Contacts of the strand formed by residues 11 - 17 (chain B) in PDB entry 4K8T


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 ILE 11 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ASN*     3.4    18.4    +      -       +      +
     10B  ALA*     1.3    79.7    -      -       -      +
     12B  VAL*     1.3    71.3    +      -       -      +
     13B  ASP*     3.7     2.0    -      -       -      +
     56B  GLY      2.6    33.6    +      -       -      -
     57B  GLY*     3.9     8.6    -      -       -      +
     88B  PHE*     3.4    12.4    -      -       -      -
    111B  ALA*     3.5    17.7    -      -       +      -
    112B  ARG      3.9     3.1    -      -       -      -
    113B  SER*     3.6    20.2    -      -       -      +
    127B  THR*     3.9    10.1    -      -       +      -
    129B  LEU*     4.8     0.7    -      -       +      -
    401B  ADN      3.4    63.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ILE*     1.3    78.0    -      -       -      +
     13B  ASP*     1.3    73.4    +      -       -      +
     14B  ILE*     4.5     2.2    -      -       +      +
     53B  GLU*     4.3    12.1    -      -       +      -
     54B  ALA      3.9    12.1    -      -       -      +
     55B  SER*     4.5     5.2    -      -       -      +
     56B  GLY      4.1     0.2    -      -       -      +
     84B  LEU*     3.5    52.5    -      -       +      +
     87B  ILE*     4.6     8.3    -      -       +      -
     88B  PHE*     4.1    17.3    -      -       +      +
    110B  THR*     4.6     4.0    -      -       +      -
    111B  ALA      3.1    10.2    +      -       -      +
    112B  ARG*     3.1    10.6    -      -       +      +
    113B  SER      3.1    21.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ILE*     3.7     3.8    -      -       -      +
     12B  VAL*     1.3    78.2    -      -       -      +
     14B  ILE*     1.3    61.3    +      -       -      +
     15B  ILE*     4.0    15.0    -      -       +      +
     53B  GLU*     3.2     5.9    -      -       -      +
     54B  ALA*     2.8    37.8    +      -       +      +
     56B  GLY*     4.0     2.9    -      -       -      -
    113B  SER*     3.4     5.5    -      -       -      -
    115B  ILE*     3.4    22.3    -      -       +      +
    272B  THR*     4.3     0.5    -      -       -      +
    312B  PRO*     3.3    16.3    -      -       -      +
    401B  ADN      2.4    50.4    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     87A  ILE*     6.2     2.5    -      -       +      -
     12B  VAL*     4.5     4.9    -      -       +      +
     13B  ASP*     1.3    77.4    -      -       -      +
     15B  ILE*     1.3    59.5    +      -       -      +
     45B  TYR*     3.9    13.5    -      -       +      +
     48B  MSE      3.4    18.3    -      -       -      +
     51B  ALA*     3.6    24.5    -      -       +      -
     52B  LEU      3.5     3.1    -      -       -      -
     53B  GLU*     3.8    19.5    -      -       +      +
     84B  LEU*     5.8     5.4    -      -       +      -
    112B  ARG*     3.8    22.9    -      -       +      -
    113B  SER      2.8    10.7    +      -       -      +
    114B  MSE      3.3    11.4    -      -       +      -
    115B  ILE      2.8    26.9    +      -       -      -
    402B  DMS      3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LEU*     6.1     0.2    -      -       +      -
     13B  ASP*     4.0    17.7    -      -       +      +
     14B  ILE*     1.3    76.7    -      -       -      +
     16B  SER*     1.3    64.5    +      -       -      +
     51B  ALA*     3.2     6.4    -      -       -      -
     52B  LEU*     2.8    48.4    +      -       +      +
     54B  ALA*     4.2    19.5    -      -       +      -
    115B  ILE*     3.5    19.7    -      -       +      +
    117B  VAL*     4.1    20.0    -      -       +      -
    270B  ASP*     4.7     4.9    -      -       -      +
    272B  THR*     5.9     2.0    -      -       +      +
    310B  ILE*     4.4    19.3    -      -       +      -
    311B  GLY*     4.1    27.8    -      -       -      +
    312B  PRO*     4.5     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ILE*     1.3    79.3    -      -       -      +
     17B  ARG*     1.3    68.6    +      -       -      +
     48B  MSE      3.5    29.5    -      -       -      +
     49B  GLY*     3.8    13.6    +      -       -      -
     50B  PRO      3.3    20.6    +      -       -      -
     51B  ALA*     4.4     0.7    -      -       -      -
    115B  ILE      3.0     9.1    +      -       -      +
    116B  PHE*     3.3     7.8    -      -       -      -
    117B  VAL*     2.9    25.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  MSE      5.7     5.2    -      -       -      +
     16B  SER*     1.3    83.1    +      -       -      +
     18B  CYS*     1.3    63.5    +      -       -      +
     49B  GLY*     6.0     0.2    -      -       -      -
    117B  VAL*     3.3    30.1    +      -       -      +
    118B  THR      3.9    16.2    +      -       -      -
    119B  GLU*     4.1    18.2    +      -       +      +
    121B  GLY*     4.4     1.4    -      -       -      -
    267B  GLU*     5.1     5.1    +      -       -      -
    268B  VAL      4.5     2.4    +      -       -      -
    269B  VAL*     3.0    45.9    +      -       -      +
    270B  ASP*     5.1     1.4    -      -       -      +
    310B  ILE*     5.1     7.1    -      -       -      +
----------------------------------------------------------
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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