Contacts of the strand formed by residues 52 - 66 (chain B) in PDB entry 1MT7


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 GLY 52 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     4.0     0.5    -      -       -      +
     51A  GLY*     3.4    12.4    -      -       -      -
     48B  GLY*     3.3     0.9    -      -       -      -
     49B  GLY      3.0    31.1    +      -       -      -
     50B  ILE      3.3     0.6    +      -       -      -
     51B  GLY*     1.3    80.4    -      -       -      +
     53B  PHE*     1.3    70.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLY*     4.8     3.0    +      -       -      +
     46B  MET*     4.1    30.7    -      -       +      +
     47B  ILE*     3.2    27.4    -      -       -      -
     48B  GLY*     3.4    20.0    -      -       -      -
     49B  GLY      5.2     0.7    -      -       -      -
     52B  GLY*     1.3    80.1    -      -       -      -
     54B  ILE*     1.3    68.2    +      -       -      +
      8P  VAL*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     3.4    46.0    -      -       +      +
     51A  GLY*     3.9     9.9    -      -       -      +
     46B  MET*     3.6     5.9    -      -       -      -
     47B  ILE*     3.0    48.1    +      -       +      +
     53B  PHE*     1.3    79.7    -      -       -      +
     55B  LYS*     1.3    65.8    +      -       -      +
     56B  VAL*     3.9    19.8    +      -       +      -
     79B  PRO*     4.3    16.4    -      -       +      +
     80B  THR*     4.2    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  LYS      3.7     6.3    -      -       -      +
     46B  MET*     3.4    27.1    -      -       +      -
     54B  ILE*     1.3    74.6    -      -       -      +
     56B  VAL*     1.3    64.9    +      -       -      +
     78B  GLY*     4.2     0.2    -      -       -      -
     79B  PRO*     3.3    22.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  VAL*     4.4     6.3    -      -       +      -
     42B  TRP*     5.3     0.2    -      -       -      -
     44B  PRO*     3.9     3.6    -      -       -      +
     45B  LYS*     3.0    49.3    +      -       +      +
     47B  ILE*     4.0    18.2    -      -       +      -
     54B  ILE*     4.0    21.3    -      -       +      -
     55B  LYS*     1.3    81.8    -      -       -      +
     57B  ARG*     1.3    63.8    +      -       -      +
     76B  LEU*     3.9    28.3    -      -       +      -
     77B  VAL      3.4    10.1    -      -       -      +
     78B  GLY*     3.9    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  GLU*     2.6    45.0    +      -       -      -
     36B  MET      3.0    18.0    +      -       -      -
     37B  ASN*     4.7     5.9    +      -       -      +
     38B  LEU      4.8     0.2    -      -       -      +
     42B  TRP*     3.2    43.6    -      -       +      +
     43B  LYS      3.9     3.1    -      -       -      -
     56B  VAL*     1.3    75.8    -      -       -      +
     58B  GLN*     1.3    61.6    +      -       -      +
     59B  TYR*     3.4    35.7    +      -       +      -
     76B  LEU*     3.3     3.7    -      -       -      -
     77B  VAL*     2.8    51.9    +      -       -      +
     78B  GLY*     5.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  TRP*     3.2    23.2    -      -       -      +
     43B  LYS*     2.9    31.3    +      -       -      +
     44B  PRO      5.2     0.7    -      -       -      +
     45B  LYS*     3.6    29.0    +      -       +      +
     56B  VAL      4.0     0.6    +      -       -      -
     57B  ARG*     1.3    71.7    -      -       -      +
     59B  TYR*     1.3    63.7    +      -       -      +
     60B  ASP*     3.2    28.5    +      -       -      +
     74B  THR*     3.5    22.9    +      -       +      +
     76B  LEU*     3.7    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LEU*     3.4    41.3    +      -       +      -
     39B  PRO      3.9    10.8    -      -       -      -
     40B  GLY*     3.8    16.2    -      -       -      -
     41B  LYS      3.7    14.6    -      -       -      -
     42B  TRP*     3.6    18.7    +      +       +      -
     57B  ARG*     3.4    53.8    +      -       +      -
     58B  GLN*     1.3    75.8    -      -       -      +
     60B  ASP*     1.3    62.0    +      -       -      +
     62B  ILE*     3.7    21.8    -      -       +      +
     74B  THR*     3.2     4.2    -      -       -      +
     75B  VAL*     2.8    38.8    +      -       +      +
     77B  VAL*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LYS      5.2     2.8    +      -       -      -
     58B  GLN*     3.2    27.8    +      -       -      +
     59B  TYR*     1.3    74.3    -      -       -      +
     61B  GLN*     1.3    79.2    +      -       +      +
     62B  ILE*     3.3    13.1    +      -       -      +
     74B  THR*     2.8    27.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  ASP*     1.3    82.2    -      -       +      +
     62B  ILE*     1.3    62.9    +      -       -      +
     63B  PRO*     3.6     8.1    -      -       -      +
     72B  ILE*     3.7    32.5    +      -       +      +
     73B  GLY*     3.6    16.0    +      -       -      -
     74B  THR*     5.0     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ILE*     3.9    27.4    -      -       +      -
     16B  GLY*     5.2     2.9    -      -       -      +
     38B  LEU*     4.8    12.6    -      -       +      -
     39B  PRO      5.4     4.7    -      -       -      +
     59B  TYR*     3.7    37.5    -      -       +      +
     60B  ASP      3.6    18.6    -      -       -      +
     61B  GLN*     1.3    77.8    -      -       -      +
     63B  PRO*     1.3    82.1    -      -       +      +
     64B  VAL*     3.4     6.3    +      -       +      +
     72B  ILE*     3.3     3.6    -      -       -      +
     73B  GLY      3.0    27.9    +      -       -      +
     75B  VAL*     4.1     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ARG      3.9     5.9    -      -       -      +
     15B  ILE*     4.1     7.3    -      -       -      +
     16B  GLY      4.5     2.3    +      -       -      -
     61B  GLN      3.6     6.5    -      -       -      +
     62B  ILE*     1.3    93.2    -      -       +      +
     64B  VAL*     1.3    63.8    +      -       -      +
     71B  ALA      3.5     9.2    -      -       -      +
     72B  ILE*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ILE*     4.5    14.4    -      -       +      -
     14B  ARG      3.3     8.5    -      -       -      +
     15B  ILE*     3.7    28.3    -      -       +      -
     31B  THR*     6.0     0.7    -      -       +      -
     33B  LEU*     5.8     0.4    -      -       +      -
     62B  ILE*     3.4    10.3    +      -       +      +
     63B  PRO*     1.3    80.1    -      -       -      +
     65B  GLU*     1.3    64.3    +      -       -      +
     66B  ILE*     4.0    20.3    +      -       +      -
     69B  HIS      3.9     0.3    -      -       -      +
     70B  LYS*     3.8     0.4    -      -       -      -
     71B  ALA*     2.8    40.9    +      -       +      +
     75B  VAL*     4.0    14.8    -      -       +      -
     85B  ILE*     5.0     2.9    -      -       +      -
     89B  LEU*     4.1    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ILE*     3.0     8.1    -      -       -      +
     14B  ARG*     2.7    61.6    +      -       +      +
     64B  VAL*     1.3    72.4    -      -       -      +
     66B  ILE*     1.3    61.8    +      -       -      +
     67B  CYS      4.0     0.8    +      -       -      -
     68B  GLY*     3.8    30.4    +      -       -      +
     69B  HIS      3.4    12.6    -      -       -      +
     70B  LYS*     3.1    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PHE*     4.4     3.6    -      -       +      -
     11B  VAL*     3.9    25.8    -      -       +      -
     12B  THR      3.9     2.7    -      -       -      -
     13B  ILE*     3.9    14.4    -      -       +      -
     24B  LEU*     4.4     8.1    -      -       +      -
     64B  VAL*     4.0    13.9    -      -       +      +
     65B  GLU*     1.3    73.5    -      -       -      +
     67B  CYS*     1.3    76.1    +      -       +      +
     68B  GLY      3.2     0.2    -      -       -      -
     69B  HIS*     2.7    31.2    +      -       -      +
     71B  ALA*     4.6     4.3    -      -       +      -
     85B  ILE*     3.9    24.0    -      -       +      -
     89B  LEU*     4.2    16.2    -      -       +      +
     93B  ILE*     3.9    37.9    -      -       +      -
----------------------------------------------------------
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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