Contacts of the strand formed by residues 368 - 376 (chain B) in PDB entry 2IFG


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 GLY 368 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  ALA*     5.0     1.3    -      -       -      +
    364B  ALA*     3.5     2.5    -      -       -      +
    365B  ASN*     2.9    37.3    +      -       -      +
    366B  PRO      3.2     1.3    -      -       -      -
    367B  PHE*     1.3    81.5    -      -       -      +
    369B  GLN*     1.3    60.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 369 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  ALA*     5.2     2.9    -      -       -      -
    314B  ARG*     3.5    15.2    -      -       -      +
    362B  LEU*     3.3    39.5    -      -       -      +
    363B  ALA      3.2    12.6    -      -       -      +
    364B  ALA*     4.1    12.9    -      -       +      +
    368B  GLY*     1.3    75.9    -      -       -      +
    370B  ALA*     1.3    71.1    +      -       -      +
    371B  SER*     4.3     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 370 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  ALA*     3.5    26.8    -      -       -      +
    287B  SER*     4.1     0.9    -      -       -      -
    288B  VAL*     3.5    30.7    -      -       +      +
    361B  LEU      3.8     0.3    -      -       -      +
    362B  LEU*     3.5     2.9    -      -       -      -
    363B  ALA*     2.8    33.5    +      -       -      +
    369B  GLN*     1.3    77.0    -      -       -      +
    371B  SER*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 371 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  VAL*     4.6     6.1    -      -       -      +
    360B  THR*     3.5    18.0    -      -       -      +
    361B  LEU      3.3     6.1    -      -       -      -
    362B  LEU*     3.4    17.9    -      -       -      +
    369B  GLN*     4.3     3.1    +      -       -      -
    370B  ALA*     1.3    76.3    -      -       -      +
    372B  ALA*     1.3    67.2    +      -       -      +
    373B  SER*     4.4     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 372 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  VAL*     3.9    21.3    -      -       +      +
    289B  GLN*     4.1     5.6    -      -       -      -
    290B  LEU*     3.6    30.7    -      -       +      +
    360B  THR*     3.3     1.8    -      -       -      -
    361B  LEU      2.8    31.0    +      -       -      -
    371B  SER*     1.3    79.5    +      -       -      +
    373B  SER*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 373 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290B  LEU*     4.3     3.4    -      -       -      +
    358B  ASN*     3.3    17.5    -      -       -      -
    359B  TYR      3.1     4.7    -      -       -      -
    360B  THR*     3.2    20.9    +      -       -      +
    371B  SER*     4.4     3.1    +      -       -      -
    372B  ALA*     1.3    77.9    -      -       -      +
    374B  ILE*     1.3    67.4    +      -       -      +
      1N  NAG      3.8    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 374 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290B  LEU*     3.4    33.0    -      -       +      +
    291B  HIS      4.4    12.6    -      -       -      +
    292B  THR*     4.7    14.8    -      -       +      +
    293B  ALA*     5.0     2.2    -      -       +      +
    301B  ILE*     3.8    21.8    -      -       +      -
    357B  GLY      3.7     0.3    -      -       -      +
    358B  ASN*     3.8     4.3    -      -       -      -
    359B  TYR*     2.7    43.5    +      -       +      +
    373B  SER*     1.3    77.2    -      -       -      +
    375B  MET*     1.3    79.7    +      -       +      +
    376B  ALA*     5.7     0.9    -      -       +      -
      1N  NAG      5.2     4.9    -      -       +      -
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Residues in contact with MET 375 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293B  ALA*     5.4     2.6    +      -       -      +
    318B  ASN*     5.9     0.2    -      -       -      +
    357B  GLY*     3.3    30.1    -      -       -      +
    358B  ASN*     3.5    25.8    -      -       -      -
    374B  ILE*     1.3    91.4    -      -       +      +
    376B  ALA*     1.3    61.2    +      -       -      +
      1N  NAG      3.6    27.3    -      -       +      +
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Residues in contact with ALA 376 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293B  ALA*     4.1    16.6    -      -       +      -
    301B  ILE*     4.4     6.5    -      -       +      -
    355B  ASN      4.0     0.3    -      -       -      +
    356B  ASN*     3.0     7.8    -      -       -      +
    357B  GLY      2.8    37.0    +      -       -      -
    359B  TYR*     4.2    13.0    -      -       +      -
    374B  ILE*     3.8     2.4    +      -       +      +
    375B  MET*     1.3    77.7    -      -       -      +
    377B  ALA*     1.3    60.6    +      -       -      +
    378B  PHE*     3.5    30.7    -      -       +      -
----------------------------------------------------------
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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