Contacts of the strand formed by residues 162 - 175 (chain B) 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 ALA 162 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA*     6.3     1.1    -      -       +      -
     16B  LEU      4.0    10.1    -      -       -      +
     17B  ARG      3.9     2.2    -      -       -      +
     18B  PRO*     3.6    24.7    -      -       +      -
     19B  LEU*     3.9     6.1    -      -       -      -
    157B  VAL*     3.4     2.6    -      -       -      +
    158B  SER*     2.9    35.5    +      -       -      +
    160B  SER*     4.4     7.6    -      -       -      +
    161B  GLY*     1.3    77.8    -      -       -      +
    163B  PHE*     1.3    66.7    +      -       -      +
    164B  LEU*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA*     4.0     0.9    -      -       -      +
     16B  LEU*     3.0    46.8    +      -       +      +
     17B  ARG*     3.2    36.5    +      -       +      -
     19B  LEU*     3.5    24.2    -      -       +      -
     23B  GLU*     3.8    23.6    -      -       -      -
     67B  TRP*     3.9    26.0    -      +       -      -
    113B  ALA*     3.9    29.8    -      -       +      -
    116B  LEU*     5.6     2.9    -      -       +      -
    155B  LEU*     4.2     7.6    -      -       +      -
    156B  TRP      3.5     4.7    -      -       -      -
    157B  VAL*     4.6     0.9    -      -       +      -
    162B  ALA*     1.3    76.5    -      -       -      +
    164B  LEU*     1.3    64.0    +      -       -      +
    303B  LEU*     4.0    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     4.7    15.9    -      -       +      +
     14B  PHE      3.6    17.7    -      -       -      +
     15B  ALA*     4.0    12.1    -      -       +      -
    154B  ASP      3.9     0.2    -      -       -      +
    155B  LEU*     3.1     9.3    -      -       -      +
    156B  TRP*     2.9    75.5    +      -       +      +
    158B  SER*     3.6    27.6    -      -       -      -
    162B  ALA*     6.1     0.2    -      -       +      -
    163B  PHE*     1.3    79.2    -      -       -      +
    165B  LEU*     1.3    60.3    +      -       -      +
    309B  VAL*     4.5    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     3.2     6.1    -      -       -      +
     14B  PHE*     2.8    44.3    +      -       +      +
     16B  LEU*     4.2    17.2    -      -       +      +
    117B  LEU*     5.2     4.5    -      -       +      -
    153B  LEU*     4.4    11.4    -      -       +      -
    154B  ASP      3.2    18.4    -      -       -      +
    155B  LEU*     3.9    11.7    -      -       +      -
    156B  TRP*     4.9     0.2    -      -       -      -
    163B  PHE      4.3     0.2    -      -       -      -
    164B  LEU*     1.3    72.4    -      -       -      +
    166B  GLU*     1.3    75.4    +      -       -      +
    167B  VAL*     4.0    19.1    -      -       +      -
    294B  ALA*     4.1    23.3    -      -       +      +
    297B  ILE*     4.7    10.8    -      -       +      -
    298B  GLY*     4.9     1.3    -      -       -      +
    301B  LEU*     4.6    10.5    -      -       +      -
    306B  PRO*     4.7    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ASN*     3.8    21.8    +      -       -      +
     13B  ARG*     4.4     3.4    -      -       +      +
    152B  VAL      4.5     0.9    -      -       -      +
    153B  LEU*     3.3     6.4    -      -       -      -
    154B  ASP*     2.9    47.3    +      -       +      +
    156B  TRP*     3.5    34.3    -      -       +      -
    164B  LEU      4.1     0.4    +      -       -      -
    165B  LEU*     1.3    74.6    -      -       -      +
    167B  VAL*     1.3    70.8    +      -       -      +
    168B  ASP*     5.9     1.6    -      -       +      +
    577B  GLY      5.7     0.7    -      -       -      +
    579B  GLY*     4.1    21.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ASN*     3.2    32.0    +      -       -      +
     14B  PHE*     4.2     5.6    -      -       +      -
    151B  ALA*     3.8    20.9    -      -       +      -
    152B  VAL      3.7     4.0    -      -       -      -
    153B  LEU*     3.7    13.0    -      -       +      -
    165B  LEU*     4.0    21.5    -      -       +      -
    166B  GLU*     1.3    82.6    -      -       -      +
    168B  ASP*     1.3    64.7    +      -       -      +
    169B  PRO*     4.6     0.2    -      -       +      -
    290B  THR*     3.6    31.0    -      -       +      +
    293B  ILE*     3.8    16.2    -      -       +      -
    294B  ALA*     4.1    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ASN*     4.0     6.2    +      -       -      +
    151B  ALA*     3.6     2.9    -      -       -      -
    152B  VAL*     2.9    41.9    +      -       +      +
    166B  GLU*     5.3     2.7    -      -       +      +
    167B  VAL*     1.3    76.8    -      -       -      +
    169B  PRO*     1.3    77.7    -      -       -      +
    170B  ALA*     4.1     2.1    -      -       -      +
    286B  ARG*     3.3    14.4    +      -       -      +
    290B  THR*     4.6     0.5    +      -       -      -
    580B  ARG*     3.0    49.4    +      -       -      +
    582B  TYR*     4.5     0.9    +      -       -      -
    615B  ARG*     4.9     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  GLY      3.2    13.5    -      -       -      +
    151B  ALA*     3.8     3.8    -      -       +      -
    167B  VAL*     4.3     1.8    -      -       +      -
    168B  ASP*     1.3    96.3    -      -       -      +
    170B  ALA*     1.3    60.9    +      -       -      +
    281B  LEU*     4.1    18.4    -      -       +      -
    286B  ARG*     2.6    47.6    +      -       +      +
    289B  ARG*     3.9    21.5    -      -       +      +
    290B  THR*     3.2    31.6    -      -       -      +
    293B  ILE*     5.0     0.7    -      -       +      -
      8E    G      4.7     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  TYR*     3.6    13.3    -      -       +      +
    149B  GLY*     3.8     0.7    -      -       -      -
    150B  GLY      2.9    32.7    +      -       -      +
    151B  ALA*     4.5     0.2    -      -       -      -
    152B  VAL*     4.2    22.7    -      -       +      +
    168B  ASP      3.6     7.2    +      -       -      +
    169B  PRO*     1.3    76.0    -      -       -      +
    171B  TYR*     1.3    70.0    +      -       -      +
    286B  ARG*     5.7     0.4    -      -       -      +
      8E    G      3.3    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  TYR*     3.8     5.5    +      -       -      -
    139B  HIS*     3.3    41.2    -      +       +      -
    147B  VAL*     4.1    10.5    -      -       +      -
    148B  LEU      3.2    14.4    -      -       -      +
    149B  GLY*     3.6    13.7    -      -       -      -
    170B  ALA*     1.3    77.7    -      -       -      +
    172B  ARG*     1.3    62.6    +      -       -      +
    173B  ILE*     6.1     0.2    -      -       +      -
    278B  ALA      4.3     1.4    +      -       -      -
    279B  LEU*     3.4    52.0    -      -       +      -
    281B  LEU*     3.3    23.4    -      -       +      +
    289B  ARG*     2.7    32.7    +      -       -      -
      8E    G      2.7    36.3    +      -       -      +
      9E    T      3.8     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  TRP*     4.3     7.0    -      -       +      -
    130B  GLU*     2.7    40.8    +      -       -      +
    135B  TYR*     3.5    35.2    -      -       +      -
    146B  ARG      3.8     0.5    -      -       -      +
    147B  VAL*     3.2     6.2    -      -       -      -
    148B  LEU*     2.9    36.0    +      -       +      +
    171B  TYR*     1.3    74.4    -      -       -      +
    173B  ILE*     1.3    75.7    +      -       -      +
    174B  LEU*     3.9    22.6    +      -       +      +
    194B  ARG*     5.0    10.1    -      -       -      +
      8E    G      4.5     0.2    -      -       -      -
      9E    T      2.7    44.7    +      -       -      -
     10E    A      3.4    36.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  TRP*     5.4     1.6    -      -       +      -
    146B  ARG      3.7     6.3    -      -       -      +
    147B  VAL*     4.3    16.2    -      -       +      -
    172B  ARG*     1.3    87.1    +      -       -      +
    174B  LEU*     1.3    71.6    +      -       -      +
    175B  CYS      4.4     0.3    +      -       -      -
    265B  LEU*     3.7    44.9    +      -       +      +
    266B  THR*     4.5     7.0    -      -       -      +
    267B  LEU*     4.1    26.0    -      -       +      -
    270B  LEU*     4.2    19.3    -      -       +      -
    279B  LEU*     4.8     3.6    -      -       +      -
      8E    G      3.7    23.3    -      -       +      +
      9E    T      2.7    15.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  TRP*     3.6    46.7    -      -       +      +
    145B  TRP*     3.2     7.0    -      -       -      +
    146B  ARG*     2.9    68.2    +      -       +      +
    148B  LEU*     3.6    32.8    -      -       +      -
    172B  ARG*     3.9    17.5    -      -       +      +
    173B  ILE*     1.3    86.6    -      -       -      +
    175B  CYS*     1.3    63.6    +      -       -      +
    176B  GLU*     4.6     0.5    -      -       -      +
    194B  ARG*     5.4     9.0    -      -       -      +
    265B  LEU*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  GLY      3.7    11.9    -      -       -      -
    145B  TRP*     4.4     2.7    -      -       +      +
    173B  ILE      4.3     0.4    -      -       -      -
    174B  LEU*     1.3    76.2    -      -       -      +
    176B  GLU*     1.3    65.3    +      -       -      +
    177B  MET      3.6    13.5    -      -       -      -
    182B  TRP*     4.2    12.6    -      -       -      -
    194B  ARG*     4.9     9.8    +      -       -      +
    262B  VAL*     4.0    11.6    -      -       +      +
    263B  PRO*     3.5    57.7    -      -       +      +
    265B  LEU*     5.0     9.7    -      -       +      +
----------------------------------------------------------
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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