Contacts of the strand formed by residues 345 - 349 (chain A) in PDB entry 4LEY


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 PHE 345 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  ILE*     6.1     0.4    -      -       +      -
    225A  LEU*     4.3    19.1    -      -       +      -
    312A  LEU      3.7     0.7    -      -       -      +
    313A  GLU*     3.8     0.3    -      -       -      -
    314A  SER*     2.9    67.3    +      -       -      -
    316A  GLY*     3.7    14.4    -      -       -      -
    317A  SER      3.4    19.7    -      -       -      -
    318A  TRP*     3.7    22.4    -      +       +      +
    319A  PRO*     4.0    18.2    -      -       +      -
    344A  PRO*     1.3    73.5    -      -       -      +
    346A  TYR*     1.3    67.1    +      -       -      +
    347A  LEU*     4.6     9.4    -      -       +      -
    365A  LEU*     3.8    25.8    -      -       +      -
    366A  SER      4.5     1.3    -      -       -      -
    367A  PHE*     3.9    17.9    -      -       +      -
    369A  HIS*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  LEU*     3.8    12.1    -      -       +      +
    215A  MET*     4.7    11.7    -      -       +      -
    217A  LYS*     3.4    31.8    -      -       +      +
    311A  ALA*     4.4    10.3    -      -       +      -
    312A  LEU      3.3     5.2    -      -       -      -
    313A  GLU*     2.7    52.7    +      -       +      -
    344A  PRO*     3.7    15.0    -      -       +      +
    345A  PHE*     1.3    76.0    -      -       -      +
    347A  LEU*     1.3    66.1    +      -       -      +
    365A  LEU*     3.4    11.4    -      -       -      +
    366A  SER*     2.9    46.8    +      -       -      +
    369A  HIS*     3.3    47.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  ILE*     4.2     9.2    -      -       +      -
    225A  LEU*     3.8    15.7    -      -       +      -
    235A  TYR*     4.8    11.2    -      -       +      -
    237A  VAL*     3.8    26.2    -      -       +      -
    310A  LEU      3.9     0.2    -      -       -      +
    311A  ALA*     3.2     6.8    -      -       -      -
    312A  LEU*     2.9    46.6    +      -       +      +
    314A  SER*     5.6     2.5    -      -       -      -
    345A  PHE*     4.6     9.4    -      -       +      -
    346A  TYR*     1.3    76.2    -      -       -      +
    348A  VAL*     1.3    62.3    +      -       -      +
    363A  TRP*     3.9    27.8    -      -       +      -
    364A  ARG      3.3    11.9    -      -       -      +
    365A  LEU*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  MET*     4.8     2.0    -      -       +      -
    292A  PRO*     3.7     6.7    -      -       +      -
    309A  ILE*     3.6    29.4    -      -       +      -
    310A  LEU      3.7     5.4    -      -       -      +
    311A  ALA*     4.5     6.1    -      -       +      -
    347A  LEU*     1.3    76.2    -      -       -      +
    349A  PRO*     1.3    71.7    -      -       +      +
    363A  TRP*     3.2    12.0    -      -       -      -
    364A  ARG*     2.9    74.9    +      -       +      +
    366A  SER*     4.2    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  ALA*     3.9    25.8    -      -       +      +
    263A  LEU*     4.2    31.4    -      -       +      -
    290A  GLY      4.5     0.7    -      -       -      +
    292A  PRO*     3.3    33.3    -      -       +      +
    310A  LEU*     3.4    22.0    -      -       +      +
    348A  VAL*     1.3    86.7    -      -       +      +
    350A  LYS*     1.3    64.4    +      -       -      +
    351A  ASN*     4.3    12.1    -      -       +      +
    362A  THR      4.2     0.4    -      -       -      +
    363A  TRP*     3.7    13.9    -      -       +      -
    364A  ARG*     4.6     1.7    +      -       -      -
----------------------------------------------------------
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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