Contacts of the strand formed by residues 193 - 199 (chain L) in PDB entry 2IG2


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 TYR 193 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119L  LEU*     4.9     0.4    -      -       -      -
    134L  LEU*     3.7    22.4    -      -       +      -
    150L  TRP*     5.0     3.8    -      +       +      -
    151L  LYS      3.5     8.1    -      -       -      -
    152L  ALA*     3.5    23.0    -      -       +      +
    157L  VAL*     4.5     6.1    -      -       +      -
    180L  LEU*     3.7    23.6    -      -       +      -
    182L  LEU*     3.7    23.2    -      -       +      +
    186L  GLN*     3.8     9.7    +      -       -      +
    187L  TRP*     3.7    41.5    -      +       -      -
    190L  HIS*     3.7    29.7    +      -       +      -
    192L  SER*     1.3    75.5    +      -       -      +
    194L  SER*     1.3    65.3    +      -       -      +
    207L  THR*     3.4     0.2    -      -       -      -
    208L  VAL*     2.7    52.3    +      -       +      +
    210L  PRO*     5.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 194 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119L  LEU*     4.6     0.9    -      -       -      -
    149L  ALA      3.6     0.9    -      -       -      +
    150L  TRP*     3.8     7.3    -      -       -      -
    151L  LYS*     2.9    48.6    +      -       -      +
    192L  SER*     4.1     3.3    +      -       -      -
    193L  TYR*     1.3    77.7    +      -       -      +
    195L  CYS*     1.3    60.4    +      -       -      +
    196L  GLN*     3.5     5.8    +      -       -      +
    205L  GLU*     3.9    21.0    +      -       -      -
    206L  LYS      3.3     8.7    -      -       -      -
    207L  THR*     2.9    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 195 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117L  VAL*     4.1     7.4    -      -       +      +
    119L  LEU*     4.2    15.9    -      -       +      +
    136L  CYS*     2.0    52.3    -      -       +      -
    148L  VAL*     3.6    24.9    -      -       -      -
    149L  ALA      3.8     3.6    -      -       -      -
    150L  TRP*     4.3    10.3    -      -       +      -
    194L  SER*     1.3    69.5    -      -       -      +
    196L  GLN*     1.3    63.0    +      -       -      +
    197L  VAL*     3.8     1.7    +      -       -      -
    204L  VAL      3.5     4.5    -      -       -      +
    205L  GLU*     3.9     0.4    -      -       -      -
    206L  LYS      3.0    27.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 196 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148L  VAL*     3.5     1.2    -      -       -      +
    149L  ALA*     2.6    60.1    +      -       +      +
    151L  LYS*     3.4    41.0    +      -       +      +
    194L  SER*     3.5     2.1    +      -       -      +
    195L  CYS*     1.3    74.3    -      -       -      +
    197L  VAL*     1.3    57.9    +      -       -      +
    198L  THR*     4.3     3.9    +      -       -      -
    203L  THR*     3.9    19.8    -      -       +      +
    204L  VAL      3.4     4.9    -      -       -      -
    205L  GLU*     3.3    38.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 197 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115L  PRO*     4.7     6.9    -      -       +      +
    117L  VAL*     3.3    45.1    -      -       +      -
    138L  ILE*     3.9    28.3    -      -       +      -
    146L  VAL*     4.2    15.0    -      -       +      -
    147L  THR      3.1    21.3    -      -       -      +
    148L  VAL*     4.0     8.5    -      -       +      -
    195L  CYS*     4.4     1.3    -      -       -      +
    196L  GLN*     1.3    76.6    -      -       -      +
    198L  THR*     1.3    59.0    +      -       -      +
    199L  HIS*     4.0     1.2    +      -       -      -
    202L  SER      3.7     0.3    -      -       -      +
    203L  THR*     3.4     1.1    -      -       -      +
    204L  VAL*     2.8    44.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 198 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145L  ALA      4.5     0.9    -      -       -      +
    146L  VAL      3.8     0.5    -      -       -      -
    147L  THR*     2.7    52.1    +      -       -      +
    149L  ALA*     6.1     0.9    -      -       -      +
    196L  GLN*     5.0     3.8    +      -       -      -
    197L  VAL*     1.3    70.2    -      -       -      +
    199L  HIS*     1.3    60.8    +      -       -      +
    200L  GLU      4.2     0.7    -      -       -      -
    201L  GLY*     4.2    14.6    -      -       -      +
    202L  SER      3.3     9.2    -      -       -      +
    203L  THR*     2.9    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 199 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  LYS*     4.8     2.7    -      -       +      -
    113L  ALA      3.3    14.3    +      -       -      -
    114L  ASN*     4.3    10.7    +      -       -      -
    115L  PRO*     3.6    33.8    -      -       +      +
    141L  PHE*     4.0     4.0    -      +       +      -
    142L  TYR      3.1    28.5    +      -       -      -
    143L  PRO*     2.7    39.1    +      -       +      +
    145L  ALA      3.5    19.1    -      -       -      -
    146L  VAL*     3.7    17.0    -      -       +      -
    197L  VAL      4.0     0.2    -      -       -      -
    198L  THR*     1.3    74.6    -      -       -      +
    200L  GLU*     1.4    77.3    +      -       +      +
    201L  GLY      3.5     0.2    -      -       -      -
    202L  SER*     2.7    21.9    +      -       -      +
----------------------------------------------------------
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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