Contacts of the strand formed by residues 261 - 275 (chain D) in PDB entry 1KD1


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLN 261 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2808A    U      3.0    38.9    +      -       -      +
   2809A    G      3.7    30.8    +      -       -      +
     19D  SER*     4.3    13.9    +      -       -      +
     21D  SER      5.2     1.4    -      -       -      +
     23D  THR      4.8     0.2    -      -       -      +
     24D  PRO*     3.2    16.3    -      -       +      +
     25D  ARG*     2.8    51.4    +      -       -      +
    203D  ALA*     5.2     0.6    -      -       -      +
    204D  GLY      3.5     9.2    -      -       -      +
    205D  VAL*     4.2     5.6    -      -       +      +
    260D  HIS*     1.3    73.9    -      -       -      +
    262D  ARG*     1.3    85.9    +      -       -      +
    263D  THR*     4.2     4.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2715A    G      2.8    46.6    +      -       -      +
   2716A    G      3.2    17.1    +      -       -      -
   2807A    U      5.6     0.4    -      -       -      -
   2808A    U      3.9     8.4    +      -       -      -
     13D  PHE*     3.4    49.5    +      -       -      +
     16D  ARG*     4.5     9.3    -      -       -      +
    202D  VAL      3.8     1.9    -      -       -      +
    203D  ALA*     3.1     2.0    -      -       -      -
    204D  GLY      2.9    33.1    +      -       -      +
    206D  THR*     3.6    24.7    -      -       +      -
    260D  HIS*     3.4    27.0    +      -       -      +
    261D  GLN*     1.3    94.8    +      -       -      +
    263D  THR*     1.3    65.2    +      -       -      +
    264D  GLU*     3.7     5.5    +      -       -      +
    302D  PRO*     4.0    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2807A    U      3.5    23.8    +      -       -      +
   2808A    U      2.6    28.5    +      -       -      -
     26D  PHE*     4.3    16.5    -      -       +      -
     27D  ASN*     5.2     0.5    +      -       -      -
    201D  ASP*     4.3     8.7    -      -       +      -
    202D  VAL      3.7     3.8    -      -       -      +
    203D  ALA*     3.6    12.1    -      -       +      +
    261D  GLN*     4.2     2.1    +      -       -      -
    262D  ARG*     1.3    73.9    -      -       -      +
    264D  GLU*     1.3    58.5    +      -       -      +
    265D  LEU*     3.2    28.1    +      -       +      +
    312D  ARG*     4.0    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2715A    G      2.5    35.8    +      -       -      +
   2716A    G      3.6    26.3    +      -       -      +
   2765A    C      3.2    10.7    -      -       -      +
   2766A    A      4.2    11.1    -      -       -      +
    201D  ASP*     3.6     1.0    -      -       -      -
    202D  VAL*     2.9    38.7    +      -       +      +
    262D  ARG*     3.7     6.0    -      -       -      +
    263D  THR*     1.3    71.1    -      -       -      +
    265D  LEU*     1.3    62.6    +      -       -      +
    267D  LYS*     3.3    34.4    +      -       +      +
    300D  SER*     4.3     3.3    +      -       -      -
    302D  PRO*     4.0    15.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 265 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2766A    A      2.2    37.9    +      -       -      +
   2767A    C      4.3    14.4    -      -       -      -
   2806A    C      3.8    12.1    -      -       -      +
   2807A    U      4.5     9.0    -      -       -      -
    201D  ASP*     3.3    19.1    -      -       -      +
    263D  THR*     3.2    33.6    +      -       +      +
    264D  GLU*     1.3    74.4    -      -       -      +
    266D  ASN*     1.3    71.6    +      -       -      +
    267D  LYS*     3.6     1.8    +      -       -      +
    312D  ARG*     4.6     1.3    -      -       -      +
    315D  VAL*     5.0     1.3    -      -       +      -
    316D  ARG*     3.4    44.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2766A    A      3.6    17.3    -      -       -      +
   2767A    C      2.6    33.9    +      -       -      +
    199D  TYR*     3.9    22.9    -      -       +      -
    200D  ALA      3.8     2.9    +      -       -      -
    201D  ASP*     3.0    14.5    +      -       -      +
    265D  LEU*     1.3    77.1    -      -       -      +
    267D  LYS*     1.3    60.3    +      -       -      +
    268D  ARG      3.9     1.7    +      -       -      -
    314D  ALA*     3.6     9.9    -      -       -      +
    316D  ARG*     3.1    27.6    +      -       -      +
    317D  PRO*     3.2    15.0    -      -       -      +
    318D  ASN*     3.0    19.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 267 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2765A    C      2.7    28.5    +      -       -      +
   2766A    A      3.9     8.4    +      -       -      +
    199D  TYR*     3.3     1.3    -      -       -      -
    200D  ALA*     2.6    46.3    +      -       +      +
    202D  VAL*     3.9    19.1    -      -       +      -
    264D  GLU*     3.3    56.3    +      -       -      +
    265D  LEU      4.4     0.2    -      -       -      +
    266D  ASN*     1.3    75.3    -      -       -      +
    268D  ARG*     1.3    61.7    +      -       -      +
    269D  LEU*     3.6     1.9    +      -       +      +
    297D  VAL*     4.0    15.3    -      -       +      -
    298D  LYS      3.8    11.2    -      -       -      +
    300D  SER*     2.6    35.0    +      -       -      +
    301D  VAL*     5.0     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 268 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  LEU*     4.9     5.9    -      -       -      +
     56D  ASP*     3.4    30.1    +      -       -      +
    197D  GLY      4.0    17.7    +      -       -      +
    198D  GLU      3.6     3.4    -      -       -      -
    199D  TYR*     3.6    32.3    +      -       +      -
    266D  ASN      3.9     1.2    +      -       -      -
    267D  LYS*     1.3    70.4    -      -       -      +
    269D  LEU*     1.3    65.7    +      -       -      +
    270D  ILE*     3.2    22.5    +      -       +      +
    297D  VAL*     3.9     2.3    -      -       -      +
    298D  LYS*     3.0    56.6    +      -       +      +
    322D  ARG*     3.4    32.8    +      -       -      +
    325D  PRO*     3.1    35.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 269 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190D  MET*     5.8     1.3    -      -       -      -
    194D  PHE*     3.5    45.8    -      -       +      -
    195D  ARG      4.6     5.4    -      -       -      +
    196D  ALA*     3.5     5.4    -      -       -      -
    197D  GLY*     2.7    34.1    +      -       -      +
    198D  GLU*     2.9    24.1    +      -       +      +
    200D  ALA*     4.1    18.8    -      -       +      -
    202D  VAL*     5.9     0.2    -      -       +      -
    267D  LYS*     4.4     2.7    -      -       +      +
    268D  ARG*     1.3    73.0    -      -       -      +
    270D  ILE*     1.3    62.8    +      -       -      +
    271D  ASP      3.3     3.2    +      -       -      +
    272D  ILE*     4.7     7.0    -      -       +      -
    295D  THR*     4.1    24.2    -      -       +      -
    296D  LEU      3.8     3.4    -      -       -      +
    297D  VAL*     4.2    15.3    -      -       +      -
    311D  PHE*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 270 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  VAL*     4.3     8.7    -      -       +      -
     53D  LEU*     3.7    43.5    -      -       +      -
     69D  VAL*     4.8     1.3    -      -       +      -
     71D  VAL*     4.4     9.0    -      -       +      -
    196D  ALA*     4.0     2.0    -      -       -      +
    197D  GLY      5.0     0.2    -      -       -      +
    268D  ARG*     3.2    30.5    +      -       +      +
    269D  LEU*     1.3    71.6    -      -       -      +
    271D  ASP*     1.3    65.0    +      -       +      +
    296D  LEU*     3.0    20.5    +      -       +      +
    298D  LYS*     3.9    33.7    -      -       +      +
    325D  PRO*     3.9    21.7    -      -       +      +
    327D  VAL*     4.3    12.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 271 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196D  ALA*     3.8    12.4    -      -       -      +
    269D  LEU      3.3     2.6    -      -       -      -
    270D  ILE*     1.3    86.3    -      -       +      +
    272D  ILE*     1.3    74.9    +      -       -      +
    273D  GLY*     4.0     5.1    +      -       -      -
    294D  TYR*     3.7    24.1    +      -       -      -
    295D  THR*     3.5     2.8    -      -       -      +
    296D  LEU*     2.7    50.7    +      -       +      +
    327D  VAL*     4.8    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 272 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76D  THR*     5.2     0.2    -      -       -      +
    190D  MET*     3.9    32.5    -      -       +      +
    191D  ASN*     3.7    24.7    -      -       -      +
    194D  PHE*     3.5    34.1    -      -       +      +
    195D  ARG*     4.1     0.4    -      -       -      -
    196D  ALA*     3.8    25.0    -      -       +      +
    269D  LEU*     4.7     6.1    -      -       +      -
    271D  ASP*     1.3    89.3    +      -       -      +
    273D  GLY*     1.3    63.5    +      -       -      +
    294D  TYR      3.5    12.3    -      -       -      +
    295D  THR*     4.4    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 273 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271D  ASP*     4.0     3.1    +      -       -      -
    272D  ILE*     1.3    77.4    -      -       -      +
    274D  GLU*     1.3    63.8    +      -       -      +
    277D  GLU*     5.6     0.2    -      -       -      -
    293D  PRO*     3.6     2.8    -      -       -      +
    294D  TYR*     3.0    48.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 274 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273D  GLY*     1.3    76.5    -      -       -      +
    275D  GLY*     1.3    65.1    +      -       -      +
    277D  GLU*     2.9    16.2    +      -       -      +
    292D  GLY*     3.0    20.2    -      -       -      +
    293D  PRO*     3.8    24.6    -      -       +      +
    294D  TYR*     3.3     7.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 275 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274D  GLU*     1.3    83.3    -      -       -      +
    276D  ASP*     1.3    59.7    +      -       -      -
    277D  GLU*     3.5     4.0    -      -       -      -
    290D  VAL*     3.6     6.6    -      -       -      +
    291D  ASP*     2.9    31.5    +      -       -      -
    292D  GLY      2.8    16.0    +      -       -      +
    294D  TYR*     4.0     4.2    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il