Contacts of the strand formed by residues 376 - 381 (chain B) in PDB entry 2P1N


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 SER 376 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  ARG      3.0    10.4    +      -       -      +
    342B  GLU*     3.0    27.1    +      -       -      +
    343B  LEU      2.8    29.6    +      -       -      -
    344B  ARG*     5.0     4.5    +      -       -      -
    374B  LEU*     3.6     1.5    -      -       -      +
    375B  GLU*     1.3    83.4    -      -       -      +
    377B  VAL*     1.3    61.7    +      -       -      +
    399B  MET*     3.9     1.0    -      -       -      -
    401B  ARG*     3.4    38.0    +      -       -      +
    601B  IHP      5.3     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 377 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343B  LEU*     3.4     9.6    -      -       +      +
    344B  ARG*     5.3     0.2    -      -       -      -
    364B  LEU*     4.0    25.4    -      -       +      -
    374B  LEU*     3.9    30.1    -      -       +      -
    376B  SER*     1.3    81.5    +      -       -      +
    378B  LEU*     1.3    63.9    +      -       -      +
    379B  TYR*     4.0    20.0    -      -       +      -
    399B  MET*     4.1    10.1    -      -       +      -
    401B  ARG*     2.6    14.1    +      -       -      +
    402B  PHE*     4.0    25.6    -      -       +      -
    403B  ARG*     2.8    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 378 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343B  LEU      2.9    10.7    +      -       -      +
    344B  ARG*     3.3    28.9    -      -       +      +
    345B  VAL      2.8    27.5    +      -       -      +
    346B  PHE*     3.9    31.6    -      -       +      -
    377B  VAL*     1.3    73.7    -      -       -      +
    379B  TYR*     1.3    69.3    +      -       -      +
    380B  PHE*     3.9    15.9    -      -       +      -
    403B  ARG*     3.2    48.7    -      -       +      +
    602B  CFA      3.6    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 379 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  LEU*     3.8    18.2    -      -       +      +
    343B  LEU*     4.7     4.9    -      -       +      -
    345B  VAL*     3.7    32.5    -      -       +      -
    359B  LEU*     3.5    17.0    -      -       +      +
    360B  THR      2.8    25.7    +      -       -      -
    363B  GLY*     3.9     1.0    -      -       -      -
    364B  LEU*     3.5    40.5    +      -       +      -
    377B  VAL*     4.0    10.8    -      -       +      -
    378B  LEU*     1.3    77.1    -      -       -      +
    380B  PHE*     1.4    62.8    +      -       -      +
    381B  CYS*     3.9    33.3    +      -       +      -
    384B  MET*     4.9     2.5    -      -       +      -
    403B  ARG      2.8    13.0    +      -       -      +
    404B  LEU*     3.6    14.9    -      -       +      +
    405B  CYS*     2.8    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 380 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  ASP*     4.7     7.6    -      -       -      +
    345B  VAL*     3.1    28.6    +      -       -      +
    346B  PHE*     4.1     9.0    -      +       -      -
    347B  PRO*     3.6    39.5    -      -       +      -
    359B  LEU*     3.5    16.6    -      -       -      +
    378B  LEU*     3.9    26.9    -      -       +      -
    379B  TYR*     1.4    75.4    -      -       -      +
    381B  CYS*     1.4    60.5    +      -       -      +
    405B  CYS*     3.5    36.1    -      -       +      -
    407B  ILE*     4.7    10.3    -      -       +      -
    602B  CFA      3.8    15.5    -      -       -      -
      6C  PRO*     5.0     0.9    -      -       +      -
      7C  PRO*     3.6    22.0    -      -       +      -
      8C  VAL*     3.7    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 381 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359B  LEU*     3.7    24.9    -      -       +      +
    360B  THR*     4.5     2.9    -      -       -      -
    361B  GLU      5.2     0.2    -      -       -      -
    379B  TYR*     3.9    15.7    -      -       +      -
    380B  PHE*     1.4    72.8    -      -       -      +
    382B  ARG*     1.3    67.2    +      -       -      +
    383B  GLN      3.5    25.1    -      -       -      +
    384B  MET*     3.9    18.2    -      -       -      -
    404B  LEU*     4.6     3.8    -      -       -      -
    405B  CYS      3.3     5.4    +      -       -      -
    406B  ILE*     3.5    16.9    -      -       -      -
    407B  ILE*     3.3    25.6    +      -       -      +
----------------------------------------------------------
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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