Contacts of the strand formed by residues 140 - 144 (chain B) in PDB entry 4IGM


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 140 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  LEU*     3.3    17.1    -      -       -      +
    115B  GLY      3.1    16.6    +      -       -      -
    133B  VAL*     5.9     0.4    -      -       -      -
    138B  PHE*     3.2    10.7    -      -       -      +
    139B  PRO*     1.3    83.5    -      -       -      +
    141B  VAL*     1.3    66.5    +      -       -      +
    169B  CYS*     3.7     9.6    -      -       -      -
    170B  SER*     3.2    14.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  LEU*     4.1     6.5    -      -       -      +
    115B  GLY*     3.2    26.0    -      -       -      +
    117B  LEU*     3.9    37.0    -      -       +      -
    129B  MET*     4.3     5.4    -      -       +      -
    132B  CYS*     4.6     9.4    -      -       +      -
    133B  VAL*     6.0     0.2    -      -       +      -
    140B  GLY*     1.3    80.8    -      -       -      +
    142B  GLN*     1.3    54.2    +      -       -      +
    143B  ILE*     4.0     7.5    +      -       +      -
    169B  CYS*     4.1    13.5    -      -       -      -
    170B  SER      3.0     3.6    +      -       -      +
    171B  LEU*     3.4    26.4    -      -       +      -
    172B  PHE*     2.7    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  HIS*     3.1    24.8    -      -       -      -
     74B  SER*     2.9    30.9    +      -       -      -
     75B  THR*     2.8    39.0    +      -       -      +
     77B  PRO*     4.3     0.8    -      -       -      +
     80B  PHE*     4.0    26.4    -      -       +      -
     82B  TYR*     4.6     0.7    +      -       -      -
    114B  LEU*     4.0     4.7    -      -       +      +
    115B  GLY      2.8    18.2    +      -       -      +
    116B  THR*     4.0    11.3    +      -       -      +
    117B  LEU      4.6     0.9    +      -       -      -
    141B  VAL*     1.3    71.6    -      -       -      +
    143B  ILE*     1.3    67.4    +      -       -      +
    172B  PHE*     3.2    24.7    -      -       +      +
    174B  HIS*     3.4    15.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  PHE*     3.8     5.2    -      -       -      -
     82B  TYR*     3.5     9.4    -      -       -      +
    117B  LEU*     4.3     6.7    -      -       +      +
    119B  MET*     3.9    43.5    -      -       +      -
    141B  VAL*     4.0    19.9    +      -       +      -
    142B  GLN*     1.3    78.5    -      -       -      +
    144B  GLY*     1.3    63.8    +      -       -      +
    152B  LEU*     4.6    12.8    -      -       +      -
    160B  VAL*     6.1     0.4    -      -       +      -
    161B  TYR*     5.0     4.5    -      -       +      -
    171B  LEU*     4.3    25.8    -      -       +      -
    172B  PHE      2.8    14.2    +      -       -      +
    173B  VAL*     3.3    15.1    -      -       +      -
    174B  HIS*     2.7    33.8    +      -       -      +
    206B  MET*     6.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  PHE*     3.5    15.5    -      -       -      -
     82B  TYR*     3.1    20.1    +      -       -      -
    143B  ILE*     1.3    79.6    -      -       -      +
    145B  THR*     1.3    66.2    +      -       -      -
    146B  HIS      3.2     4.6    +      -       -      -
    147B  VAL*     5.5     1.1    -      -       -      +
    152B  LEU*     3.8    12.1    -      -       -      +
    173B  VAL*     3.7     8.8    -      -       -      +
    174B  HIS      3.1    13.7    -      -       -      -
    176B  TRP*     5.1     2.0    -      -       -      -
----------------------------------------------------------
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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