Contacts of the strand formed by residues 312 - 317 (chain A) in PDB entry 2LTZ


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 ARG 312 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  ASN*     3.2     6.2    +      -       -      -
    308A  THR*     2.7    46.3    +      -       -      +
    310A  THR*     3.0    43.7    +      -       +      +
    311A  GLY*     1.3    84.2    -      -       -      +
    313A  VAL*     1.3    59.3    +      -       -      +
    314A  TYR*     3.8     0.5    -      -       -      -
    325A  PHE*     3.0    38.3    -      -       +      -
    205B  GLU*     3.8    20.6    -      -       +      +
    206B  SER*     2.7    42.9    +      -       -      -
    207B  PRO      4.4     6.1    +      -       -      -
    209B  PRO*     5.7     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  ILE*     4.4     6.3    -      -       +      -
    306A  ARG      3.5    17.5    -      -       -      +
    307A  ASN*     3.4    26.2    -      -       +      +
    311A  GLY      5.5     0.7    -      -       -      -
    312A  ARG*     1.3    73.4    -      -       -      +
    314A  TYR*     1.3    60.5    +      -       -      +
    315A  PHE*     3.3    25.8    -      -       +      -
    324A  GLN      3.2     1.7    -      -       -      +
    325A  PHE*     2.8    24.1    -      -       -      -
    327A  ASP*     2.8    30.2    +      -       -      +
    329A  ARG*     3.4    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306A  ARG*     2.8    67.5    +      -       +      +
    308A  THR*     3.2    37.0    -      -       +      +
    312A  ARG      3.8     6.7    -      -       -      -
    313A  VAL*     1.3    72.9    -      -       -      +
    315A  PHE*     1.3    63.7    +      -       -      +
    316A  VAL*     3.8     5.6    +      -       +      +
    323A  THR*     3.3    25.4    -      -       -      +
    324A  GLN      2.9     8.7    -      -       -      +
    325A  PHE*     3.7    17.5    -      +       +      +
    208B  PRO*     4.5     0.2    -      -       +      -
    209B  PRO*     3.5    22.2    -      -       +      +
    215B  PRO*     3.1    37.3    +      -       +      +
    217B  ASP*     3.8     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  LEU*     4.1    14.4    -      -       +      -
    300A  PRO*     6.0     0.4    -      -       +      -
    303A  TRP*     3.2    33.2    -      +       +      -
    304A  GLU      3.0     7.4    -      -       -      +
    305A  ILE*     3.7    37.0    -      -       +      -
    313A  VAL*     3.3    17.5    -      -       +      -
    314A  TYR*     1.3    77.4    -      -       -      +
    316A  VAL*     1.3    60.6    +      -       -      +
    324A  GLN*     2.8    42.9    +      -       +      +
    327A  ASP*     3.2    27.6    -      -       +      -
    328A  PRO*     3.5    28.0    -      -       +      -
    329A  ARG*     3.6    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  TRP*     5.2     0.2    -      -       -      -
    304A  GLU*     2.8    56.7    +      -       +      +
    306A  ARG*     5.9     2.5    -      -       +      -
    314A  TYR*     3.8    10.2    +      -       +      +
    315A  PHE*     1.3    71.3    -      -       -      +
    317A  ASP*     1.3    61.8    +      -       -      +
    318A  HIS*     3.6     1.9    +      -       +      -
    322A  THR      3.2     2.9    -      -       -      -
    323A  THR*     3.5    30.3    -      -       -      +
    209B  PRO      5.5     0.7    -      -       -      +
    210B  PRO      5.7     0.2    -      -       -      +
    211B  TYR*     3.2    30.1    -      -       +      -
    212B  SER      4.1     7.4    -      -       -      +
    213B  ARG      3.3    26.2    -      -       -      +
    215B  PRO*     4.7     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  GLY      4.5     2.7    -      -       -      -
    303A  TRP*     3.1    37.5    -      -       -      +
    304A  GLU      5.0     0.2    -      -       -      +
    316A  VAL*     1.3    72.5    -      -       -      +
    318A  HIS*     1.3    53.9    +      -       -      +
    319A  ASN*     3.0    22.7    +      -       +      +
    320A  ASN*     4.0    13.3    -      -       +      +
    321A  ARG*     2.7    31.2    +      -       -      +
    322A  THR*     2.8    34.9    +      -       -      +
    324A  GLN*     3.3    20.9    -      -       -      +
    211B  TYR*     2.9     7.7    +      -       -      -
----------------------------------------------------------
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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