Contacts of the strand formed by residues 72 - 77 (chain K) in PDB entry 3GTL


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 72 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  TYR*     4.1    12.7    +      -       -      +
     32K  VAL*     4.0    25.6    -      -       +      -
     33K  ILE      3.5     4.3    -      -       -      +
     34K  THR*     4.0    20.0    -      -       +      +
     60K  ALA      3.5     1.0    -      -       -      +
     61K  TYR*     2.9    27.1    -      -       -      +
     62K  LYS*     3.1    20.3    +      -       +      +
     64K  GLU*     3.4    37.8    +      -       +      +
     70K  ARG*     5.4     8.3    -      -       -      +
     71K  PHE*     1.3    81.5    -      -       -      +
     73K  LEU*     1.3    59.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31K  VAL      3.7     0.9    -      -       -      +
     32K  VAL*     3.2     3.6    -      -       -      -
     33K  ILE*     2.8    43.6    +      -       +      +
     35K  PHE*     3.7    24.6    -      -       +      -
     43K  GLY      5.2     0.7    -      -       -      +
     46K  ILE*     3.5    29.4    -      -       +      -
     47K  ARG*     4.0    20.6    -      -       +      +
     50K  LEU*     4.0     2.0    -      -       +      -
     59K  ALA      5.3     0.2    -      -       -      -
     60K  ALA      3.2    18.8    -      -       -      +
     61K  TYR*     3.6    17.9    -      -       +      -
     71K  PHE*     4.4     5.4    +      -       +      -
     72K  LYS*     1.3    72.6    -      -       -      +
     74K  ARG*     1.3    59.7    +      -       -      +
     75K  ILE*     3.6    28.9    +      -       +      -
     87K  LEU*     4.1     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 74 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  TYR*     3.6    37.8    -      -       +      +
    556A  TRP*     3.8    23.0    -      -       -      -
    558A  GLY*     4.1     5.8    -      -       -      -
     24K  ASP*     2.9    46.2    +      -       -      +
     26K  LYS*     5.0     1.6    -      -       -      +
     27K  ALA*     3.9    10.9    -      -       -      +
     30K  ALA*     3.5    13.3    -      -       -      +
     31K  VAL      3.0    20.0    -      -       -      +
     32K  VAL*     4.3     3.4    -      -       +      -
     58K  PHE*     3.1    42.1    -      -       +      -
     59K  ALA*     3.4     1.0    -      -       -      -
     60K  ALA      2.8    33.2    +      -       -      -
     73K  LEU*     1.3    73.4    -      -       -      +
     75K  ILE*     1.3    61.6    +      -       -      +
     76K  GLN*     4.0    18.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  ASN      4.1     1.6    -      -       -      +
     30K  ALA*     3.5     3.0    -      -       -      -
     31K  VAL*     2.8    34.8    +      -       +      +
     33K  ILE*     4.1    19.7    -      -       +      -
     50K  LEU*     3.4    46.7    -      -       +      -
     56K  VAL*     3.8     8.1    -      -       +      -
     58K  PHE*     3.2    12.3    -      -       -      +
     59K  ALA*     4.8     2.2    -      -       -      -
     73K  LEU*     3.6    22.2    -      -       +      -
     74K  ARG*     1.3    79.6    -      -       -      +
     76K  GLN*     1.3    63.1    +      -       -      +
     77K  THR*     4.3     9.4    -      -       +      -
     83K  PRO*     4.4    15.9    -      -       +      +
     86K  ALA*     4.7     4.5    -      -       +      -
     87K  LEU*     4.2    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 76 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  TRP*     6.1     0.2    -      -       -      -
    558A  GLY      4.5     5.3    +      -       -      -
    560A  ILE*     5.9     1.8    -      -       -      +
     78H  SER*     4.3    15.9    +      -       -      -
     27K  ALA*     3.3    20.8    -      -       -      +
     28K  PRO*     3.0    33.3    -      -       -      +
     29K  ASN      3.9     2.7    -      -       -      +
     30K  ALA*     4.0     9.6    -      -       +      -
     56K  VAL*     3.3     7.4    -      -       -      +
     57K  LEU*     2.8    43.6    +      -       +      +
     58K  PHE*     2.9    30.7    +      -       +      +
     74K  ARG*     4.0    14.8    -      -       -      +
     75K  ILE*     1.3    74.4    -      -       -      +
     77K  THR*     1.3    67.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 77 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  ASN*     2.7    37.8    +      -       -      +
     55K  LYS      3.7    15.7    -      -       -      +
     56K  VAL*     3.8    10.3    -      -       +      -
     57K  LEU*     3.6    16.6    -      -       -      +
     75K  ILE*     4.3     4.5    -      -       +      -
     76K  GLN*     1.3    82.0    -      -       -      +
     78K  THR*     1.3    65.0    +      -       -      +
     79K  GLU      3.7     0.3    +      -       -      -
     81K  TYR*     3.0    23.8    +      -       +      -
     83K  PRO*     3.4    12.5    -      -       +      +
     86K  ALA*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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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