Contacts of the strand formed by residues 59 - 72 (chain B) 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 LYS 59 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  GLN      3.6    11.0    +      -       -      +
     58B  SER*     1.3    81.0    -      -       -      +
     60B  LEU*     1.3    62.7    +      -       -      +
     61B  THR*     4.7     4.5    -      -       +      +
     86B  THR      4.5     0.7    -      -       -      +
     87B  VAL      4.6     0.7    -      -       -      +
     88B  GLU      3.9    22.4    +      -       -      +
    276C  PHE*     4.6     0.2    -      -       -      -
    277C  GLN*     4.3     7.9    -      -       +      -
    278C  LYS*     3.0    51.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  SER*     4.2     0.9    -      -       -      -
     59B  LYS*     1.3    73.5    -      -       -      +
     61B  THR*     1.3    70.9    +      -       -      +
     62B  VAL*     3.8    16.2    -      -       +      -
     85B  VAL*     4.2    12.6    -      -       +      -
     86B  THR      3.1    17.5    -      -       -      +
     87B  VAL*     4.0    16.2    -      -       +      +
    244C  MET*     3.8    21.1    -      -       +      -
    267C  VAL*     3.9    20.2    -      -       +      -
    269C  ILE*     5.4     0.4    -      -       +      -
    274C  TYR*     4.6    10.8    -      -       +      -
    275C  THR      5.5     0.4    -      -       -      +
    276C  PHE*     3.9    30.2    -      -       +      +
    278C  LYS      3.0     7.0    +      -       -      +
    279C  ALA*     3.0    31.7    -      -       +      -
    280C  GLN*     3.0     2.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  LYS      4.7     4.0    -      -       -      +
     60B  LEU*     1.3    85.0    -      -       -      +
     62B  VAL*     1.3    65.7    +      -       -      +
     63B  LYS*     5.1    12.9    -      -       -      +
     84B  GLN      3.5     2.1    +      -       -      +
     85B  VAL*     3.4     4.3    -      -       -      +
     86B  THR*     2.6    48.6    +      -       -      +
    280C  GLN*     3.1    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LEU*     3.8    18.8    -      -       +      -
     61B  THR*     1.3    76.2    -      -       -      +
     63B  LYS*     1.3    63.2    +      -       -      +
     80B  VAL*     4.3    11.7    -      -       +      -
     83B  CYS*     4.0    26.9    -      -       +      -
     84B  GLN      3.7     2.0    -      -       -      -
     85B  VAL*     4.3    14.4    -      -       +      -
    111B  LEU*     4.6    11.9    -      -       +      -
    113B  ILE*     4.8     0.9    -      -       +      -
    244C  MET*     4.2    14.8    -      -       +      -
    280C  GLN      2.6    11.8    +      -       -      +
    281C  VAL*     3.2    23.8    -      -       +      +
    282C  GLU*     2.8    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  THR*     5.1    12.6    -      -       -      +
     62B  VAL*     1.3    82.2    -      -       -      +
     64B  GLY*     1.3    58.5    +      -       -      +
     83B  CYS*     2.9     4.6    -      -       -      +
     84B  GLN*     2.7    49.2    +      -       +      +
    280C  GLN      5.7     0.2    -      -       -      +
    282C  GLU*     3.3    40.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  VAL      4.3     0.2    -      -       -      -
     63B  LYS*     1.3    75.8    -      -       -      +
     65B  ASN*     1.3    66.0    +      -       -      -
     80B  VAL*     3.9     4.2    -      -       -      +
     82B  ASN      3.8     7.6    -      -       -      -
     83B  CYS*     3.5    14.1    -      -       -      -
    282C  GLU      3.2     7.7    +      -       -      +
    283C  ALA*     2.9    24.1    -      -       -      +
    284C  GLU*     3.2     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  GLY*     1.3    77.1    -      -       -      -
     66B  LEU*     1.3    60.0    +      -       -      +
     67B  ASP*     3.1     5.2    +      -       +      -
     80B  VAL*     3.5     1.4    -      -       -      -
     81B  LYS*     2.9    44.4    +      -       +      +
     82B  ASN*     4.0    13.3    -      -       -      +
    283C  ALA*     4.1     1.3    -      -       -      -
    284C  GLU*     3.7    24.5    +      -       -      +
    286C  VAL*     4.3    16.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  ARG*     2.9    20.4    +      -       -      -
     65B  ASN*     1.3    69.0    -      -       -      +
     67B  ASP*     1.3    60.3    +      -       -      +
     68B  THR      2.8    31.6    -      -       -      +
     69B  TYR*     3.8    21.1    -      -       +      -
     78B  PHE*     4.2    15.0    -      -       +      -
     79B  ILE      3.7    11.4    -      -       -      +
     80B  VAL*     4.6     2.9    -      -       +      +
    258C  TRP*     3.7    39.0    -      -       +      +
    283C  ALA*     3.4    25.4    -      -       +      +
    284C  GLU      3.2     6.9    +      -       -      +
    285C  TRP*     3.2    27.8    -      -       +      +
    286C  VAL      4.2     0.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ARG*     5.1     4.5    +      -       -      -
     91A  ASN*     4.0     2.4    +      -       -      +
    107A  ARG*     3.4    29.6    +      -       -      +
     65B  ASN*     3.1     4.8    +      -       -      +
     66B  LEU*     1.3    73.4    -      -       -      +
     68B  THR*     1.3    70.5    +      -       -      +
     79B  ILE*     2.8    26.4    +      -       +      +
     81B  LYS*     3.8    44.2    +      -       +      +
    285C  TRP*     3.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ARG*     3.9    45.3    +      -       +      +
     91A  ASN*     3.4    12.3    +      -       -      +
     66B  LEU*     2.8    17.6    -      -       -      +
     67B  ASP*     1.3    93.1    +      -       -      +
     69B  TYR*     1.3    77.0    +      -       -      +
     77B  THR      4.5     0.4    -      -       -      -
     78B  PHE*     3.4     0.9    -      -       -      -
     79B  ILE*     2.9    35.7    +      -       +      +
    231C  ILE*     4.7     5.4    -      -       +      -
    285C  TRP*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ARG*     4.7     0.2    -      -       -      -
     91A  ASN*     2.8    76.3    +      -       +      -
     92A  ALA      3.9     5.2    -      -       -      -
     93A  GLU*     4.0    16.2    -      -       +      -
    103A  ILE      4.9     0.5    +      -       -      -
    104A  MET*     4.7     0.3    -      -       -      -
    105A  ARG*     2.8    39.1    +      -       -      +
     66B  LEU*     3.8     6.3    -      -       +      -
     68B  THR*     1.3    81.4    -      -       -      +
     70B  GLY*     1.3    64.6    +      -       -      +
     76B  TRP*     4.4     5.6    -      +       -      -
     77B  THR*     3.2     9.4    -      -       -      -
     78B  PHE*     3.7    22.0    -      -       +      -
    231C  ILE*     5.7     0.7    -      -       -      +
    258C  TRP*     3.6    27.8    -      +       +      -
    285C  TRP*     3.8    27.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ALA      3.4    11.2    -      -       -      -
     69B  TYR*     1.3    80.6    -      -       -      +
     71B  PHE*     1.3    62.3    +      -       -      -
     72B  CYS      4.2     0.4    -      -       -      -
     75B  VAL      3.5     1.0    -      -       -      +
     76B  TRP*     3.3    10.6    -      -       -      -
     77B  THR*     2.9    36.7    +      -       -      -
    231C  ILE*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ALA*     5.1     0.5    -      -       -      +
     92A  ALA      3.0     8.8    +      -       -      +
     93A  GLU*     3.2    20.4    -      -       +      +
     94A  TYR      2.8    42.6    +      -       -      -
     95A  ASN*     3.5    37.9    -      -       +      -
     70B  GLY*     1.3    75.3    -      -       -      +
     72B  CYS*     1.3    61.6    +      -       -      +
     74B  ASP*     3.7    31.2    -      -       -      -
     75B  VAL      3.2    14.4    -      -       -      -
     76B  TRP*     3.3    47.1    -      +       +      -
    248C  TYR*     3.7    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  LYS*     4.1    17.5    -      -       -      -
     86A  ALA*     3.7    27.4    -      -       +      +
     87A  LEU*     3.5    31.9    -      -       +      -
     92A  ALA      5.9     0.2    -      -       -      +
     94A  TYR*     4.0    14.8    -      -       -      -
     70B  GLY      4.2     0.4    -      -       -      -
     71B  PHE*     1.3    75.8    -      -       -      +
     73B  ASP*     1.3    76.4    +      -       -      +
     74B  ASP      3.2     2.9    -      -       -      +
     75B  VAL*     3.0    22.3    +      -       -      +
----------------------------------------------------------
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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