Contacts of the strand formed by residues 111 - 119 (chain B) in PDB entry 1NMS


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 ARG 111 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  TYR*     3.9     3.4    -      -       -      -
     43B  GLU*     3.3    31.9    +      -       +      +
     45B  GLY*     3.8    24.2    -      -       -      -
     46B  LEU*     3.7    21.5    -      -       -      +
     84B  GLU*     4.3     5.7    +      -       -      -
     86B  ARG*     4.1     4.6    -      -       -      +
    106B  GLU*     2.9    31.3    +      -       -      +
    107B  ASP      3.9    15.4    +      -       -      +
    108B  HIS*     3.0    49.8    +      -       +      +
    109B  SER      3.2     0.2    -      -       -      -
    110B  LYS*     1.3    82.0    -      -       +      +
    112B  SER*     1.3    63.7    +      -       -      +
    113B  SER      3.4     5.4    -      -       -      +
    151B  LEU*     5.3     0.2    -      -       +      -
    154B  LYS*     2.9    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LYS      3.9     4.3    -      -       -      +
     39B  MET*     3.3    40.1    +      -       -      +
     41B  TYR*     3.2    35.7    +      -       -      +
     43B  GLU      2.8    14.8    +      -       -      -
     44B  MET*     3.3    11.3    +      -       -      -
    111B  ARG*     1.3    73.6    -      -       -      +
    113B  SER*     1.3    60.5    +      -       -      +
    154B  LYS*     3.4    22.3    -      -       -      +
    155B  PRO*     3.5     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  MET*     3.9     8.5    -      -       -      +
     44B  MET      2.7    24.8    +      -       -      +
     45B  GLY*     3.4    13.7    -      -       -      -
     46B  LEU      4.1     0.9    +      -       -      -
     83B  TYR*     2.8    27.5    +      -       -      -
    108B  HIS*     5.2     0.9    +      -       -      -
    111B  ARG*     3.4     4.1    -      -       -      +
    112B  SER*     1.3    79.7    -      -       -      +
    114B  PHE*     1.3    63.9    +      -       -      +
    115B  VAL*     5.5     1.1    -      -       -      -
    151B  LEU*     4.1     9.6    -      -       -      +
    154B  LYS*     4.6     4.0    -      -       -      +
    155B  PRO*     3.4    28.5    -      -       -      -
    157B  LEU*     5.8     2.5    -      -       -      -
    273B  LEU*     5.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  LEU*     3.9    18.8    -      -       +      -
     48B  ILE*     3.9    17.7    -      -       +      -
    100B  MET*     4.9     3.1    -      -       +      -
    103B  VAL*     3.5    24.9    -      -       +      -
    108B  HIS*     4.2    12.6    -      +       -      +
    113B  SER*     1.3    77.9    -      -       -      +
    115B  VAL*     1.3    77.5    +      -       -      +
    116B  CYS*     3.7    25.4    -      -       +      -
    143B  PHE*     3.6    35.4    -      +       -      -
    151B  LEU*     3.7    22.7    -      -       +      -
    155B  PRO      3.0     7.1    +      -       -      +
    156B  LYS*     3.5     6.8    -      -       +      -
    157B  LEU*     2.9    26.3    +      -       -      +
    158B  PHE*     4.0    18.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  LEU      2.9    13.4    +      -       -      +
     47B  CYS*     3.3    24.0    -      -       +      -
     48B  ILE      2.9    23.4    +      -       -      -
     78B  PHE*     4.1    10.5    -      -       +      -
     83B  TYR*     3.6    30.1    -      -       +      +
    113B  SER*     4.9     0.2    -      -       -      +
    114B  PHE*     1.3    89.0    -      -       -      +
    116B  CYS*     1.3    64.2    +      -       -      +
    117B  VAL*     4.1     4.3    -      -       +      -
    157B  LEU*     3.4    26.2    -      -       +      +
    159B  ILE*     4.0    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ILE*     3.4     9.9    -      -       +      +
     50B  ILE*     4.8     1.6    -      -       -      -
    100B  MET*     4.1    25.8    -      -       -      -
    114B  PHE*     3.7    11.9    -      -       +      -
    115B  VAL*     1.3    76.0    -      -       -      +
    117B  VAL*     1.3    64.2    +      -       -      +
    118B  LEU*     3.7    30.1    +      -       -      +
    139B  ILE*     5.1     0.4    -      -       -      -
    157B  LEU      2.8     6.7    +      -       -      -
    158B  PHE*     3.3    30.6    -      -       +      +
    159B  ILE*     2.9    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  CYS*     4.2    11.9    -      -       -      -
     48B  ILE      2.7    16.4    +      -       -      +
     49B  ILE*     4.3    12.1    -      -       +      -
     50B  ILE      2.8    28.4    +      -       -      +
     74B  LEU*     3.7    33.4    -      -       +      -
     78B  PHE*     4.9     0.9    -      -       +      -
    115B  VAL*     4.1    14.8    -      -       +      -
    116B  CYS*     1.3    78.8    -      -       -      +
    118B  LEU*     1.3    67.1    +      -       -      +
    119B  LEU*     3.8    15.7    -      -       +      -
    159B  ILE*     3.3    33.4    -      -       +      +
    216B  ILE*     4.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ILE*     3.6    36.6    -      -       +      -
     96B  ILE*     5.2     2.5    -      -       +      -
    116B  CYS*     3.7    18.6    -      -       -      +
    117B  VAL*     1.3    79.2    -      -       -      +
    119B  LEU*     1.3    64.2    +      -       -      +
    120B  SER      4.0     0.4    -      -       -      -
    127B  ILE*     4.0    26.7    -      -       +      -
    136B  LEU*     3.6    31.2    -      -       +      -
    139B  ILE*     4.3    20.0    -      -       +      -
    158B  PHE*     5.2     3.6    -      -       +      -
    159B  ILE      2.8    12.7    +      -       -      +
    160B  ILE*     4.5    12.2    -      -       +      +
    161B  GLN      2.9    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ILE*     4.2     9.2    -      -       +      -
     50B  ILE*     2.9    16.5    +      -       -      +
     51B  ASN*     3.7    20.2    -      -       -      +
     52B  ASN*     3.0    23.7    +      -       -      +
     64B  ARG*     3.3     9.0    +      -       -      +
     67B  THR*     3.7    16.4    -      -       -      +
     70B  ASP*     4.1     6.7    -      -       +      +
     71B  ALA*     4.1    26.7    -      -       -      +
     74B  LEU*     4.2    12.3    -      -       +      -
    117B  VAL*     3.8    20.0    -      -       +      -
    118B  LEU*     1.3    80.0    -      -       -      +
    120B  SER*     1.3    61.5    +      -       -      +
    161B  GLN*     3.6    21.8    -      -       +      -
    216B  ILE*     4.2     7.4    -      -       +      -
----------------------------------------------------------
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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