Contacts of the strand formed by residues 121 - 125 (chain N) in PDB entry 7K60


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 THR 121 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25N  GLN*     2.9    27.6    +      -       -      +
     27N  PRO*     2.9    30.1    +      -       +      +
     28N  SER*     3.5     4.4    -      -       -      +
     29N  SER*     4.8     0.7    -      -       -      +
     30N  MET*     5.1     3.8    -      -       +      +
     40N  ILE*     3.7    25.4    -      -       +      +
    103N  ALA      3.7     0.9    -      -       -      +
    104N  THR*     3.1     6.3    +      -       -      -
    105N  TYR*     2.8    36.5    +      -       -      -
    120N  GLY*     1.3    71.7    +      -       -      -
    122N  LYS*     1.3    65.2    -      -       -      +
    123N  LEU*     3.5    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 122 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28N  SER      3.3    10.8    +      -       -      +
     29N  SER*     3.6    12.9    +      -       -      +
     30N  MET      3.1    27.4    +      -       -      +
    103N  ALA      3.9     5.1    -      -       -      -
    104N  THR*     4.1    22.1    -      -       -      +
    120N  GLY      5.5     1.8    -      -       -      +
    121N  THR*     1.3    73.5    -      -       -      +
    123N  LEU*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30N  MET*     3.7    20.6    -      -       +      +
     32N  ALA*     5.4     3.1    -      -       +      -
     38N  VAL*     3.6    36.1    -      -       +      -
     40N  ILE*     3.8     9.6    -      -       +      -
     94N  ILE*     5.7     1.8    -      -       +      -
     97N  LEU*     5.4     7.0    -      -       +      -
    101N  ASP      4.3     7.9    -      -       -      +
    102N  THR*     3.2    25.6    -      -       -      +
    103N  ALA      3.0    16.0    +      -       -      +
    105N  TYR*     3.5    33.4    -      -       +      +
    121N  THR*     3.5    19.7    -      -       +      -
    122N  LYS*     1.3    80.3    -      -       -      +
    124N  GLU*     1.3    63.0    +      -       -      +
    125N  ILE*     5.6     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 124 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30N  MET      3.4     7.2    +      -       -      +
     31N  HIS*     3.5    37.4    +      -       +      +
     32N  ALA*     3.1    22.7    +      -       -      +
    102N  THR*     4.1     8.3    -      -       +      -
    123N  LEU*     1.3    75.3    -      -       -      +
    125N  ILE*     1.3    71.1    +      -       -      +
    126N  LYS*     3.4    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 125 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32N  ALA*     3.3    21.1    -      -       +      +
     33N  SER      4.0     5.4    -      -       -      +
     34N  LEU*     3.8    32.3    -      -       +      -
     38N  VAL*     5.6     0.4    -      -       +      -
     97N  LEU*     3.8    35.4    -      -       +      -
     98N  GLU      3.5    23.8    -      -       -      +
     99N  SER*     4.4     9.4    +      -       -      -
    101N  ASP*     4.7     0.4    -      -       +      -
    102N  THR*     3.3    25.5    +      -       -      +
    123N  LEU*     5.5     4.5    -      -       +      -
    124N  GLU*     1.3    84.6    +      -       -      +
    126N  LYS*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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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