Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 1RMO


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 TYR 92 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  VAL*     4.2     3.1    -      -       -      -
     69A  GLN      3.6    10.6    +      -       -      -
     70A  CYS*     3.6    25.7    +      -       +      -
     83A  PHE*     4.3    11.4    -      +       +      -
     84A  PHE*     3.5    35.6    -      +       +      -
     87A  ALA*     4.0    11.0    -      -       +      -
     88A  MET*     3.4    18.4    -      -       +      -
     91A  GLY*     1.3    73.1    -      -       -      +
     93A  VAL*     1.4    67.8    +      -       -      +
     94A  GLN*     3.8     7.9    +      -       -      -
    111A  GLU*     3.6     2.1    -      -       -      -
    112A  VAL*     2.8    69.2    +      -       +      +
    185A  ASN*     3.4    27.4    -      -       -      -
    186A  THR      3.4    18.8    -      -       -      +
    187A  PRO*     4.2     2.2    -      -       +      -
    188A  ILE*     3.8     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  TYR*     1.4    73.7    -      -       -      +
     94A  GLN*     1.3    65.3    +      -       -      +
     95A  GLU*     3.9    20.9    -      -       +      +
    109A  ARG*     3.4    33.9    -      -       +      +
    110A  ALA      3.4    10.8    -      -       -      +
    111A  GLU*     4.4    11.0    -      -       +      -
    184A  GLN      3.7     0.5    -      -       -      +
    185A  ASN*     3.1    27.4    -      -       -      +
    186A  THR*     2.7    25.8    +      -       -      +
    187A  PRO      5.2     0.9    -      -       -      +
    188A  ILE*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  THR*     5.3     1.2    +      -       -      +
     66A  CRO      3.0    42.1    +      -       -      -
     69A  GLN*     3.6     7.1    -      -       -      +
     92A  TYR*     3.8    16.1    +      -       +      -
     93A  VAL*     1.3    75.1    -      -       -      +
     95A  GLU*     1.4    64.8    +      -       -      +
     96A  ARG*     3.4    21.9    -      -       +      +
    108A  THR*     4.1     2.3    +      -       -      +
    109A  ARG*     3.6     1.4    -      -       -      -
    110A  ALA*     2.8    45.3    +      -       +      +
    112A  VAL*     4.9     2.7    -      -       +      -
    183A  GLN*     3.3    22.0    +      -       +      +
    184A  GLN      3.6     2.7    -      -       -      -
    185A  ASN*     2.9    27.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.9    21.0    -      -       +      +
     94A  GLN*     1.4    77.7    -      -       -      +
     96A  ARG*     1.3    65.0    +      -       -      +
    108A  THR      3.3     9.4    -      -       -      +
    109A  ARG*     4.3    21.4    +      -       +      +
    183A  GLN*     3.3     4.3    -      -       -      +
    184A  GLN*     2.9    47.0    +      -       +      +
    186A  THR*     5.0     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  THR*     2.8    30.3    +      -       -      -
     63A  THR*     4.0     7.5    +      -       -      +
     66A  CRO      2.7    29.1    +      -       -      +
     69A  GLN*     4.1     2.0    -      -       -      +
     94A  GLN*     3.4    18.3    -      -       +      +
     95A  GLU*     1.3    80.3    -      -       -      +
     97A  THR*     1.4    65.2    +      -       -      +
     98A  ILE*     4.3    11.0    -      -       +      -
    106A  TYR      4.4     0.2    -      -       -      -
    107A  LYS*     3.3     4.7    -      -       -      +
    108A  THR*     2.9    45.6    +      -       -      +
    165A  PHE*     3.8    18.5    -      -       -      -
    181A  HIS*     3.7    25.2    -      -       -      -
    182A  TYR      3.2    11.0    -      -       -      +
    183A  GLN*     2.8    36.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ARG*     1.4    75.1    +      -       -      +
     98A  ILE*     1.3    65.5    +      -       -      +
     99A  PHE*     3.4    41.5    +      -       +      -
    105A  ASN*     4.6     2.7    -      -       +      -
    106A  TYR      3.2     9.6    -      -       -      +
    107A  LYS*     3.4    34.2    +      -       +      +
    180A  ASP      3.7     1.7    -      -       -      +
    181A  HIS*     3.8     0.7    -      -       -      -
    182A  TYR*     3.0    37.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR      5.2     2.9    -      -       -      +
     62A  THR*     4.0     3.4    -      -       -      +
     63A  THR*     3.9    21.1    -      -       -      +
     96A  ARG*     4.3    14.6    -      -       +      -
     97A  THR*     1.3    75.8    -      -       -      +
     99A  PHE*     1.3    61.6    +      -       -      +
    100A  PHE*     3.7    25.2    +      -       +      -
    105A  ASN*     3.1     6.2    -      -       -      -
    106A  TYR*     2.8    50.7    +      -       +      +
    108A  THR*     4.9     2.7    -      -       +      -
    179A  ALA*     4.0     7.2    -      -       +      -
    180A  ASP      3.4     3.4    -      -       -      +
    181A  HIS*     3.5    51.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  THR*     3.4    30.3    -      -       +      -
     98A  ILE*     1.3    72.5    -      -       -      +
    100A  PHE*     1.3    65.2    +      -       -      +
    101A  LYS*     3.5     2.3    +      -       -      -
    105A  ASN*     4.1    22.2    -      -       +      -
    107A  LYS*     5.3     2.7    -      -       -      -
    178A  LEU      3.8     0.2    -      -       -      +
    179A  ALA*     3.4     1.9    -      -       -      -
    180A  ASP*     2.9    39.9    +      -       +      +
    182A  TYR*     3.8    36.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR*     4.0    23.3    -      -       +      -
     98A  ILE*     3.7    27.6    -      -       +      -
     99A  PHE*     1.3    72.9    -      -       -      +
    101A  LYS*     1.3    66.9    +      -       -      +
    102A  ASP      3.3     0.5    +      -       -      -
    103A  ASP*     2.9    32.7    +      -       +      +
    104A  GLY      2.9    22.2    +      -       -      +
    106A  TYR*     3.7    38.1    -      +       -      -
    130A  PHE*     3.7    15.9    -      +       +      -
    136A  ILE*     4.1    13.9    -      -       +      -
    169A  HIS*     3.9    16.6    -      +       -      -
    177A  GLN*     3.9    16.8    -      -       +      +
    178A  LEU      3.6     1.6    -      -       -      -
    179A  ALA*     3.6    21.3    -      -       +      -
    181A  HIS*     5.8     0.2    -      +       -      -
----------------------------------------------------------
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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