Contacts of the strand formed by residues 116 - 124 (chain B) in PDB entry 3MXN


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 CYS 116 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  SER*     3.3    22.0    -      -       -      +
     84B  ARG*     5.5    16.2    -      -       +      +
    109B  GLN*     2.8    33.3    +      -       +      -
    110B  ALA*     2.9    29.4    +      -       +      +
    114B  GLU*     3.3    19.7    -      -       -      -
    115B  PRO*     1.3    75.4    -      -       -      +
    117B  LEU*     1.3    65.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  LEU*     4.5     5.6    -      -       +      -
     58B  VAL*     3.6    27.6    -      -       +      -
     60B  MET*     3.8    29.8    -      -       +      -
     81B  PHE*     4.3    12.6    -      -       +      -
     82B  SER      2.8    13.6    +      -       -      +
     83B  VAL*     3.4     7.5    -      -       +      -
     84B  ARG*     2.9    30.3    +      -       -      +
    104B  VAL*     4.0    22.9    -      -       +      +
    106B  GLY*     4.2    11.4    -      -       -      +
    107B  VAL      3.3     5.8    -      -       -      +
    108B  VAL*     3.8    18.8    -      -       +      +
    109B  GLN*     4.2     3.8    -      -       -      -
    115B  PRO*     5.4     1.6    -      -       +      -
    116B  CYS*     1.3    83.5    -      -       -      +
    118B  GLN*     1.3    60.4    +      -       -      +
    119B  ALA      3.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  ARG*     3.8    20.2    -      -       -      +
     85B  GLY*     3.8    21.6    -      -       -      +
     87B  GLU*     5.6     0.2    +      -       -      -
     88B  ARG*     5.3     7.5    -      -       -      +
    106B  GLY*     3.2     1.5    -      -       -      -
    107B  VAL*     2.8    41.2    +      -       +      +
    109B  GLN*     3.8    30.5    -      -       +      +
    117B  LEU*     1.3    72.3    -      -       -      +
    119B  ALA*     1.3    68.2    +      -       -      +
    120B  VAL*     3.6     2.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  VAL*     3.6    22.2    -      -       +      -
     84B  ARG      2.9    20.4    +      -       -      +
     85B  GLY*     4.5     5.2    -      -       -      +
     86B  LEU*     3.7    18.8    -      -       +      -
     88B  ARG*     5.6     2.3    -      -       -      +
     89B  VAL*     3.7    16.8    -      -       +      +
    104B  VAL*     4.5     5.4    -      -       +      -
    105B  MET      3.8     4.5    -      -       -      -
    106B  GLY*     4.3     1.8    -      -       -      -
    117B  LEU      3.8     1.2    +      -       -      -
    118B  GLN*     1.3    77.7    -      -       -      +
    120B  VAL*     1.3    61.0    +      -       -      +
    121B  LYS      4.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515A  VAL*     5.0     9.2    -      -       +      +
     17B  LEU*     5.6    15.0    -      -       +      +
     18B  PRO*     4.8     6.5    -      -       +      -
     89B  VAL*     3.4    16.3    -      -       -      +
     90B  PRO*     3.6     8.0    -      -       -      +
    105B  MET*     2.7    48.2    +      -       +      +
    106B  GLY*     4.5     2.9    -      -       -      -
    107B  VAL*     4.2    25.1    -      -       +      -
    118B  GLN      4.3     1.8    -      -       -      +
    119B  ALA*     1.3    77.0    -      -       -      +
    121B  LYS*     1.3    65.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  PHE*     4.0    23.3    -      -       +      +
    514A  ILE*     2.8    33.3    +      -       -      +
    515A  VAL*     3.9    14.8    -      -       -      +
    585A  LEU      4.5     0.6    +      -       -      -
    586A  ILE*     2.8    41.0    +      -       -      +
    588A  LEU      5.0     0.6    +      -       -      -
     89B  VAL*     4.1     9.4    -      -       -      -
     90B  PRO*     4.5    15.5    -      -       +      -
    103B  MET*     4.4     5.8    -      -       -      -
    104B  VAL*     3.2     9.9    -      -       -      +
    105B  MET*     3.0    37.5    +      -       +      +
    119B  ALA*     4.6     1.1    -      -       -      +
    120B  VAL*     1.3    89.6    +      -       +      +
    122B  MET*     1.3    60.1    +      -       -      +
    123B  THR*     3.9    14.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  VAL*     5.0     0.7    -      -       -      -
     72B  ALA*     4.4     0.2    -      -       +      -
     74B  LEU*     4.0    24.0    -      -       +      -
     83B  VAL*     4.6     2.5    -      -       +      -
     86B  LEU*     3.7    38.8    -      -       +      -
     89B  VAL*     4.1    11.1    -      -       +      +
     90B  PRO      4.5     9.6    +      -       -      +
     92B  GLY*     5.5     1.6    +      -       -      -
     95B  CYS*     4.0    22.8    -      -       -      +
     96B  LEU*     3.8    25.6    -      -       +      -
    102B  VAL*     4.0    18.4    -      -       +      -
    103B  MET      3.2    11.9    -      -       -      +
    104B  VAL*     3.6    19.5    -      -       +      -
    121B  LYS*     1.3    75.5    -      -       -      +
    123B  THR*     1.3    68.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  PHE*     6.1     0.9    -      -       -      +
    586A  ILE*     3.3    37.3    +      -       +      +
    587A  ASP*     3.5    25.4    +      -       -      +
    588A  LEU      5.5     1.2    +      -       -      -
    589A  CYS*     5.5     1.2    -      -       -      +
     90B  PRO      5.3     0.7    -      -       -      +
     92B  GLY      5.5     0.9    -      -       -      +
     93B  ARG      5.7     0.4    -      -       -      -
     95B  CYS*     3.7     7.0    -      -       -      -
    102B  VAL*     3.3     3.5    -      -       -      +
    103B  MET*     3.0    50.2    +      -       -      +
    121B  LYS*     3.9    16.7    +      -       +      -
    122B  MET*     1.3    82.0    -      -       -      +
    124B  ASP*     1.3    63.3    +      -       -      +
    125B  LEU*     4.2     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    587A  ASP*     4.2    13.8    +      -       -      +
     93B  ARG*     3.4    48.9    +      -       +      +
     94B  PRO      4.4     2.6    -      -       -      +
     95B  CYS*     3.6    27.0    -      -       +      +
    100B  LYS*     3.4    26.0    +      -       -      +
    101B  TYR      3.2     4.3    -      -       -      +
    102B  VAL*     4.1     0.3    -      -       -      +
    123B  THR*     1.3    74.5    +      -       -      +
    125B  LEU*     1.3    71.3    +      -       -      +
    126B  SER*     2.6    30.4    +      -       -      -
    127B  ASP*     4.9     0.7    -      -       -      +
----------------------------------------------------------
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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