Contacts of the strand formed by residues 91 - 100 (chain N) in PDB entry 2O5J


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 91 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22N  SER*     3.5     6.0    +      -       -      -
     23N  TYR      3.9     1.1    -      -       -      -
     24N  GLY      3.6     7.9    -      -       -      -
     26N  VAL*     4.5     0.4    -      -       -      -
     49N  ILE*     4.1     1.6    -      -       -      -
     50N  PHE*     3.2    17.7    -      -       -      -
     90N  MET*     1.3    76.4    -      -       -      +
     92N  HIS*     1.3    60.6    +      -       -      +
    518N  PRO*     3.1     6.2    -      -       -      +
    519N  VAL*     2.2    48.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 92 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18N  ILE*     3.8    18.4    -      -       +      -
     19N  ARG*     3.5    37.2    +      -       +      +
     22N  SER*     2.4    33.1    +      -       -      +
     24N  GLY*     2.7    36.5    +      -       -      -
     25N  GLU*     3.0    45.5    +      -       +      +
     26N  VAL      3.5     2.8    +      -       -      -
     91N  GLY*     1.3    74.2    -      -       -      +
     93N  ILE*     1.3    58.5    -      -       -      +
     94N  GLU*     5.0     4.3    -      -       -      -
    516N  ALA*     5.2     1.1    -      -       +      -
    517N  VAL      2.9    13.2    -      -       -      +
    519N  VAL*     3.2     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 93 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25N  GLU*     4.0     4.5    -      -       -      +
     26N  VAL*     4.1    10.8    -      -       +      +
     92N  HIS*     1.3    74.7    -      -       -      +
     94N  GLU*     1.3    60.5    +      -       -      +
     95N  LEU*     3.1     9.0    -      -       +      +
    516N  ALA*     4.6     0.7    -      -       -      -
    517N  VAL*     2.4    63.4    +      -       +      +
    519N  VAL*     3.5    21.8    -      -       +      -
    544N  TYR*     4.1    15.7    -      -       +      -
    547N  LEU*     3.9    21.3    -      -       +      -
    548N  ILE*     4.1    29.8    -      -       +      -
    551N  ASN*     3.8    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 94 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19N  ARG*     2.7    42.8    +      -       -      -
     25N  GLU*     3.1    24.1    +      -       -      +
     92N  HIS*     5.0     3.6    -      -       +      -
     93N  ILE*     1.3    69.3    -      -       -      +
     95N  LEU*     1.3    64.1    +      -       -      +
     96N  ALA      3.7     0.3    +      -       -      -
    515N  GLU*     2.8    27.7    -      -       -      +
    516N  ALA*     4.5     2.5    -      -       -      +
    551N  ASN*     2.5    22.4    +      -       -      -
    555N  LYS*     3.9    17.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93N  ILE*     3.1    18.3    +      -       +      +
     94N  GLU*     1.3    79.0    -      -       -      +
     96N  ALA*     1.3    70.3    +      -       -      +
     97N  THR      4.6     9.1    -      -       -      +
     98N  PRO*     4.7     0.2    -      -       +      -
     99N  ALA*     4.4    11.2    -      -       +      +
    514N  LEU*     3.3    27.1    -      -       +      +
    515N  GLU*     3.2    34.6    +      -       -      +
    516N  ALA      3.3     0.9    -      -       -      +
    517N  VAL*     3.2    31.2    -      -       +      +
    547N  LEU*     5.3     4.3    -      -       +      -
    551N  ASN*     3.0    13.7    -      -       -      +
    574N  LEU*     4.9     3.1    -      -       +      -
    578N  VAL*     4.4    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 96 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94N  GLU      4.7     0.4    -      -       -      -
     95N  LEU*     1.3    77.9    -      -       -      +
     97N  THR*     1.3    63.0    +      -       -      +
     98N  PRO*     3.8     6.2    -      -       -      +
    515N  GLU*     6.0     0.2    -      -       -      +
    551N  ASN*     2.6    19.7    +      -       -      +
    554N  LEU*     3.2    35.9    -      -       +      -
    555N  LYS*     4.5     9.2    -      -       +      +
    558N  LEU*     4.3    15.7    -      -       +      -
    574N  LEU*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 97 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95N  LEU*     4.6     4.0    -      -       -      +
     96N  ALA*     1.3    81.3    -      -       -      +
     98N  PRO*     1.3    83.5    -      -       +      +
     99N  ALA*     3.7     0.7    +      -       -      +
    456N  MET      5.5     1.6    -      -       -      +
    458N  ALA      5.2     1.1    -      -       -      +
    459N  GLU*     3.2    28.4    +      -       +      +
    554N  LEU*     4.0     2.4    -      -       -      +
    558N  LEU*     6.0     1.4    -      -       -      +
    568N  ARG*     5.6     2.9    -      -       -      +
    571N  LYS*     2.9    52.0    +      -       +      +
    574N  LEU*     3.6    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 98 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95N  LEU*     4.7     2.2    -      -       +      -
     96N  ALA      3.8     7.4    -      -       -      +
     97N  THR*     1.3   105.4    -      -       +      +
     99N  ALA*     1.3    59.6    +      -       -      +
    458N  ALA*     3.1    33.5    +      -       +      +
    459N  GLU*     5.2     2.5    -      -       -      +
    462N  GLN*     4.2    27.1    -      -       +      +
    513N  ILE*     5.0     9.2    -      -       +      -
    514N  LEU      3.4    20.6    -      -       -      +
    515N  GLU*     4.3    18.8    -      -       +      +
    575N  GLN*     5.3     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 99 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95N  LEU*     4.4     5.1    -      -       +      +
     97N  THR      4.7     1.6    -      -       -      +
     98N  PRO*     1.3    74.1    -      -       -      +
    100N  ALA*     1.3    64.3    +      -       -      +
    458N  ALA*     3.4    12.2    -      -       -      +
    513N  ILE*     4.5     0.7    -      -       -      -
    514N  LEU*     3.5    25.9    +      -       -      +
    574N  LEU*     5.3     1.6    -      -       +      -
    575N  GLN*     3.8    38.6    -      -       +      +
    578N  VAL*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 100 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99N  ALA*     1.3    80.2    -      -       -      +
    101N  HIS*     1.3    64.9    +      -       -      +
    102N  ILE*     3.3     3.8    +      -       -      +
    105N  VAL*     4.1    19.9    -      -       +      +
    128N  TYR*     5.8     5.4    -      -       +      -
    458N  ALA*     4.4     6.5    -      -       +      +
    512N  MET      4.7     9.0    -      -       -      +
    513N  ILE*     5.1     6.5    -      -       +      -
    514N  LEU*     4.1     7.6    -      -       -      -
    575N  GLN*     4.6    12.0    +      -       -      +
    578N  VAL*     4.6     6.1    -      -       -      +
    579N  ASP*     4.3    11.8    -      -       -      +
    582N  LEU*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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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