Contacts of the strand formed by residues 28 - 33 (chain A) in PDB entry 4NLG


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 LEU 28 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ALA*     3.6    34.8    -      -       +      +
     16A  GLU*     4.0    15.9    -      -       +      -
     17A  GLU*     4.1    13.5    -      -       +      +
     23A  TYR*     3.8    24.0    -      -       +      +
     26A  LYS      3.9     2.0    -      -       -      +
     27A  PRO*     1.3    75.1    -      -       -      +
     29A  VAL*     1.3    67.5    +      -       -      +
     30A  VAL*     4.3     0.9    -      -       +      -
     45A  THR      4.2     0.2    -      -       -      +
     46A  ALA*     3.3     4.7    -      -       -      +
     47A  ASN*     2.9    45.5    +      -       -      +
     50A  ALA*     3.8     1.4    -      -       -      +
     72A  ILE*     3.5    38.4    -      -       +      +
     74A  VAL*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  LEU*     1.3    80.0    -      -       -      +
     30A  VAL*     1.3    62.2    +      -       -      +
     31A  CYS*     3.5    19.8    -      -       -      -
     43A  VAL*     3.7    32.5    -      -       +      -
     45A  THR      3.6     2.0    -      -       -      -
     46A  ALA*     4.4     0.2    -      -       -      +
     50A  ALA*     4.1     6.7    -      -       +      -
     55A  VAL*     4.0    19.1    -      -       +      -
     71A  ALA*     3.9    17.0    -      -       +      -
     72A  ILE      2.8     8.9    +      -       -      -
     73A  TYR*     3.4    30.1    -      -       +      +
     74A  VAL*     2.9    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     3.9    13.0    -      -       +      +
     13A  ALA*     3.7    35.4    -      -       +      +
     16A  GLU*     4.1     5.4    -      -       +      -
     28A  LEU*     4.9     1.3    -      -       +      -
     29A  VAL*     1.3    71.3    -      -       -      +
     31A  CYS*     1.3    55.5    +      -       -      +
     43A  VAL*     3.7     2.1    -      -       -      -
     44A  ALA*     2.7    36.9    +      -       +      -
     45A  THR*     2.7    22.0    +      -       +      +
     74A  VAL*     3.3    20.4    -      -       +      +
     76A  MET*     3.8    34.3    -      -       +      -
     81A  TYR*     3.9     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     3.5    21.1    -      -       -      -
     30A  VAL*     1.3    73.7    -      -       -      +
     32A  VAL*     1.3    63.8    +      -       -      +
     33A  TYR*     3.5    17.5    +      -       +      -
     42A  ALA      3.5     3.6    -      -       -      -
     43A  VAL*     4.8     1.3    -      -       -      -
     61A  ILE*     3.3    31.6    -      -       +      -
     73A  TYR*     3.4    39.3    -      -       -      -
     74A  VAL      2.7    11.4    +      -       -      -
     75A  PRO*     3.5     5.5    -      -       -      +
     76A  MET*     3.0    23.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  CYS*     1.3    73.2    -      -       -      +
     33A  TYR*     1.3    60.7    +      -       -      +
     34A  SER      3.3     1.0    +      -       -      -
     41A  GLY*     2.9    26.7    -      -       -      -
     42A  ALA      2.7    17.2    +      -       -      +
     44A  ALA*     4.0    11.7    -      -       +      -
     61A  ILE*     4.2     0.7    -      -       -      -
     76A  MET*     4.1    19.5    -      -       +      -
      5T    G      3.4    62.8    -      -       +      +
      6T    C      3.7    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  CYS*     3.5    13.6    +      -       +      +
     32A  VAL*     1.3    72.0    -      -       -      +
     34A  SER*     1.3    64.8    +      -       -      +
     35A  GLY*     3.2     6.5    +      -       -      +
     37A  THR      5.2     2.0    -      -       -      +
     38A  LYS*     3.4    28.3    -      -       -      -
     39A  THR*     4.5     3.1    -      -       +      -
     40A  SER      3.5     8.3    -      -       -      +
     61A  ILE*     3.8    23.2    -      -       +      +
     65A  MET*     6.1     0.3    -      -       -      -
     73A  TYR*     3.6    30.7    +      -       -      +
     75A  PRO*     3.8    42.8    -      -       +      -
      6T    C      4.6     4.7    +      -       -      -
----------------------------------------------------------
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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