Contacts of the strand formed by residues 257 - 268 (chain C) in PDB entry 1RM1


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 ARG 257 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  THR      4.0     0.2    -      -       -      +
    253C  ARG*     3.2     2.3    -      -       -      -
    254C  THR*     2.9    66.2    +      -       -      +
    255C  LYS*     3.5    25.9    -      -       -      +
    256C  ALA*     1.3    78.6    -      -       +      +
    258C  TRP*     1.3    62.9    +      -       -      +
    259C  LYS*     5.0     7.4    -      -       +      +
    283C  ALA      4.1     2.7    -      -       -      -
    284C  GLU*     4.3    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLU*     4.1     8.7    -      -       -      -
    105A  ARG*     4.3     0.9    -      -       -      -
     66B  LEU*     3.7    22.4    -      -       +      +
     69B  TYR*     3.6    43.3    -      +       -      -
     76B  TRP*     3.7    26.0    -      +       -      -
     78B  PHE*     4.1    12.3    -      +       +      -
    251C  VAL*     3.7    23.6    -      -       +      -
    252C  THR      3.4     4.0    -      -       -      -
    253C  ARG*     3.5    40.1    -      -       +      +
    256C  ALA*     3.4    18.2    +      -       -      +
    257C  ARG*     1.3    75.5    -      -       -      +
    259C  LYS*     1.3    65.2    +      -       -      +
    260C  CYS*     4.3     7.4    -      -       -      -
    281C  VAL*     5.1     0.4    -      -       +      -
    282C  GLU*     3.4     6.6    -      -       -      +
    283C  ALA*     2.9    37.3    +      -       +      +
    285C  TRP*     3.6    18.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  LYS*     3.7     2.6    -      -       -      +
    251C  VAL*     3.7     2.9    -      -       -      -
    252C  THR*     2.8    47.3    +      -       -      +
    257C  ARG*     5.0     8.3    -      -       +      +
    258C  TRP*     1.3    79.2    -      -       -      +
    260C  CYS*     1.3    62.2    +      -       -      +
    261C  SER      4.2     0.2    -      -       -      -
    280C  GLN*     5.7     2.2    -      -       -      +
    281C  VAL      3.2     5.4    -      -       -      +
    282C  GLU*     3.2    33.4    +      -       +      -
      6D    T      5.2    19.0    -      -       -      +
      7D    C      5.5     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  PHE*     3.6    37.9    -      -       +      -
    250C  LYS      3.8     2.7    -      -       -      -
    251C  VAL*     4.1    13.2    -      -       +      -
    258C  TRP*     5.0     6.7    -      -       -      -
    259C  LYS*     1.3    80.5    -      -       -      +
    261C  SER*     1.3    60.0    +      -       -      +
    262C  LEU*     3.7    17.0    +      -       +      -
    279C  ALA      3.4     6.1    -      -       -      +
    280C  GLN*     3.5     5.4    +      -       -      +
    281C  VAL*     2.8    59.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 261 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248C  TYR*     3.6     0.2    -      -       -      -
    249C  ASP*     2.8    34.7    +      -       -      +
    250C  LYS*     2.8    44.0    +      -       -      +
    259C  LYS      4.1     0.4    +      -       -      -
    260C  CYS*     1.3    69.2    -      -       -      +
    262C  LEU*     1.3    68.2    +      -       -      +
    280C  GLN*     3.7    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  PHE*     5.6     3.8    -      -       +      -
    113B  ILE*     4.5     7.6    -      -       +      -
    115B  ALA*     4.8     4.3    -      -       +      -
    244C  MET*     4.2    13.2    -      -       -      -
    246C  CYS*     3.7    17.0    -      -       -      -
    247C  LEU      3.3    16.4    -      -       -      +
    248C  TYR*     3.9    13.9    -      -       +      +
    249C  ASP*     4.4     4.8    -      -       -      +
    251C  VAL*     5.5     1.6    -      -       +      -
    260C  CYS*     3.9    16.6    -      -       +      +
    261C  SER*     1.3    86.7    -      -       -      +
    263C  LYS*     1.3    64.6    +      -       -      +
    276C  PHE*     4.0     0.7    -      -       +      -
    278C  LYS*     3.4     8.7    -      -       -      +
    279C  ALA*     2.9    45.1    +      -       +      +
    280C  GLN*     5.1     0.9    +      -       -      -
    281C  VAL*     3.3    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LYS*     6.2     0.7    -      -       -      -
    118B  SER*     4.3    15.1    -      -       -      -
    246C  CYS*     3.5     2.1    -      -       -      +
    247C  LEU*     3.1    39.1    +      -       +      +
    249C  ASP*     2.9    37.1    +      -       -      +
    262C  LEU*     1.3    78.4    -      -       -      +
    264C  ASP*     1.3    88.0    +      -       -      +
    265C  GLY      3.2     3.6    +      -       -      -
    276C  PHE*     4.0     2.2    -      -       -      -
    277C  GLN      3.0    16.6    -      -       -      +
    278C  LYS*     4.2    11.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 264 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  TYR*     2.6    30.2    +      -       -      +
     49B  ALA*     4.7     3.3    -      -       -      +
     52B  LEU*     3.6    24.5    -      -       +      +
     53B  LYS*     3.6    41.2    -      -       +      +
    246C  CYS*     3.8     0.9    -      -       -      -
    247C  LEU*     4.0    18.3    +      -       +      +
    263C  LYS*     1.3    88.5    -      -       -      +
    265C  GLY*     1.3    55.5    +      -       -      +
    276C  PHE      3.4     8.0    +      -       -      -
    277C  GLN*     3.0    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 265 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  LEU*     3.7     9.7    -      -       -      +
    245C  LEU      3.3    12.8    -      -       -      -
    246C  CYS*     3.3    10.5    -      -       -      -
    263C  LYS      3.2     2.0    +      -       -      -
    264C  ASP*     1.3    76.4    -      -       -      +
    266C  VAL*     1.3    59.7    +      -       -      +
    275C  THR*     3.3     3.3    -      -       -      -
    276C  PHE*     2.8    48.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 266 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  TYR*     4.0    22.2    -      -       +      -
     13B  SER*     4.1    21.8    -      -       -      -
     14B  THR      5.7     0.4    -      -       -      +
     15B  ILE*     6.0     0.9    -      -       +      -
     48B  VAL*     5.7     1.6    -      -       +      -
     52B  LEU*     4.6     7.9    -      -       +      -
     10C  TYR*     3.4    28.9    -      -       +      +
    243C  LEU      4.0     0.7    -      -       -      +
    244C  MET*     3.5     1.0    -      -       -      +
    245C  LEU*     3.0    37.3    +      -       +      +
    265C  GLY*     1.3    76.5    -      -       -      +
    267C  VAL*     1.3    66.7    +      -       -      +
    268C  THR*     5.7     0.9    -      -       -      +
    273C  ASP*     4.5     4.5    -      -       -      +
    274C  TYR      3.4    12.3    -      -       -      +
    275C  THR*     4.2    11.7    -      -       +      -
    276C  PHE*     3.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 267 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LEU*     3.9    20.9    -      -       +      -
    111B  LEU*     4.3     6.3    -      -       +      -
    243C  LEU      3.3    19.5    -      -       -      +
    244C  MET*     3.9    23.3    -      -       +      -
    266C  VAL*     1.3    78.4    -      -       -      +
    268C  THR*     1.3    65.9    +      -       -      +
    269C  ILE*     3.5    25.1    -      -       +      -
    272C  ASN      3.7     0.9    -      -       -      +
    273C  ASP*     3.2     6.0    -      -       -      +
    274C  TYR*     2.8    66.5    +      -       +      +
    276C  PHE*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 268 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  SER*     5.8     0.2    -      -       -      -
     14B  THR*     3.0    19.1    +      -       -      +
     51C  VAL*     5.0     2.7    -      -       +      -
    239C  PRO*     4.2    20.9    -      -       +      +
    241C  GLU      4.2    11.0    -      -       -      +
    242C  ASN*     3.1    25.5    -      -       -      +
    243C  LEU*     3.0    14.7    +      -       -      -
    266C  VAL*     5.7     0.5    -      -       -      +
    267C  VAL*     1.3    72.0    -      -       -      +
    269C  ILE*     1.3    63.4    +      -       -      +
    270C  ASN      4.9     0.4    -      -       -      +
    271C  ARG*     4.3    12.8    -      -       -      +
    272C  ASN      3.3     7.6    -      -       -      +
    273C  ASP*     2.6    22.0    +      -       -      +
----------------------------------------------------------
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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