Contacts of the strand formed by residues 617 - 623 (chain A) in PDB entry 4N41


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 LEU 617 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  VAL*     4.0    18.2    -      -       +      -
    574A  ARG      3.7    10.1    -      -       -      +
    575A  LYS*     4.2     2.0    -      -       -      -
    602A  LEU*     3.3     7.0    -      -       -      +
    603A  LEU*     2.8    39.6    +      -       +      +
    605A  THR*     4.0    15.0    -      -       +      +
    615A  ARG      3.5     0.4    +      -       -      -
    616A  PRO*     1.3    73.8    -      -       -      +
    618A  LYS*     1.3    59.8    +      -       -      +
    619A  LEU*     3.5    17.6    -      -       +      +
    635A  ILE*     5.5     0.7    -      -       +      -
    651A  ARG*     3.4    66.6    -      -       +      +
    652A  LEU*     4.1    16.8    -      -       +      -
    653A  PRO*     4.5     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  VAL*     3.8     0.3    -      -       -      -
    574A  ARG*     2.9    65.2    +      -       +      +
    577A  GLY      3.8    19.3    +      -       -      +
    578A  GLY*     4.0    17.2    -      -       -      +
    596A  LEU*     5.5     7.0    -      -       +      -
    597A  GLU*     4.5    16.3    +      -       -      -
    600A  THR*     5.0     6.5    -      -       -      -
    601A  PHE      3.7     4.7    -      -       -      +
    602A  LEU*     4.2    11.9    -      -       +      -
    616A  PRO      3.7     1.2    +      -       -      -
    617A  LEU*     1.3    73.7    -      -       -      +
    619A  LEU*     1.3    65.1    +      -       -      +
    620A  VAL*     4.9     9.0    -      -       +      -
      3D    A      5.5     0.2    +      -       -      -
      4D    C      4.1    18.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571A  VAL*     4.0     6.7    -      -       +      -
    572A  SER      3.1     9.9    -      -       -      +
    573A  VAL*     4.0    14.4    -      -       +      -
    599A  LYS      4.0     0.2    -      -       -      +
    600A  THR*     3.3     5.0    -      -       -      -
    601A  PHE*     2.9    63.2    +      -       +      +
    603A  LEU*     3.6    18.2    -      -       +      -
    617A  LEU*     3.5    32.1    -      -       +      +
    618A  LYS*     1.3    80.0    -      -       -      +
    620A  VAL*     1.3    66.1    +      -       -      +
    621A  HIS      4.2     0.2    -      -       -      -
    635A  ILE*     3.6    40.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571A  VAL*     3.4     4.9    -      -       -      -
    572A  SER*     2.9    40.8    +      -       -      -
    574A  ARG*     4.0    29.8    -      -       -      +
    599A  LYS*     3.5    11.2    -      -       +      +
    600A  THR*     3.8    21.1    -      -       +      -
    618A  LYS*     4.9     7.4    -      -       -      -
    619A  LEU*     1.3    79.6    -      -       -      +
    621A  HIS*     1.3    66.9    +      -       -      +
    622A  GLU*     3.3    22.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569A  ASP*     2.8    22.8    +      -       +      -
    570A  LEU      3.6     9.2    -      -       -      -
    571A  VAL*     4.3     6.2    -      -       +      +
    599A  LYS*     2.8    48.9    +      -       +      +
    601A  PHE*     5.1     1.9    -      -       +      -
    619A  LEU      4.2     0.2    -      -       -      -
    620A  VAL*     1.3    71.7    -      -       -      +
    622A  GLU*     1.3    59.1    +      -       -      +
    623A  ALA      3.0    21.3    +      -       -      -
    624A  GLY      3.4    19.7    +      -       -      -
    625A  ASP*     4.3     1.1    -      -       -      -
    626A  THR      3.1    27.9    +      -       -      -
    628A  LEU*     3.5    26.0    -      -       +      +
    631A  LEU*     3.6    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545A  ARG*     2.7    36.4    +      -       -      -
    551A  GLN*     3.3    40.9    +      -       -      +
    570A  LEU*     2.9    36.0    +      -       +      +
    572A  SER*     3.6    14.7    -      -       -      -
    574A  ARG*     4.6     7.6    +      -       -      -
    599A  LYS*     5.5     5.3    -      -       -      +
    620A  VAL*     3.6    23.1    -      -       +      +
    621A  HIS*     1.3    74.8    -      -       -      +
    623A  ALA*     1.3    62.9    +      -       -      +
     75B  LEU*     5.8     2.3    -      -       -      +
     76B  GLU*     4.9     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 623 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  GLN*     5.2     1.6    -      -       -      +
    558A  LEU*     3.9    27.4    -      -       +      -
    568A  TYR*     4.2     9.9    -      -       +      -
    569A  ASP*     3.2     2.1    -      -       -      -
    570A  LEU*     2.9    33.6    +      -       +      -
    621A  HIS*     3.0    13.5    +      -       -      -
    622A  GLU*     1.3    80.3    -      -       +      +
    624A  GLY*     1.3    62.2    +      -       -      +
     76B  GLU*     3.6    12.1    -      -       -      +
----------------------------------------------------------
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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