Contacts of the strand formed by residues 1335 - 1339 (chain C) in PDB entry 6K4Y


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 ILE1335 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1330C  ILE*     3.3    28.2    -      -       +      +
   1331C  ARG*     3.7    10.5    -      -       -      +
   1333C  LEU*     3.1    15.7    +      -       +      -
   1334C  GLY*     1.3    87.1    -      -       -      +
   1336C  ASN*     1.3    62.3    +      -       -      +
   1337C  ILE*     3.3    21.6    +      -       +      +
     22D  ILE*     4.3    10.1    -      -       +      -
     23D  ALA      3.8     8.1    -      -       -      +
     24D  LEU*     4.3    10.3    -      -       +      -
     33D  TRP*     4.8     0.9    -      -       -      -
    113D  HIS*     5.7     1.6    -      -       -      +
    115D  TRP*     4.7    19.5    -      -       +      -
    116D  PHE*     4.3    12.3    -      -       +      -
   1332D  LEU*     5.0     8.3    -      -       +      +
   1336D  ALA*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN1336 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334C  GLY      3.8     3.0    +      -       -      -
   1335C  ILE*     1.3    70.5    -      -       -      +
   1337C  ILE*     1.3    70.6    +      -       -      +
   1338C  GLU*     3.4    28.9    +      -       -      +
     21D  LYS      4.2     0.2    -      -       -      +
     22D  ILE*     3.4     1.6    -      -       -      -
     23D  ALA*     2.6    46.1    +      -       +      +
     24D  LEU      3.3    22.5    +      -       -      +
     25D  ALA*     4.4     3.3    -      -       -      +
     26D  SER      5.9     0.2    -      -       -      +
     29D  MET*     3.7    26.8    -      -       -      +
     33D  TRP*     3.2    31.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1323C  PHE*     5.7     7.0    -      -       +      -
   1326C  LEU*     5.8     3.8    -      -       +      -
   1327C  LEU*     3.7    31.4    -      -       +      +
   1330C  ILE*     3.7    37.7    -      -       +      -
   1331C  ARG*     3.0    27.1    +      -       +      +
   1335C  ILE*     3.3     8.3    +      -       +      +
   1336C  ASN*     1.3    85.9    -      -       -      +
   1338C  GLU*     1.3    62.8    +      -       -      +
     20D  ILE*     4.5    13.5    -      -       +      -
     21D  LYS      3.2     9.4    -      -       -      +
     22D  ILE*     3.7    27.6    -      -       +      -
   1319D  PHE*     5.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1327C  LEU*     5.2     1.8    -      -       -      +
   1331C  ARG*     4.2     8.5    -      -       -      +
   1336C  ASN*     3.4    29.2    +      -       -      +
   1337C  ILE*     1.3    83.6    -      -       -      +
   1339C  LEU*     1.3    72.6    +      -       -      +
   1340C  GLU*     3.5    19.9    -      -       -      +
     20D  ILE*     3.4    22.2    -      -       -      +
     21D  LYS*     2.9    24.3    +      -       +      +
     29D  MET*     4.7     9.9    -      -       -      +
     33D  TRP*     6.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1319C  MET*     4.2    22.4    -      -       +      -
   1323C  PHE*     4.7    11.7    -      -       +      -
   1327C  LEU*     4.8    22.2    -      -       +      -
   1331C  ARG*     5.3     1.5    -      -       -      +
   1338C  GLU*     1.3    80.8    -      -       -      +
   1340C  GLU*     1.3    70.9    +      -       -      +
     17D  PHE*     3.6    35.7    -      -       +      -
     19D  ALA      4.8     1.6    -      -       -      -
     20D  ILE*     3.7    19.3    -      -       +      -
----------------------------------------------------------
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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