Contacts of the strand formed by residues 49 - 56 (chain A) in PDB entry 3I7O


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 LEU 49 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     3.7    27.6    -      -       +      -
     33A  ILE*     5.2     1.8    -      -       +      -
     42A  TYR*     3.6    26.0    -      -       +      -
     43A  VAL      3.6     1.3    -      -       -      -
     44A  VAL*     4.5     9.0    -      -       +      -
     45A  THR*     4.7     0.9    -      -       -      -
     47A  GLU*     3.9    10.2    +      -       -      +
     48A  GLY*     1.3    77.3    -      -       -      +
     50A  ARG*     1.3    59.3    +      -       -      +
     51A  PRO*     3.3     9.9    -      -       -      +
    317A  LEU*     3.8    27.6    -      -       +      -
    323A  PHE*     4.6     8.3    -      -       +      -
    333A  LEU*     3.5    28.0    -      -       +      +
    353A  PHE*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     3.1     3.4    -      -       -      -
     43A  VAL*     2.5    58.6    +      -       -      +
     45A  THR*     3.4    29.4    -      -       +      +
     48A  GLY      3.5     1.0    +      -       -      -
     49A  LEU*     1.3    71.0    -      -       -      +
     51A  PRO*     1.4    72.1    -      -       +      +
     52A  VAL*     3.7    14.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ILE      3.5     0.9    -      -       -      +
     42A  TYR*     3.5    28.2    -      -       +      -
     49A  LEU      3.3    11.9    -      -       -      +
     50A  ARG*     1.4    91.4    -      -       +      +
     52A  VAL*     1.3    64.3    +      -       -      +
     53A  LYS      5.3     0.7    -      -       -      +
    663A  ASN*     4.4    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  THR*     4.4     9.2    -      -       +      +
     41A  ILE*     2.6    22.3    +      -       +      +
     43A  VAL*     3.5    31.2    -      -       +      -
     50A  ARG*     3.7    13.9    -      -       -      +
     51A  PRO*     1.3    81.0    -      -       -      +
     53A  LYS*     1.3    65.9    +      -       +      +
     91A  TYR*     3.1    35.3    +      -       +      +
     98A  ILE*     4.6     7.1    -      -       +      +
    663A  ASN*     6.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLU*     3.6     1.7    -      -       -      +
     41A  ILE*     2.8    49.6    +      -       +      +
     51A  PRO*     5.3     0.4    -      -       -      +
     52A  VAL*     1.3    86.4    -      -       +      +
     54A  GLU*     1.3    68.1    +      -       -      +
     55A  VAL*     3.8    19.6    -      -       +      +
     91A  TYR*     4.3     9.2    -      -       +      -
     98A  ILE*     3.7    46.5    +      -       +      +
     99A  ASP*     4.9     2.9    -      -       -      +
    100A  ILE*     3.8    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LYS*     2.5    39.0    +      -       -      +
     38A  ARG*     2.5    45.1    +      -       -      +
     39A  LEU      3.4     3.1    -      -       -      +
     40A  GLU*     3.3    38.4    -      -       +      +
     53A  LYS*     1.3    80.4    +      -       -      +
     55A  VAL*     1.3    62.5    +      -       -      +
     56A  GLY      4.1     0.2    +      -       -      -
    663A  ASN*     6.1     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ARG*     3.4     7.0    -      -       -      -
     39A  LEU*     2.7    59.6    +      -       +      +
     41A  ILE*     5.1     0.9    -      -       +      -
     53A  LYS*     3.8    23.6    -      -       +      +
     54A  GLU*     1.3    75.3    -      -       -      +
     56A  GLY*     1.3    58.2    +      -       -      +
     57A  MET*     5.7     1.3    -      -       +      -
    100A  ILE*     3.3    39.5    -      -       +      +
   1065A  VAL*     4.1    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  THR      3.2     7.9    -      -       -      -
     38A  ARG*     2.9    30.5    -      -       -      +
     54A  GLU      4.1     0.2    +      -       -      -
     55A  VAL*     1.3    73.4    -      -       -      +
     57A  MET*     1.3    63.4    +      -       -      +
     58A  TYR*     6.1     0.4    -      -       -      -
   1065A  VAL*     3.2    26.7    +      -       -      +
----------------------------------------------------------
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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