Contacts of the strand formed by residues 99 - 102 (chain A) in PDB entry 4R95


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 PHE 99 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  MET*     3.9    22.7    -      -       +      -
     81A  VAL*     3.7    21.1    -      -       +      -
     90A  ILE*     4.0    11.4    -      -       +      -
     97A  SER      4.2     0.8    +      -       -      -
     98A  ASN*     1.4    68.8    +      -       -      +
    100A  ALA*     1.3    57.9    +      -       -      +
    101A  VAL*     3.6    20.6    -      -       +      -
    146A  VAL*     3.8    35.9    -      -       +      -
    158A  ALA*     5.0     0.2    -      -       +      -
    159A  ASN      3.5    24.3    +      -       -      +
    160A  ILE*     3.6    19.4    -      -       +      -
    161A  ALA*     2.9    26.5    +      -       -      +
    179A  ILE      3.5    13.2    -      -       -      -
    180A  LEU*     3.8    17.9    -      -       +      -
    181A  GLY      4.5     2.0    +      -       -      +
    194A  LEU*     6.3     0.2    -      -       -      +
    196A  PRO*     6.1     0.2    -      -       -      +
    197A  PHE*     4.4    20.5    -      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ASN*     3.4     2.9    +      -       +      +
     99A  PHE*     1.3    74.0    -      -       -      +
    101A  VAL*     1.4    59.0    +      -       -      +
    137A  TRP*     3.7    37.2    -      -       +      -
    161A  ALA*     3.4     6.7    -      -       +      -
    163A  ILE*     3.7    18.3    -      -       +      +
    169A  PHE*     4.9     0.2    -      -       +      -
    178A  GLY*     3.2     1.9    -      -       -      -
    179A  ILE*     2.8    49.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  VAL*     5.4     0.9    -      -       +      -
     88A  LEU*     4.3    13.2    -      -       +      -
     90A  ILE*     3.7    15.0    -      -       +      -
     99A  PHE*     3.6    34.3    -      -       +      -
    100A  ALA*     1.4    78.0    -      -       -      +
    102A  GLY*     1.3    59.3    +      -       -      +
    103A  ALA      3.3     0.3    +      -       -      -
    113A  TYR*     3.6    32.8    -      -       +      -
    160A  ILE*     3.7    21.1    -      -       +      -
    161A  ALA      2.9     8.3    +      -       -      +
    162A  ALA*     3.6     0.7    -      -       -      -
    163A  ILE*     2.8    33.8    +      -       -      +
    177A  GLU      3.7     8.3    -      -       -      +
    178A  GLY*     3.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LEU*     5.2     0.7    -      -       -      +
    101A  VAL*     1.3    71.6    -      -       -      +
    103A  ALA*     1.3    58.3    +      -       -      -
    104A  ALA      3.7     0.4    -      -       -      -
    109A  LEU*     4.2    10.5    -      -       -      -
    112A  TYR*     3.3    10.2    -      -       -      +
    113A  TYR*     2.9    25.8    +      -       -      +
    163A  ILE*     4.1     4.5    -      -       -      -
    170A  PHE*     3.6    23.6    -      -       -      -
    177A  GLU      2.8    19.7    +      -       -      +
----------------------------------------------------------
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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