Contacts of the strand formed by residues 100 - 105 (chain A) in PDB entry 5EAA


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 ALA 100 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  GLN*     2.9    36.7    +      -       +      +
     88A  PHE*     4.5    10.3    -      -       +      -
     94A  LEU*     3.9    10.8    +      -       +      +
     95A  ILE*     5.6     1.5    -      -       -      +
     98A  LYS*     3.4     6.1    +      -       -      +
     99A  ARG*     1.3    80.2    -      -       -      +
    101A  ARG*     1.3    71.3    +      -       -      +
    271A  THR*     4.5     2.7    -      -       +      -
    272A  LEU      3.4     8.7    -      -       -      +
    273A  VAL*     4.2    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ASP*     3.1    26.1    +      -       -      -
     84A  GLN*     4.6     3.6    +      -       -      -
     98A  LYS*     5.7     9.0    -      -       -      +
    100A  ALA*     1.3    80.2    +      -       -      +
    102A  THR*     1.3    72.6    +      -       -      +
    271A  THR*     3.7     0.5    -      -       -      +
    272A  LEU*     2.9    32.5    +      -       -      +
    280A  VAL*     3.5    22.6    -      -       +      +
    281A  ASP*     3.7    22.8    -      -       -      +
    284A  PHE*     3.5    48.2    -      -       +      -
    288A  LYS*     5.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ASP*     3.9    10.0    -      -       -      +
     79A  PHE*     5.3     0.4    -      -       +      -
     80A  GLY*     4.0    32.2    -      -       -      +
     83A  THR*     4.5     3.4    -      -       +      -
     84A  GLN*     3.3    23.2    +      -       -      +
    101A  ARG*     1.3    87.8    +      -       -      +
    103A  ALA*     1.3    65.2    +      -       -      +
    269A  ALA*     3.9    21.5    -      -       +      -
    270A  CYS      3.7     3.4    -      -       -      +
    271A  THR*     2.8    27.2    +      -       -      +
    284A  PHE*     3.5    11.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ASP*     3.5     8.7    -      -       -      -
    102A  THR*     1.3    77.2    -      -       -      +
    104A  GLN*     1.3    65.5    +      -       -      +
    105A  THR*     3.9     1.6    +      -       -      +
    269A  ALA*     3.2     3.1    -      -       -      -
    270A  CYS*     2.8    45.1    +      -       +      +
    284A  PHE*     3.9    19.3    -      -       +      -
    287A  MET*     5.0     2.7    -      -       -      -
    291A  ILE*     4.0    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     3.7     2.9    -      -       -      +
     73A  ILE      4.5     3.6    -      -       -      +
     74A  ASP      2.7    18.3    +      -       -      +
     75A  GLY*     3.3     5.4    -      -       -      -
     76A  ILE*     3.0    41.6    -      -       -      +
     79A  PHE*     3.8    30.1    -      -       +      -
     80A  GLY*     6.2     0.4    -      -       -      -
    102A  THR      4.2     0.4    -      -       -      -
    103A  ALA*     1.3    76.7    -      -       -      +
    105A  THR*     1.3    67.1    +      -       -      +
    266A  ARG      5.7     0.6    -      -       -      +
    267A  VAL*     6.2     0.7    -      -       +      -
    268A  GLY      4.4     1.6    -      -       -      +
    291A  ILE*     5.3     0.2    -      -       -      +
    295A  TYR*     3.7     6.1    +      -       -      -
    298A  PRO*     3.5    29.4    -      -       +      +
    299A  PRO*     3.0    28.2    -      -       -      +
    303A  ALA*     3.2    19.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ALA*     3.9     8.9    +      -       -      +
    104A  GLN*     1.3    80.3    -      -       -      +
    106A  PRO*     1.3    66.8    -      -       -      +
    107A  GLY      2.8    33.2    +      -       -      +
    110A  GLY      3.3     4.5    +      -       -      -
    111A  ALA*     2.9    35.2    +      -       +      +
    114A  VAL*     4.2     5.5    -      -       -      +
    266A  ARG      3.7     4.9    -      -       -      +
    267A  VAL*     4.1     0.2    -      -       -      -
    268A  GLY      2.7    33.1    +      -       -      +
    269A  ALA*     4.2     2.0    -      -       -      -
    270A  CYS*     4.0     6.8    -      -       -      +
    291A  ILE*     5.4     0.2    -      -       -      +
    295A  TYR*     3.5    11.0    +      -       -      -
    298A  PRO*     5.0     1.8    -      -       -      -
    299A  PRO*     5.2     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