Contacts of the strand formed by residues 1553 - 1558 (chain A) in PDB entry 2LVM


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 PHE1553 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1500A  TYR*     5.5     0.9    -      -       -      -
   1545A  THR*     4.2     8.7    -      -       +      -
   1546A  ALA      3.6     4.5    -      -       -      -
   1547A  LEU*     3.7    18.2    -      -       +      -
   1552A  TYR*     1.3    73.5    -      -       -      +
   1554A  SER*     1.3    76.6    +      -       -      +
   1555A  ALA*     6.1     1.6    -      -       +      -
     15B  ALA*     3.9    28.8    -      -       +      +
     16B  LYS*     3.1    29.8    -      -       -      +
     17B  ARG*     3.9     3.4    -      -       -      -
     18B  HIS*     2.9    50.9    -      +       +      +
----------------------------------------------------------
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Residues in contact with SER1554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1545A  THR*     3.3     9.1    -      -       -      +
   1546A  ALA*     2.8    36.6    +      -       -      +
   1552A  TYR*     5.4     1.0    -      -       -      +
   1553A  PHE*     1.3    86.2    +      -       -      +
   1555A  ALA*     1.3    61.6    +      -       -      +
   1574A  LYS*     3.0    39.6    +      -       -      -
   1581A  TYR*     5.7     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA1555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1543A  GLU*     5.2     9.6    -      -       +      -
   1544A  VAL      3.3    14.4    -      -       -      +
   1545A  THR*     4.0    12.3    -      -       -      +
   1546A  ALA*     4.6     1.6    -      -       -      +
   1553A  PHE*     6.1     1.6    -      -       +      -
   1554A  SER*     1.3    73.9    -      -       -      +
   1556A  GLY*     1.3    57.6    +      -       -      +
   1572A  ILE*     5.3     0.7    -      -       -      -
   1574A  LYS*     3.4    21.3    -      -       -      +
   1589A  SER*     5.5     0.9    -      -       -      +
   1592A  GLN*     6.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1556 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1543A  GLU*     3.4     9.2    -      -       -      +
   1544A  VAL      2.9    29.4    +      -       -      -
   1555A  ALA*     1.3    74.4    -      -       -      +
   1557A  VAL*     1.3    62.8    +      -       -      +
   1572A  ILE*     3.8    11.9    -      -       -      +
   1573A  GLU      3.5    13.0    -      -       -      -
   1574A  LYS*     4.3     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1541A  ASP*     3.5    27.1    -      -       -      +
   1542A  THR      3.4     2.2    -      -       -      +
   1543A  GLU*     3.6    27.8    -      -       +      +
   1544A  VAL*     4.6     0.2    -      -       -      -
   1556A  GLY*     1.3    78.3    -      -       -      +
   1558A  VAL*     1.3    75.9    -      -       -      +
   1559A  LYS*     3.4    19.5    +      -       +      -
   1572A  ILE*     3.3     5.5    -      -       -      +
   1573A  GLU*     2.8    42.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1538A  ILE*     3.7    35.0    -      -       +      +
   1539A  PRO      3.9     8.3    -      -       -      +
   1540A  LEU*     3.7    20.4    -      -       +      -
   1541A  ASP      2.8    26.7    +      -       -      -
   1542A  THR      3.0     8.3    +      -       -      +
   1544A  VAL*     3.8     9.6    -      -       +      -
   1557A  VAL*     1.3    77.1    -      -       -      +
   1559A  LYS*     1.3    62.5    +      -       -      +
   1560A  GLY      3.7    18.6    -      -       -      +
   1561A  HIS*     4.7     0.4    -      -       +      -
   1570A  TYR*     3.8    17.7    -      -       +      -
   1571A  SER      3.7     4.7    -      -       -      -
   1572A  ILE*     3.6    19.1    -      -       +      -
----------------------------------------------------------
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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