Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 3KDM


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 ALA 92 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ARG*     4.0    10.3    -      -       +      -
     39B  GLN      3.5    29.2    -      -       -      +
     40B  ALA*     3.7     4.9    -      -       +      +
     41B  PRO*     4.4     4.5    -      -       -      -
     89B  GLU      5.6     0.4    -      -       -      +
     90B  ASP      3.3     9.0    +      -       -      +
     91B  THR*     1.3    79.9    -      -       -      +
     93B  VAL*     1.3    60.0    +      -       -      +
     94B  TYR*     3.2    17.6    -      -       +      -
    117B  LEU*     3.8     7.4    -      -       -      +
    118B  VAL      3.0    30.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL      4.0     0.5    -      -       -      +
     38B  ARG*     3.2     5.4    -      -       -      -
     39B  GLN*     2.9    41.4    +      -       +      +
     41B  PRO*     6.4     1.3    -      -       +      -
     92B  ALA*     1.3    73.2    -      -       -      +
     94B  TYR*     1.3    61.7    +      -       -      +
     95B  TYR*     3.7    34.3    +      -       +      +
    114B  GLN      5.2     0.4    -      -       -      +
    115B  GLY*     3.8    18.4    -      -       -      -
    116B  THR      3.6     8.3    -      -       -      +
    117B  LEU*     4.0    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLU*     2.6    24.0    -      -       -      +
     20B  LEU*     3.4    30.7    -      -       +      -
     36B  TRP*     4.3     5.2    -      +       +      -
     37B  VAL      3.7     3.6    -      -       -      -
     38B  ARG*     3.1    41.8    +      -       +      -
     48B  VAL*     4.5     5.8    -      -       +      -
     68B  PHE*     4.0    24.9    -      +       -      -
     81B  LEU*     4.3    10.8    -      -       +      -
     83B  MET*     4.2     8.6    -      -       -      -
     86B  LEU*     5.5     0.2    -      -       -      +
     90B  ASP*     2.9    28.1    +      -       -      +
     92B  ALA*     3.2    31.9    -      -       +      -
     93B  VAL*     1.3    72.7    -      -       -      +
     95B  TYR*     1.3    56.9    +      -       -      +
    115B  GLY*     3.2     0.9    -      -       -      -
    116B  THR      2.9    22.5    +      -       -      +
    118B  VAL*     3.8    24.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLN*     3.4    18.9    +      -       -      -
     43A  GLY      5.8     0.3    -      -       -      -
     44A  LYS      3.8     7.7    +      -       -      -
     45A  ALA*     3.6    26.7    -      -       +      -
     46A  PRO*     4.2     3.1    -      -       +      -
      6B  GLU*     3.4     2.0    -      -       -      -
     36B  TRP*     3.2    10.6    -      -       -      -
     37B  VAL*     2.9    43.8    +      -       +      +
     38B  ARG*     5.0     0.7    -      -       -      -
     39B  GLN*     3.6    21.7    +      -       +      -
     45B  LEU*     4.5     2.9    -      -       +      -
     93B  VAL*     3.7    26.3    -      -       +      +
     94B  TYR*     1.3    73.5    -      -       -      +
     96B  CYS*     1.3    62.2    +      -       -      +
     97B  ALA*     5.4     0.2    -      -       -      +
    112B  TRP*     3.5    31.6    -      +       +      -
    113B  GLY      3.6    12.1    -      -       -      -
    114B  GLN      4.0     4.7    -      -       -      -
    115B  GLY*     3.5    25.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.9     1.6    -      -       -      -
      6B  GLU*     3.1    26.9    +      -       -      -
     22B  CYS*     2.0    54.5    -      -       +      -
     35B  SER      3.3     4.7    -      -       -      +
     36B  TRP*     3.7    13.7    -      -       +      -
     79B  LEU*     3.9    11.0    -      -       +      -
     95B  TYR*     1.3    75.9    -      -       -      +
     97B  ALA*     1.3    64.0    +      -       -      +
    112B  TRP*     3.2     2.3    -      -       -      +
    113B  GLY*     2.6    37.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.8     2.6    -      -       -      +
     34B  MET*     3.5     8.0    -      -       -      +
     35B  SER*     2.6    43.1    +      -       -      +
     37B  VAL*     5.8     1.1    -      -       +      -
     96B  CYS*     1.3    78.6    -      -       -      +
     98B  ARG*     1.3    60.1    +      -       -      +
    109B  MET*     3.9    23.6    -      -       +      -
    111B  VAL      3.0    15.0    -      -       -      +
    112B  TRP*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  VAL*     4.3     4.4    -      -       -      +
      4B  LEU*     4.6     3.8    -      -       +      -
     27B  PHE*     3.1    60.2    -      -       +      +
     32B  TYR*     3.7    33.2    -      -       +      -
     33B  ALA      3.6     5.8    -      -       -      +
     34B  MET*     3.8    14.4    -      -       -      -
     97B  ALA*     1.3    75.0    -      -       -      +
     99B  ASP*     1.3    62.4    +      -       -      +
    100B  PRO*     3.5    17.9    -      -       -      +
    109B  MET*     3.1     7.7    -      -       -      -
    110B  ASP*     3.0    61.8    +      -       -      -
    111B  VAL*     3.1    24.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  TYR*     3.4    20.8    -      -       -      +
     33B  ALA*     3.0    19.8    +      -       +      +
     34B  MET*     5.0     0.2    -      -       -      +
     97B  ALA      4.3     0.4    +      -       -      -
     98B  ARG*     1.3    71.7    -      -       -      +
    100B  PRO*     1.3    61.5    -      -       -      +
    101B  GLY      3.0    15.8    +      -       -      +
    105B  TYR*     3.6     6.7    -      -       +      -
    106B  TYR      2.9    20.7    +      -       -      -
    107B  TYR*     2.9    23.0    +      -       -      -
    108B  GLY      3.1    10.5    -      -       -      +
    109B  MET*     4.3     1.2    -      -       -      +
    226B  TES      2.7    47.0    +      -       +      +
----------------------------------------------------------
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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