Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 3I5D


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 64 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  THR      3.8     1.8    +      -       -      -
     63A  VAL*     1.3    73.3    -      -       -      +
     65A  SER*     1.3    59.4    +      -       -      +
    195A  ASN      4.3     0.2    -      -       -      +
    196A  ILE*     3.5     4.7    -      -       -      -
    197A  ARG*     3.0    43.8    +      -       +      +
    199A  PRO*     4.6    14.1    -      -       +      -
    259C  GLN*     6.5     1.8    -      -       +      -
    280C  ARG*     5.5     3.0    +      -       -      +
    325C  MET*     5.4    13.2    -      -       +      -
    327C  PHE*     5.4    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     3.9     5.4    +      -       -      -
     64A  LEU*     1.3    75.0    -      -       -      +
     66A  SER*     1.3    72.2    +      -       -      +
     67A  VAL*     4.2     1.2    -      -       -      +
    194A  ASN*     3.2    11.8    +      -       -      -
    195A  ASN      3.9     3.8    -      -       -      -
    196A  ILE*     4.0     2.9    -      -       -      -
    326A  VAL*     3.1    45.2    -      -       -      +
    325C  MET*     4.0    16.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  SER*     1.3    79.5    +      -       -      +
     67A  VAL*     1.3    65.2    +      -       -      +
     68A  THR*     5.5     0.7    +      -       -      -
    194A  ASN*     2.9    15.2    +      -       -      -
    195A  ASN*     3.1    27.4    +      -       -      +
    255C  VAL*     5.1     3.8    -      -       -      +
    280C  ARG*     6.1     0.7    -      -       -      -
    282C  LEU*     3.6    27.9    -      -       -      +
    321C  ARG*     4.6     0.3    +      -       -      -
    323C  ASP*     3.0    24.8    +      -       -      -
    325C  MET*     4.5     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  SER*     4.2     1.3    -      -       -      +
     66A  SER*     1.3    79.4    +      -       -      +
     68A  THR*     1.3    66.6    +      -       -      +
     69A  THR*     5.4     0.7    -      -       +      -
     99A  ASP      4.4     0.9    -      -       -      +
    100A  GLY*     3.2    37.0    -      -       -      +
    192A  ILE*     5.2     3.1    -      -       +      -
    193A  LYS      3.3     8.7    -      -       -      +
    194A  ASN*     3.7    19.7    -      -       +      +
    260A  ILE*     5.1     0.2    -      -       +      -
    324A  VAL*     3.6    34.5    -      -       +      +
    326A  VAL*     3.8    11.2    -      -       +      -
    321C  ARG*     2.8    25.5    +      -       -      +
    323C  ASP*     4.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  SER*     5.5     0.9    +      -       -      -
     67A  VAL*     1.3    83.1    +      -       -      +
     69A  THR*     1.3    73.7    +      -       -      +
     70A  LYS*     5.9     0.9    -      -       +      -
     99A  ASP      4.8     1.8    -      -       -      -
    191A  LEU*     3.5     1.5    -      -       +      +
    192A  ILE*     3.5     2.6    -      -       -      +
    193A  LYS*     2.8    56.4    +      -       +      +
    255C  VAL*     4.5     9.5    -      -       -      +
    292C  ALA*     6.5     0.7    -      -       +      -
    295C  TYR*     3.9    28.2    -      -       +      -
    321C  ARG*     3.2    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  VAL*     5.4     1.1    -      -       +      -
     68A  THR*     1.3    88.5    -      -       -      +
     70A  LYS*     1.3    63.4    +      -       -      +
     71A  VAL*     5.5     0.8    -      -       -      +
     98A  GLU      4.9     3.1    +      -       -      -
     99A  ASP      4.3     6.9    +      -       -      -
    100A  GLY      3.6    25.0    +      -       -      +
    102A  PHE*     3.8    33.5    -      -       +      +
    190A  VAL*     4.0    11.2    -      -       +      -
    191A  LEU*     3.1     8.5    -      -       -      +
    192A  ILE*     4.4     7.4    -      -       +      -
    324A  VAL*     4.3    12.3    -      -       +      -
    295C  TYR*     5.7     1.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR*     5.9     1.3    -      -       +      -
     69A  THR*     1.3    76.2    -      -       -      +
     71A  VAL*     1.3    64.8    +      -       -      +
     72A  LYS*     3.8     2.6    +      -       -      +
    189A  THR      3.8     0.3    -      -       -      +
    190A  VAL*     3.6     0.5    -      -       -      -
    191A  LEU*     2.9    48.6    +      -       +      +
    292C  ALA*     5.4     7.0    -      -       +      -
    296C  ASN      5.6     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  THR*     5.5     0.7    -      -       -      +
     70A  LYS*     1.3    73.2    -      -       -      +
     72A  LYS*     1.3    66.2    +      -       -      +
     89A  VAL*     3.7    37.1    -      -       +      +
     90A  ALA*     4.5    13.0    -      -       -      +
     94A  ILE*     3.6    18.5    -      -       +      +
    102A  PHE*     3.5    39.3    -      -       +      -
    104A  VAL*     4.7     4.5    -      -       +      -
    188A  PHE*     4.4     9.9    -      -       +      -
    189A  THR      3.4     8.5    -      -       -      +
    190A  VAL*     3.7    14.6    -      -       +      -
    235A  LEU*     5.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  LYS      3.8     1.8    +      -       -      +
     71A  VAL*     1.3    75.2    -      -       -      +
     73A  GLY*     1.3    58.5    +      -       -      +
     89A  VAL*     3.7     3.8    -      -       -      -
     90A  ALA*     6.2     0.4    -      -       -      -
    188A  PHE*     3.6     3.3    -      -       -      +
    189A  THR*     2.7    50.6    +      -       +      +
----------------------------------------------------------
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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