Contacts of the strand formed by residues 44 - 48 (chain A) in PDB entry 3L2W


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 GLY 44 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ARG*     2.7    44.8    +      -       -      +
     42A  PRO      3.1     1.7    -      -       -      -
     43A  GLU*     1.3    74.3    -      -       -      +
     45A  VAL*     1.3    62.7    +      -       -      -
     46A  LYS*     3.8     8.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PHE*     3.8    27.1    -      -       +      -
     33A  GLU*     5.8     0.2    -      -       -      +
     38A  LYS*     4.4    15.3    -      -       +      -
     39A  VAL      3.4    11.4    -      -       -      +
     40A  SER*     3.8    23.8    -      -       -      +
     44A  GLY*     1.3    74.4    -      -       -      -
     46A  LYS*     1.3    71.1    +      -       -      +
     47A  ILE*     6.0     0.2    -      -       -      +
     79A  LEU      5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LYS*     3.4     6.3    -      -       -      +
     39A  VAL*     2.9    37.9    +      -       +      +
     41A  ARG*     5.5     5.4    -      -       +      -
     43A  GLU*     3.7    40.4    +      -       -      +
     44A  GLY*     3.7     9.6    -      -       -      +
     45A  VAL*     1.3    83.3    -      -       -      +
     47A  ILE*     1.3    62.9    +      -       -      +
     77A  ALA      2.9    26.9    -      -       -      +
     78A  ASN*     3.2    23.1    -      -       -      +
     79A  LEU*     3.6     9.2    -      -       -      +
     80A  TYR      4.2     3.6    -      -       -      +
     81A  TRP*     3.8    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LYS*     4.2    34.3    -      -       +      +
     37A  VAL      3.7    10.5    -      -       -      +
     38A  LYS*     4.2    23.8    -      -       +      -
     46A  LYS*     1.3    73.4    -      -       -      +
     48A  ILE*     1.3    70.7    +      -       -      +
     49A  PRO*     3.4     6.0    -      -       +      +
     79A  LEU*     2.9    25.6    +      -       +      +
     80A  TYR*     3.2    30.2    -      -       +      +
     81A  TRP      2.9    21.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     4.3    10.4    -      -       +      +
     15A  LEU*     4.5     6.3    -      -       +      -
     24A  TYR*     4.1    15.3    -      -       +      -
     30A  TYR*     3.6    34.3    -      -       +      -
     36A  LYS*     5.8     0.2    -      -       -      +
     37A  VAL*     2.9    41.3    +      -       +      +
     38A  LYS      4.3     3.1    -      -       -      -
     39A  VAL*     3.8    28.9    -      -       +      +
     47A  ILE*     1.3    77.8    -      -       -      +
     49A  PRO*     1.3    63.3    -      -       -      +
     50A  PRO*     3.9     2.8    -      -       -      +
     54A  ARG*     3.8    20.6    -      -       -      +
     81A  TRP*     3.4    21.8    -      -       +      +
     82A  TRP*     4.4     2.0    -      -       +      -
----------------------------------------------------------
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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