Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 1RP1


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 VAL 99 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  THR*     3.6    23.0    -      -       -      -
     43A  ASN*     3.2     7.0    +      -       -      +
     68A  LYS*     4.3     4.5    -      -       -      +
     69A  LYS*     3.0    35.2    -      -       +      +
     70A  THR      4.1     0.9    -      -       -      +
     71A  ARG*     4.1    16.2    -      -       +      +
     93A  MET*     4.0    22.7    -      -       +      -
     94A  PHE*     3.8    14.3    -      -       +      -
     97A  GLU*     3.4    32.5    -      -       +      +
     98A  GLU*     1.3    74.0    -      -       -      +
    100A  ASN*     1.3    75.4    +      -       -      +
    101A  CYS*     3.7     0.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  LEU*     3.8    14.4    -      -       +      -
     41A  TYR      3.9     3.8    -      -       -      -
     42A  THR*     3.9     8.6    -      -       -      +
     63A  ASN      4.2     0.2    -      -       -      +
     64A  PHE*     3.5    22.3    -      -       +      -
     65A  GLN*     2.9    49.0    +      -       -      +
     68A  LYS*     4.0     4.8    +      -       -      +
     69A  LYS      3.0    14.1    +      -       -      -
     70A  THR*     3.2    27.3    +      -       +      +
     71A  ARG      2.9    26.7    +      -       -      +
     99A  VAL*     1.3    74.3    -      -       -      +
    101A  CYS*     1.3    61.0    +      -       -      +
    102A  ILE      3.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU      3.5     2.1    -      -       -      +
     40A  LEU*     3.6     0.8    -      -       -      +
     41A  TYR*     2.8    46.0    +      -       -      +
     71A  ARG*     3.4     6.7    -      -       -      +
     73A  ILE*     3.5    17.0    -      -       -      -
     90A  CYS*     2.0    57.4    -      -       +      -
     93A  MET*     3.7    15.0    -      -       -      -
     94A  PHE*     4.1    10.5    -      -       +      -
     99A  VAL*     3.7     2.0    +      -       +      -
    100A  ASN*     1.3    72.5    -      -       -      +
    102A  ILE*     1.3    60.7    +      -       -      +
    103A  CYS*     3.9     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  PHE*     4.0    29.2    -      -       +      -
     39A  LEU      3.2     9.6    -      -       -      +
     40A  LEU*     3.8    16.6    -      -       +      -
     52A  LEU*     3.9    20.0    -      -       +      -
     64A  PHE*     4.3    10.1    -      -       +      -
     70A  THR*     3.6    19.7    -      -       +      -
     71A  ARG      3.0     7.1    +      -       -      -
     72A  PHE*     3.1    46.0    -      -       +      +
     73A  ILE*     2.8    30.4    +      -       -      -
    101A  CYS*     1.3    75.7    -      -       -      +
    103A  CYS*     1.3    61.9    +      -       -      +
    104A  VAL*     3.7     0.7    +      -       -      +
    131A  MET*     5.2     2.7    -      -       +      -
    135A  LEU*     5.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ARG      3.4     2.8    -      -       -      +
     38A  PHE*     3.6     1.2    -      -       -      -
     39A  LEU*     2.7    52.4    +      -       +      +
     41A  TYR*     3.9    16.6    -      -       +      -
     73A  ILE*     3.5     7.6    -      -       -      +
     86A  LEU*     3.7    36.1    -      -       +      -
     87A  LEU*     4.1     2.2    -      -       -      -
     90A  CYS*     3.6    28.0    -      -       -      -
    102A  ILE*     1.3    72.3    -      -       -      +
    104A  VAL*     1.3    62.0    +      -       -      +
    105A  ASP*     3.7     1.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  THR*     3.9    25.1    -      -       +      -
     37A  ARG      3.4     4.5    -      -       -      +
     38A  PHE*     3.9    15.9    -      -       +      -
     72A  PHE*     3.8    29.4    -      -       +      -
     73A  ILE      2.8    18.0    +      -       -      +
     74A  ILE*     4.0    20.9    -      -       +      -
     75A  HIS*     3.2    21.1    +      -       -      -
     86A  LEU*     4.3     3.0    -      -       -      +
    102A  ILE*     4.2     1.8    -      -       +      +
    103A  CYS*     1.3    73.4    -      -       -      +
    105A  ASP*     1.3    59.5    +      -       -      +
    106A  TRP*     3.8     5.2    -      -       +      -
    124A  VAL*     4.1    17.3    -      -       +      -
    128A  VAL*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  GLY      3.9     3.5    -      -       -      +
     36A  THR*     3.5     2.1    -      -       -      -
     37A  ARG*     2.7    71.2    +      -       +      +
     39A  LEU*     4.7    13.4    -      -       +      +
     75A  HIS*     3.5     9.7    -      -       +      +
     86A  LEU*     6.1     1.1    -      -       +      -
    103A  CYS*     3.7     2.8    +      -       +      +
    104A  VAL*     1.3    73.4    -      -       -      +
    106A  TRP*     1.3    62.3    +      -       -      +
    107A  LYS*     3.0    26.8    +      -       -      +
----------------------------------------------------------
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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