Contacts of the strand formed by residues 121 - 129 (chain A) in PDB entry 6LU7


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 SER 121 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  CYS*     4.1     1.1    -      -       -      -
    118A  TYR*     3.0    33.1    +      -       -      +
    119A  ASN*     3.1     4.7    -      -       -      -
    120A  GLY*     1.3    78.6    -      -       -      +
    122A  PRO*     1.3    73.6    +      -       -      +
    123A  SER*     3.5     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     3.7    37.2    -      -       +      +
     17A  MET*     4.3     5.6    -      -       +      -
    115A  LEU*     3.6    34.3    -      -       +      -
    116A  ALA      3.7     6.5    -      -       -      +
    117A  CYS*     3.9     8.5    -      -       -      -
    120A  GLY      3.7     8.1    -      -       -      +
    121A  SER*     1.3    91.2    +      -       -      +
    123A  SER*     1.3    59.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ALA*     2.9    15.8    +      -       -      +
    118A  TYR*     3.7    26.5    -      -       -      -
    121A  SER      3.5     2.4    +      -       -      -
    122A  PRO*     1.3    74.3    -      -       -      +
    124A  GLY*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  LEU*     3.3    10.8    -      -       -      +
    116A  ALA*     2.8    32.1    +      -       -      -
    122A  PRO      3.9     0.2    -      -       -      -
    123A  SER*     1.3    82.8    +      -       -      +
    125A  VAL*     1.3    62.0    -      -       -      -
    126A  TYR*     4.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ALA*     3.7    23.4    -      -       +      +
      8A  PHE      4.0    13.2    -      -       -      +
     10A  SER*     4.4    18.8    -      -       -      +
    113A  SER*     4.5     6.3    -      -       -      -
    114A  VAL      3.1    15.7    -      -       -      +
    115A  LEU*     4.3     9.2    -      -       +      -
    124A  GLY*     1.3    76.1    -      -       -      +
    126A  TYR*     1.3    69.4    +      -       -      +
    150A  PHE*     4.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ALA*     3.9    11.0    -      -       -      -
    113A  SER*     3.3     1.0    -      -       -      -
    114A  VAL*     2.6    55.7    +      -       +      -
    116A  ALA*     4.3    12.3    -      -       +      -
    124A  GLY      4.9     1.1    -      -       -      -
    125A  VAL*     1.3    83.7    -      -       -      +
    127A  GLN*     1.3    70.0    +      -       -      +
    128A  CYS*     3.4    24.5    -      -       -      -
    137A  LYS      4.9     0.4    -      -       -      -
    138A  GLY*     3.9     6.7    -      -       -      -
    139A  SER*     2.9    41.2    +      -       -      -
    140A  PHE*     3.3    23.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  LYS*     3.9    38.1    +      -       +      +
      6A  MET      3.2    27.9    +      -       -      +
      7A  ALA*     3.5     2.5    -      -       -      +
      8A  PHE*     4.3     6.5    +      -       -      -
    111A  THR*     3.6    26.2    +      -       +      -
    112A  PHE*     3.5    13.7    -      -       -      +
    113A  SER*     2.6    29.1    +      -       -      -
    126A  TYR*     1.3    84.2    -      -       -      +
    128A  CYS*     1.3    67.3    +      -       -      +
    151A  ASN*     5.0     0.6    +      -       -      -
    290A  GLU*     4.8     5.5    -      -       -      +
    291A  PHE*     6.4     1.1    -      -       +      -
    295A  ASP*     3.8    15.9    +      -       -      -
    298A  ARG*     4.7     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  THR*     3.2     6.6    -      -       -      -
    112A  PHE*     2.6    54.7    +      -       +      +
    114A  VAL*     3.9    17.7    -      -       +      -
    126A  TYR*     3.4    31.4    +      -       -      -
    127A  GLN*     1.3    75.8    -      -       -      +
    129A  ALA*     1.3    59.3    +      -       -      +
    136A  ILE*     4.3    11.9    -      -       +      -
    137A  LYS      3.7    22.9    -      -       -      -
    138A  GLY*     4.0     6.5    -      -       -      -
    290A  GLU*     4.1     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  GLY      5.0     3.6    -      -       -      +
    110A  GLN      3.5     5.6    -      -       -      +
    111A  THR*     3.7    19.7    -      -       +      +
    112A  PHE*     4.4     0.4    -      -       -      -
    128A  CYS*     1.3    76.9    -      -       -      +
    130A  MET*     1.3    65.4    +      -       -      +
    131A  ARG*     3.3    14.3    +      -       -      +
    135A  THR      3.9     1.0    -      -       -      +
    136A  ILE*     3.7    17.5    -      -       -      +
    137A  LYS      4.8     1.2    +      -       -      +
    200A  ILE*     5.2     2.5    -      -       +      -
    289A  ASP      5.1     1.3    -      -       -      +
    290A  GLU*     3.4    38.4    +      -       +      +
----------------------------------------------------------
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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