Contacts of the strand formed by residues 11 - 19 (chain B) in PDB entry 3KG2


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 SER 11 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ASN*     1.3    71.6    -      -       -      +
     12B  ILE*     1.3    62.2    +      -       -      +
     13B  GLN*     3.7     4.0    +      -       -      +
     42B  ARG*     3.7     5.2    -      -       -      -
     44B  THR*     3.2    21.5    +      -       -      +
     71B  TYR*     4.4     9.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ASN*     5.0     2.0    -      -       +      -
     11B  SER*     1.3    73.7    +      -       -      +
     13B  GLN*     1.3    61.5    +      -       -      +
     14B  ILE*     3.6    14.7    +      -       +      +
     41B  PHE*     3.9    27.1    -      -       +      -
     42B  ARG      3.0    14.4    +      -       -      +
     43B  LEU*     3.5    11.5    -      -       +      -
     44B  THR*     2.9    24.0    +      -       -      -
     71B  TYR*     3.7    31.0    -      -       +      -
    296B  PHE*     3.6    33.4    -      -       +      +
    306B  ILE*     6.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     3.7     5.0    +      -       -      +
     12B  ILE*     1.3    72.7    -      -       -      +
     14B  ILE*     1.3    61.9    +      -       -      +
     44B  THR*     3.5    17.9    -      -       +      +
     46B  HIS*     6.6     0.2    -      -       +      -
     68B  ARG      5.4     2.7    -      -       -      +
     69B  GLY      4.3    15.0    -      -       -      +
     70B  VAL*     3.4     8.2    -      -       +      -
     71B  TYR*     3.0    37.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ILE*     4.1    18.4    -      -       +      +
     13B  GLN*     1.3    81.2    -      -       -      +
     15B  GLY*     1.3    64.5    +      -       -      +
     29B  PHE*     4.6    18.4    -      -       +      -
     33B  MET*     5.1     1.8    -      -       -      -
     43B  LEU*     4.1    27.6    -      -       +      -
     44B  THR      3.0    11.8    +      -       -      +
     45B  PRO*     3.9    10.5    -      -       +      -
     46B  HIS*     3.0    28.8    +      -       -      +
     70B  VAL*     3.8     6.6    -      -       -      +
     72B  ALA*     3.3    22.0    -      -       +      +
     74B  PHE*     5.8     0.7    -      -       +      -
    292B  MET*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ILE*     1.3    78.6    -      -       -      +
     16B  GLY*     1.3    58.3    +      -       -      -
     17B  LEU*     4.2     0.4    -      -       -      -
     29B  PHE*     5.6     1.1    -      -       -      -
     45B  PRO*     5.7     0.4    -      -       -      -
     46B  HIS*     4.0     6.3    -      -       -      -
     65B  GLN*     4.6    11.7    -      -       -      -
     70B  VAL*     3.8    11.2    -      -       -      +
     72B  ALA      2.9    13.6    +      -       -      +
     73B  ILE*     4.2    11.4    -      -       -      -
     74B  PHE*     2.8    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  GLY*     1.3    74.3    -      -       -      -
     17B  LEU*     1.3    64.9    +      -       -      +
     18B  PHE*     3.6    19.1    +      -       -      -
     29B  PHE*     5.5     2.7    -      -       -      -
     45B  PRO*     6.1     0.2    -      -       -      -
     46B  HIS      3.1    12.9    +      -       -      +
     47B  ILE*     3.5    10.3    -      -       -      -
     48B  ASP*     2.8    30.5    +      -       -      +
     74B  PHE*     3.1     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  GLY*     4.6     1.3    -      -       -      -
     16B  GLY*     1.3    78.6    -      -       -      +
     18B  PHE*     1.3    60.7    +      -       -      +
     19B  PRO*     3.6     2.1    -      -       -      +
     48B  ASP*     3.7    11.4    -      -       +      +
     58B  VAL*     4.6    22.0    -      -       +      +
     61B  ALA*     4.2    39.3    -      -       +      +
     62B  PHE*     4.8     3.6    -      -       +      +
     65B  GLN*     5.1     4.0    -      -       +      -
     73B  ILE*     3.6    25.1    -      -       +      -
     74B  PHE      2.9     9.1    +      -       -      -
     75B  GLY*     3.1    26.0    -      -       -      -
     76B  PHE*     3.3    18.7    +      -       -      +
     85B  ILE*     4.6    12.3    -      -       +      -
     96B  PHE*     4.6     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  GLY*     3.8    19.5    -      -       -      -
     17B  LEU*     1.3    76.7    -      -       -      +
     19B  PRO*     1.3    69.7    -      -       +      +
     20B  ARG      3.5     0.2    +      -       -      -
     22B  ALA*     4.4     9.0    -      -       +      +
     25B  GLU      4.0     6.5    -      -       -      -
     26B  TYR*     3.7    50.0    -      +       +      -
     29B  PHE*     3.4    22.7    -      +       +      -
     47B  ILE*     4.1    12.6    -      -       +      -
     48B  ASP      3.4     6.6    +      -       -      -
     49B  ASN*     3.3    38.0    -      -       -      +
     50B  LEU      3.6     3.0    +      -       -      -
     74B  PHE*     3.3    39.0    -      +       -      -
     76B  PHE*     3.9    13.7    -      +       -      -
    285B  THR*     4.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU      3.6     3.4    -      -       -      +
     18B  PHE*     1.3    84.9    -      -       +      +
     20B  ARG*     1.3    68.0    +      -       -      +
     22B  ALA*     3.0    29.6    +      -       +      +
     49B  ASN*     5.6     0.6    -      -       -      -
     50B  LEU      3.4    11.2    -      -       -      +
     52B  VAL*     3.7    37.5    -      -       +      +
     76B  PHE*     3.4    35.9    -      -       +      -
----------------------------------------------------------
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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