Contacts of the strand formed by residues 112 - 122 (chain A) in PDB entry 1G13


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 112 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  SER*     3.2     4.8    -      -       -      -
     41A  THR      3.0    31.3    +      -       -      +
    110A  LYS      3.5     2.1    +      -       -      -
    111A  GLU*     1.3    75.5    -      -       -      +
    113A  THR*     1.3    63.1    +      -       -      -
    114A  TYR*     3.9    10.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG*     3.3    21.4    +      -       -      +
     38A  MSE      3.5    36.6    -      -       +      -
     39A  GLY      3.4     5.8    -      -       -      +
     40A  SER*     3.7     3.5    -      -       -      -
    112A  GLY*     1.3    74.0    -      -       -      -
    114A  TYR*     1.3    71.1    +      -       -      +
    115A  SER*     4.2     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  VAL      4.0     1.1    -      -       -      +
     38A  MSE      3.2     5.4    -      -       -      +
     39A  GLY*     2.8    37.5    +      -       -      +
     40A  SER*     4.9     2.5    -      -       -      -
     41A  THR*     4.4     9.9    -      -       +      -
     45A  LEU*     6.2     0.4    -      -       +      -
    103A  LEU*     4.1    15.3    -      -       +      -
    104A  PRO*     3.5    39.4    -      -       +      +
    109A  PHE*     3.7    11.2    -      +       +      -
    110A  LYS*     2.5    50.2    +      -       +      +
    111A  GLU      5.5     0.2    -      -       -      -
    112A  GLY*     3.9    18.4    -      -       -      -
    113A  THR*     1.3    79.4    -      -       -      +
    115A  SER*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  VAL      3.6     3.1    -      -       -      -
     38A  MSE      3.1    23.8    -      -       -      +
    101A  TYR*     4.2     6.6    -      -       -      +
    103A  LEU*     3.7    21.2    -      -       -      +
    113A  THR*     4.2     6.5    +      -       -      +
    114A  TYR*     1.3    72.1    -      -       -      +
    116A  LEU*     1.3    60.3    +      -       -      +
    117A  PRO*     3.8     7.9    -      -       -      +
     71B  TYR*     4.6     7.5    +      -       -      -
     86B  MSE      4.3    19.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     4.2    21.8    -      -       +      +
     36A  SER*     3.2     3.1    -      -       -      -
     37A  VAL*     2.8    47.2    +      -       +      +
     97A  PRO*     3.8    11.7    -      -       +      -
     98A  LEU*     5.2     5.8    -      -       +      -
    101A  TYR*     3.6    19.5    -      -       +      -
    103A  LEU*     3.7    20.0    -      -       +      -
    115A  SER*     1.3    74.7    -      -       -      +
    117A  PRO*     1.3    67.9    -      -       -      +
    119A  SER*     3.5    21.3    -      -       -      +
    121A  PHE*     4.2    24.9    -      -       +      -
     86B  MSE      3.5     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  SER*     3.9     0.2    -      -       -      -
    101A  TYR*     3.5    44.4    -      -       +      +
    115A  SER*     3.8     4.7    -      -       -      +
    116A  LEU*     1.3    91.7    -      -       -      +
    118A  LYS*     1.3    69.4    +      -       -      +
    119A  SER*     2.9    15.1    +      -       -      -
     71B  TYR*     3.9     9.6    -      -       -      +
     79B  HIS      5.1     0.7    -      -       -      +
     82B  ASP*     3.2    13.5    -      -       +      +
     83B  VAL*     3.7    30.5    -      -       +      +
     86B  MSE      3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  THR*     4.0    18.3    -      -       -      +
     23A  GLU*     3.0    36.1    +      -       -      +
     34A  THR*     3.6    15.7    -      -       +      -
     35A  LEU      3.3     7.9    -      -       -      -
     36A  SER*     3.3    11.9    -      -       -      -
    101A  TYR*     4.7     4.2    +      -       -      -
    117A  PRO*     1.3    72.5    -      -       -      +
    119A  SER*     1.3    60.1    +      -       -      +
     78B  GLU*     4.2     3.1    -      -       -      +
     79B  HIS*     3.4    43.5    +      -       +      +
     82B  ASP*     2.7    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  THR*     3.4     4.9    -      -       -      +
     35A  LEU      2.9    29.0    +      -       -      -
     97A  PRO*     3.8    27.8    -      -       -      +
    101A  TYR*     3.8     7.1    -      -       -      -
    116A  LEU*     3.5    12.8    -      -       -      +
    117A  PRO      2.9    18.0    +      -       -      -
    118A  LYS*     1.3    75.2    +      -       -      +
    120A  GLU*     1.3    64.8    -      -       -      +
    121A  PHE*     3.5    15.3    -      -       -      -
     78B  GLU*     3.3    11.1    +      -       -      -
     79B  HIS*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ASN*     4.3    22.7    -      -       +      +
     33A  VAL      3.5     4.3    -      -       -      +
     34A  THR*     2.7    26.1    +      -       -      -
     97A  PRO*     5.5     2.3    -      -       -      +
    119A  SER*     1.3    73.5    -      -       -      +
    121A  PHE*     1.3    68.6    +      -       -      +
     78B  GLU*     3.0    31.3    +      -       +      +
     79B  HIS*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ASN*     3.3     5.6    -      -       -      -
     33A  VAL*     2.9    44.2    +      -       +      +
     35A  LEU*     3.9    32.1    -      -       +      -
     96A  GLU      5.0     0.9    -      -       -      -
     97A  PRO*     3.6    38.1    -      -       +      -
     98A  LEU*     6.4     0.4    -      -       +      -
    116A  LEU*     4.2    10.5    -      -       +      -
    119A  SER*     3.5    28.3    -      -       -      -
    120A  GLU*     1.3    75.8    -      -       -      +
    122A  VAL*     1.3    65.4    +      -       -      +
    123A  VAL      3.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  GLY      4.1     3.4    -      -       -      +
     32A  ASN*     3.2    23.6    -      -       -      +
     33A  VAL*     5.4     0.2    -      -       -      -
    121A  PHE*     1.3    76.3    -      -       -      +
    123A  VAL*     1.3    75.0    +      -       -      +
    124A  PRO*     3.4     5.9    -      -       -      +
    125A  ASP*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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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