Contacts of the strand formed by residues 42 - 48 (chain N) in PDB entry 1G3I


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 VAL 42 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  ARG*     3.8     5.0    +      -       -      +
     37N  LEU*     2.9    57.0    +      -       +      +
     38N  TYR*     4.3     3.1    -      -       +      -
     40N  GLY      4.9     0.8    -      -       -      -
     41N  LYS*     1.3    86.9    +      -       +      +
     43N  LEU*     1.3    69.2    +      -       -      +
     44N  ALA*     5.9     0.9    -      -       +      -
     60N  PHE*     5.3     2.0    -      -       +      -
     64N  LEU*     3.4    25.6    -      -       +      -
     69N  GLY*     5.1     6.1    -      -       -      +
     71N  LEU*     4.0    23.1    -      -       +      -
     97N  VAL*     6.2     0.2    -      -       +      -
     98N  ALA      3.7     5.4    -      -       -      +
     99N  ASP*     3.6    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12N  VAL*     3.7    24.0    -      -       +      +
     14N  VAL*     4.3    18.6    -      -       +      -
     34N  VAL*     5.1     0.4    -      -       +      -
     35N  ARG      4.0     2.9    -      -       -      +
     36N  ARG*     3.6    30.5    -      -       +      +
     42N  VAL*     1.3    74.6    -      -       -      +
     44N  ALA*     1.3    61.1    +      -       -      +
     96N  ILE      3.6     1.5    -      -       -      +
     97N  VAL*     3.1     8.0    -      -       -      +
     98N  ALA      2.7    36.0    +      -       -      +
    170N  GLU*     3.3    49.6    -      -       +      +
    172N  LEU*     3.6    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14N  VAL*     4.7     0.2    -      -       -      -
     33N  LYS      3.9     0.5    -      -       -      +
     34N  VAL*     3.1     7.6    -      -       -      +
     35N  ARG*     2.8    39.6    +      -       -      +
     37N  LEU*     4.8     9.6    -      -       +      -
     42N  VAL*     5.9     0.9    -      -       +      -
     43N  LEU*     1.3    76.6    -      -       -      +
     45N  GLY*     1.3    59.4    +      -       -      +
     46N  PHE*     4.3     2.2    +      -       -      -
     57N  PHE*     3.4    34.3    -      -       +      -
     95N  LEU*     5.1     2.0    -      -       +      -
     96N  ILE      3.3     3.8    -      -       -      -
     97N  VAL*     4.1    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 45 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3N  ILE*     4.1    21.1    -      -       -      -
     14N  VAL*     4.4     2.1    -      -       -      +
     33N  LYS      3.3     9.0    -      -       -      -
     34N  VAL*     4.1     5.8    -      -       -      -
     44N  ALA*     1.3    75.1    -      -       -      +
     46N  PHE*     1.3    61.3    +      -       -      -
     95N  LEU*     3.4     5.3    -      -       -      +
     96N  ILE*     2.7    42.5    +      -       -      -
    123N  ILE*     3.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 46 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1N  THR*     3.9     3.6    -      -       -      +
      3N  ILE*     3.4    17.1    -      -       -      +
     32N  ARG      3.1    23.3    -      -       -      -
     33N  LYS*     3.0    37.8    +      -       +      +
     35N  ARG*     4.1    15.5    -      -       +      -
     44N  ALA      4.7     3.1    -      -       -      -
     45N  GLY*     1.3    76.8    -      -       -      -
     47N  ALA*     1.3    65.0    +      -       -      +
     50N  THR*     6.3     0.4    -      -       -      -
     53N  ALA*     3.6    30.5    -      -       +      +
     54N  PHE*     3.5    33.9    -      +       -      -
     57N  PHE*     4.8    13.9    -      +       +      -
     94N  MET      3.5     5.4    -      -       -      -
     95N  LEU*     3.3    20.0    -      -       +      -
    444U  LEU*     4.7    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1N  THR*     3.6    23.1    -      -       +      -
      3N  ILE*     3.9     2.9    -      -       +      -
     46N  PHE*     1.3    80.4    -      -       -      +
     48N  GLY*     1.3    58.8    +      -       -      +
     53N  ALA*     5.2     0.4    -      -       -      -
     93N  ALA*     3.1     4.0    -      -       -      -
     94N  MET*     2.8    36.4    +      -       +      +
    123N  ILE*     3.6    19.7    -      -       +      -
    124N  GLY*     3.9    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 48 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1N  THR*     4.7    10.7    +      -       -      -
     46N  PHE*     5.6     0.2    -      -       -      -
     47N  ALA*     1.3    75.2    -      -       -      +
     49N  GLY*     1.3    63.0    +      -       -      -
     50N  THR*     3.4     4.7    +      -       -      +
     53N  ALA*     4.6     4.8    -      -       -      +
     92N  GLU      3.4    10.8    -      -       -      -
     93N  ALA*     3.6     4.7    -      -       -      -
----------------------------------------------------------
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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