Contacts of the strand formed by residues 123 - 131 (chain A) in PDB entry 6S1M


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 PRO 123 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  HIS*     3.7    26.5    -      -       +      +
    104A  TYR      3.4     7.4    -      -       -      +
    105A  VAL*     4.5     3.6    -      -       +      -
    121A  SER*     3.9     8.7    -      -       -      +
    122A  VAL*     1.3    90.9    -      -       +      +
    124A  VAL*     1.3    61.1    +      -       -      +
    125A  LEU*     4.6     5.2    -      -       -      +
    143A  GLY      4.9     1.9    +      -       -      -
    144A  PHE      3.6    30.7    +      -       -      +
    146A  PRO*     4.9     0.4    -      -       +      -
    215A  ALA      3.9    22.4    -      -       -      +
    216A  LEU*     4.0     9.4    -      -       +      -
    217A  PRO*     4.1    10.8    -      -       +      -
    250A  PHE*     4.3     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  HIS*     4.3     0.9    +      -       -      -
    104A  TYR*     2.7    69.2    +      -       +      +
    106A  GLY*     4.7     7.2    -      -       -      +
    107A  PRO      5.9     2.9    -      -       -      +
    109A  GLN*     6.5     0.2    -      -       +      -
    121A  SER      4.0    15.3    -      -       -      +
    122A  VAL      3.3     6.0    +      -       -      +
    123A  PRO*     1.3    78.4    -      -       -      +
    125A  LEU*     1.3    62.0    +      -       -      +
    126A  ARG*     6.0     0.2    -      -       +      -
    140A  HIS*     5.1     7.9    -      -       -      +
    141A  ILE      3.5    11.9    -      -       -      +
    142A  HIS*     3.4    36.3    -      -       +      +
    143A  GLY      5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     5.9     6.3    -      -       +      -
    102A  ASP      3.5    12.8    -      -       -      +
    103A  HIS*     5.3     1.3    -      -       -      +
    123A  PRO      4.6     5.8    -      -       -      +
    124A  VAL*     1.3    78.5    -      -       -      +
    126A  ARG*     1.3    66.0    +      -       -      +
    139A  CYS      3.6     0.7    -      -       -      +
    140A  HIS*     3.5     6.1    +      -       -      +
    141A  ILE*     2.9    48.3    +      -       +      +
    144A  PHE*     4.9     7.4    -      -       +      -
    250A  PHE*     3.9    34.8    -      -       +      -
    251A  GLU*     5.4    10.3    -      -       +      -
    254A  PHE*     3.6    52.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     3.4     7.0    -      -       -      +
    102A  ASP*     2.7    67.9    +      -       +      +
    103A  HIS      4.2     5.1    +      -       -      -
    104A  TYR*     3.9    44.5    -      -       +      +
    124A  VAL*     6.0     0.2    -      -       +      -
    125A  LEU*     1.3    81.3    -      -       -      +
    127A  ALA*     1.3    62.0    +      -       -      +
    128A  PHE*     3.9    24.2    -      -       +      -
    138A  CYS*     5.0     3.4    -      -       -      -
    139A  CYS      3.5     4.5    -      -       -      +
    140A  HIS*     4.2    26.0    -      -       +      +
    141A  ILE*     5.7     0.2    -      -       -      -
    282A  THR*     5.2     2.5    -      -       -      -
    424A  VAL*     3.8    31.1    -      -       -      +
    427A  LEU*     5.2     6.9    -      -       -      +
    452A  VAL*     5.2     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PHE*     4.4    10.0    -      -       +      -
     98A  GLN*     4.8     9.4    -      -       +      +
    100A  GLU      3.6     6.7    -      -       -      +
    101A  ILE*     4.8     8.5    -      -       +      -
    126A  ARG*     1.3    75.4    -      -       -      +
    128A  PHE*     1.3    63.6    +      -       -      +
    137A  VAL      3.7     1.0    -      -       -      +
    138A  CYS*     3.6     2.1    -      -       -      -
    139A  CYS*     2.9    49.6    +      -       +      +
    141A  ILE*     4.8    13.7    -      -       +      -
    266A  LEU*     5.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PHE*     4.4     1.6    -      -       -      -
     98A  GLN*     3.3     6.3    -      -       -      +
     99A  LEU*     2.8    26.3    +      -       +      -
    100A  GLU*     3.0    29.8    +      -       +      +
    102A  ASP*     4.1    14.1    -      -       +      -
    126A  ARG*     3.9    37.7    -      -       +      -
    127A  ALA*     1.3    74.1    -      -       -      +
    129A  GLY*     1.3    59.6    +      -       -      +
    137A  VAL      3.5     3.8    -      -       -      +
    138A  CYS*     4.0    28.3    -      -       +      -
    282A  THR*     5.2     5.6    -      -       +      -
    284A  CYS*     4.7     5.4    -      -       -      -
    423A  ARG*     4.0    33.9    -      -       +      +
    424A  VAL*     5.2     6.1    -      -       +      -
    452A  VAL*     5.0     3.6    -      -       +      -
    453A  GLY*     3.9    34.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PHE*     3.7    13.4    -      -       -      -
     97A  GLN      3.1    13.5    -      -       -      -
     98A  GLN*     3.9     0.4    -      -       -      -
     99A  LEU*     4.2     6.1    -      -       -      -
    128A  PHE*     1.3    76.0    -      -       -      +
    130A  VAL*     1.3    68.3    +      -       -      +
    136A  SER*     3.7     2.6    -      -       -      -
    137A  VAL      2.9    31.7    +      -       -      -
    423A  ARG*     5.4     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  ARG*     3.9    21.3    -      -       -      +
     96A  PHE*     3.9     4.9    -      -       -      -
     97A  GLN*     2.9    35.1    +      -       +      +
     99A  LEU*     5.2     2.7    -      -       +      -
    129A  GLY*     1.3    79.5    -      -       -      +
    131A  THR*     1.3    65.9    +      -       -      +
    134A  GLY*     5.4     2.9    -      -       -      -
    135A  PHE      3.4    12.8    -      -       -      +
    136A  SER*     4.6     2.5    -      -       -      -
    137A  VAL*     4.9     0.4    -      -       -      +
    265A  TRP*     4.4     0.2    -      -       -      -
    308A  ALA*     3.8    24.4    -      -       +      +
    309A  PRO*     5.5     6.5    -      -       +      +
    310A  LEU*     3.8    18.8    -      -       +      -
    391A  ASP*     3.7    22.2    -      -       -      +
    423A  ARG*     5.7     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  LEU*     5.0     6.1    -      -       +      -
     95A  ILE      4.1    15.7    -      -       -      +
     96A  PHE*     4.1     2.7    -      -       +      -
    130A  VAL*     1.3    79.0    -      -       -      +
    132A  ASP*     1.3    60.5    +      -       -      +
    133A  GLU*     3.1     6.8    +      -       -      -
    134A  GLY*     3.1     9.5    +      -       -      -
    135A  PHE*     2.9    48.4    +      -       +      +
    137A  VAL*     3.7    25.6    -      -       +      -
    265A  TRP*     4.8     2.9    -      -       -      -
    286A  LEU*     4.3     7.2    -      -       +      -
    308A  ALA*     4.0    13.2    -      -       -      +
    309A  PRO*     4.6     1.7    -      -       -      +
----------------------------------------------------------
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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