Contacts of the strand formed by residues 1626 - 1632 (chain B) in PDB entry 4ZLP


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 LEU1626 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1419B  LEU*     3.5    41.3    -      -       +      +
   1515B  LEU*     3.6    36.8    -      -       +      -
   1516B  THR      3.6    15.9    -      -       -      +
   1517B  VAL*     4.0     9.0    -      -       +      +
   1535B  LEU*     5.3     4.9    -      -       +      -
   1611B  LEU*     5.4     2.7    -      -       +      -
   1620B  LEU*     4.6    11.0    -      -       +      -
   1622B  PHE*     4.2    24.5    -      -       +      -
   1624B  TYR      2.6    13.7    +      -       -      +
   1625B  PRO*     1.3    70.2    -      -       -      +
   1627B  ARG*     1.3    61.2    +      -       -      +
   1628B  ASP      3.9     7.0    -      -       -      +
   1629B  VAL*     4.0     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1627 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1399B  GLN*     5.2    12.5    -      -       -      +
   1416B  ASP      5.5     2.3    -      -       -      +
   1419B  LEU*     3.5    19.2    -      -       -      +
   1420B  SER*     4.8     0.3    +      -       -      -
   1516B  THR*     2.8    39.8    +      -       +      +
   1518B  LEU*     4.6    19.3    -      -       +      -
   1558B  TYR*     3.5    29.5    +      -       -      -
   1625B  PRO      3.5     4.2    +      -       -      +
   1626B  LEU*     1.3    72.0    -      -       -      +
   1628B  ASP*     1.3    97.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP1628 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1419B  LEU*     3.5     7.2    -      -       -      -
   1420B  SER*     3.3    25.1    -      -       -      +
   1514B  VAL      4.6     1.0    -      -       -      +
   1515B  LEU*     3.5     3.5    -      -       -      -
   1516B  THR*     2.8    38.0    +      -       -      -
   1626B  LEU*     3.9     3.0    -      -       -      +
   1627B  ARG*     1.3   120.7    +      -       +      +
   1629B  VAL*     1.3    73.1    +      -       -      +
   1630B  ARG*     4.3    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1629 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1419B  LEU*     3.1    44.7    +      -       +      +
   1420B  SER*     3.6     6.6    +      -       -      -
   1421B  VAL*     3.8    10.8    -      -       +      +
   1513B  LEU*     4.7     2.9    -      -       +      -
   1514B  VAL      3.4     7.2    -      -       -      +
   1515B  LEU*     4.0    18.2    -      -       +      -
   1605B  GLN*     5.4     0.2    +      -       -      -
   1608B  ALA*     3.3    36.1    -      -       +      +
   1611B  LEU*     4.2    12.8    -      -       +      -
   1626B  LEU*     4.0    10.3    -      -       +      -
   1628B  ASP*     1.3    81.8    -      -       -      +
   1630B  ARG*     1.3    66.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1630 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1420B  SER*     5.5     1.1    -      -       -      +
   1513B  LEU*     3.6     6.3    -      -       -      +
   1514B  VAL*     2.9    63.8    +      -       +      +
   1516B  THR*     4.8     4.2    +      -       -      -
   1581B  VAL*     5.4     4.8    -      -       -      +
   1583B  MET*     6.0     2.0    -      -       -      +
   1605B  GLN*     3.7     7.4    -      -       -      +
   1608B  ALA*     3.8    12.7    -      -       -      +
   1628B  ASP*     4.3    16.3    +      -       -      +
   1629B  VAL*     1.3    79.2    -      -       -      +
   1631B  GLY*     1.3    59.9    +      -       -      +
   1632B  GLU*     3.1    31.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1631 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1512B  VAL      3.6     5.4    -      -       -      -
   1604B  ALA*     4.0     2.7    -      -       -      -
   1605B  GLN*     2.6    47.8    +      -       -      +
   1630B  ARG*     1.3    74.7    -      -       -      +
   1632B  GLU*     1.3    74.0    +      -       -      +
   1633B  PRO*     4.6     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1632 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1511B  GLY*     3.1     3.8    -      -       -      -
   1512B  VAL*     2.6    54.6    +      -       +      +
   1514B  VAL*     3.8    18.8    -      -       +      -
   1604B  ALA*     4.6     0.4    -      -       -      +
   1630B  ARG*     3.1    31.0    +      -       -      +
   1631B  GLY*     1.3    81.9    -      -       -      +
   1633B  PRO*     1.3    76.2    -      -       +      +
----------------------------------------------------------
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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