Contacts of the strand formed by residues 263 - 271 (chain D) in PDB entry 3IT8


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 TYR 263 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  ASP*     2.5    39.3    +      -       +      +
    206D  SER*     2.8    22.0    +      -       -      -
    207D  PHE*     2.8    34.9    +      -       +      -
    208D  TYR*     3.8     9.4    -      +       -      -
    210D  PRO*     3.7    28.7    -      -       +      -
    254D  ILE*     3.9    19.5    -      -       +      -
    255D  LYS*     3.7     3.8    -      -       -      -
    256D  LYS*     3.7    41.2    +      -       +      +
    257D  ASP*     3.4     7.4    -      -       -      -
    261D  ASN      3.3    15.3    -      -       -      -
    262D  THR*     1.3    81.4    +      -       -      +
    264D  SER*     1.3    58.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204D  VAL      3.5     8.5    -      -       -      -
    205D  ASN*     3.8    10.7    +      -       -      +
    206D  SER*     3.0    13.2    +      -       -      -
    207D  PHE*     3.7     3.4    -      -       -      -
    253D  ASN      3.7     0.7    -      -       -      +
    254D  ILE*     3.2     5.7    -      -       -      +
    255D  LYS*     3.0    35.9    +      -       -      +
    257D  ASP*     2.7    28.1    +      -       -      +
    258D  LYS*     5.3     0.9    +      -       -      -
    263D  TYR*     1.3    71.9    -      -       -      +
    265D  LEU*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    202D  CYS      5.1     0.2    -      -       -      +
    203D  THR*     3.4     3.5    -      -       -      -
    204D  VAL*     2.9    47.7    +      -       +      +
    205D  ASN*     5.3     0.5    -      -       -      +
    207D  PHE*     3.9    14.4    -      -       +      -
    212D  VAL*     3.5    31.9    -      -       +      +
    214D  THR*     5.1     7.0    -      -       -      +
    252D  TRP*     4.3    20.6    -      -       +      -
    253D  ASN      3.2    30.3    -      -       -      +
    254D  ILE*     4.0    11.0    -      -       +      -
    264D  SER*     1.3    76.6    -      -       -      +
    266D  THR*     1.3    88.3    +      -       -      +
    267D  ASP*     4.2     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201D  GLU*     3.9    31.3    +      -       +      +
    202D  CYS      3.6     3.8    -      -       -      +
    203D  THR*     4.2     8.6    -      -       +      +
    253D  ASN*     3.1    38.9    +      -       +      +
    265D  LEU*     1.3    81.4    +      -       -      +
    267D  ASP*     1.3    64.0    +      -       -      +
    268D  LEU*     4.1     4.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 267 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201D  GLU*     3.4     2.6    -      -       -      -
    202D  CYS*     2.7    48.9    +      -       +      +
    214D  THR*     2.9    26.8    -      -       +      +
    216D  TRP*     2.7    32.4    +      -       -      -
    239D  ARG*     3.4    32.9    +      -       -      -
    252D  TRP*     3.7     7.9    -      -       +      -
    253D  ASN      5.9     0.3    +      -       -      -
    265D  LEU*     4.2    11.3    -      -       +      +
    266D  THR*     1.3    74.3    -      -       -      +
    268D  LEU*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 268 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  ASN*     5.2     0.4    -      -       -      +
    193D  LEU*     4.1    22.7    -      -       +      -
    199D  THR*     3.8    24.5    -      -       +      +
    200D  LEU      3.3    15.5    -      -       -      +
    201D  GLU*     3.4    32.5    -      -       +      +
    239D  ARG*     4.8     6.6    +      -       -      -
    266D  THR*     4.1     4.8    +      -       +      -
    267D  ASP*     1.3    80.2    +      -       -      +
    269D  VAL*     1.3    74.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 269 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199D  THR*     3.2     8.8    +      -       -      -
    200D  LEU*     2.7    40.7    +      -       +      +
    216D  TRP*     3.0    56.5    -      -       +      +
    237D  TRP*     5.3     8.1    -      -       +      -
    239D  ARG*     5.3     5.4    -      -       -      -
    267D  ASP*     4.4     0.4    -      -       -      +
    268D  LEU*     1.3    81.4    -      -       -      +
    270D  ARG*     1.3    71.1    +      -       -      +
    271D  THR*     3.2     6.1    +      -       -      +
    275D  MET*     5.3     0.9    -      -       +      -
    279D  PRO*     4.7    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 270 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193D  LEU*     6.1     5.7    -      -       +      +
    195D  ASP*     3.2    22.2    +      -       -      -
    196D  GLY*     3.0    37.9    -      -       -      +
    197D  ASN*     3.5    17.0    +      -       -      +
    198D  MET      4.3     6.0    +      -       -      -
    199D  THR*     4.6     4.7    -      -       -      +
    269D  VAL*     1.3    77.4    -      -       -      +
    271D  THR*     1.3    52.3    +      -       -      +
    272D  THR*     2.6    42.5    +      -       -      +
    275D  MET*     4.5     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 271 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197D  ASN*     2.5    32.2    +      -       -      +
    198D  MET*     2.9    44.9    +      -       +      +
    200D  LEU*     3.5    33.6    +      -       +      +
    269D  VAL*     3.2     3.5    +      -       -      +
    270D  ARG*     1.3    67.4    -      -       -      +
    272D  THR*     1.3    53.8    +      -       -      +
    275D  MET*     3.8    28.3    -      -       +      -
    278D  GLN*     5.3     4.3    -      -       +      -
    279D  PRO*     4.8     4.9    -      -       +      +
----------------------------------------------------------
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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