Contacts of the strand formed by residues 1334 - 1339 (chain B) in PDB entry 1XTB


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 THR1334 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  GLU*     4.2     2.1    +      -       -      +
    334A  THR*     3.7    22.2    -      -       +      -
    377A  ILE*     3.5    30.9    -      -       +      +
   1327B  ILE*     6.0     0.7    -      -       -      +
   1332B  CYS*     3.5     4.5    -      -       -      +
   1333B  GLU*     1.3    88.0    -      -       +      +
   1335B  GLN*     1.3    61.5    +      -       -      +
   1376B  PRO*     4.2     4.3    -      -       -      +
   1377B  ILE*     3.2    19.5    -      -       +      +
   1379B  TRP*     3.1    23.2    +      -       +      +
   1400B  MET      5.5     0.4    +      -       -      -
   1401B  ILE*     3.6    12.0    -      -       -      +
   1402B  PRO*     3.3    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1323B  GLY*     5.1     8.7    -      -       -      -
   1326B  TYR*     5.8     0.2    -      -       -      -
   1334B  THR*     1.3    76.2    -      -       -      +
   1336B  ALA*     1.3    81.0    +      -       -      +
   1337B  VAL*     3.9     8.0    +      -       +      -
   1355B  ASP*     5.5     1.6    -      -       -      +
   1376B  PRO*     4.1    20.6    -      -       +      -
   1377B  ILE      2.9     5.7    +      -       -      +
   1378B  VAL*     3.4    14.8    -      -       +      +
   1379B  TRP*     3.1    25.7    +      -       -      +
   1402B  PRO*     3.3    34.2    +      -       -      +
   1404B  ASP*     3.7    21.0    +      -       -      +
   1496B  LYS*     3.7    25.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1336 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334B  THR      4.3     0.2    -      -       -      -
   1335B  GLN*     1.3    78.5    +      -       -      +
   1337B  VAL*     1.3    61.6    +      -       -      +
   1338B  LEU*     4.0    13.5    -      -       +      -
   1379B  TRP*     3.2    25.3    -      -       +      +
   1394B  ILE*     5.3     0.2    -      -       +      -
   1401B  ILE*     4.0    11.1    -      -       +      +
   1402B  PRO      3.0     8.4    +      -       -      +
   1403B  CYS*     3.7    26.0    -      -       -      -
   1404B  ASP*     2.9    27.1    +      -       -      +
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Residues in contact with VAL1337 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1335B  GLN*     4.6     8.3    -      -       +      +
   1336B  ALA*     1.3    75.5    -      -       -      +
   1338B  LEU*     1.3    69.9    +      -       -      +
   1339B  PRO*     3.4    11.7    -      -       +      +
   1347B  PHE*     3.7    33.7    -      -       +      -
   1348B  ALA*     3.9    20.0    -      -       +      +
   1351B  PHE*     5.3     7.0    -      -       +      -
   1378B  VAL*     4.0    23.8    -      -       +      -
   1379B  TRP      2.9     8.2    +      -       -      +
   1380B  GLY*     3.5    11.8    -      -       -      -
   1381B  GLU      3.9     0.9    +      -       -      -
   1404B  ASP*     3.8     9.6    -      -       +      +
   1406B  LEU*     4.1    12.1    -      -       +      -
   1493B  TYR*     5.3     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1338 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1336B  ALA*     4.3     8.1    -      -       +      +
   1337B  VAL*     1.3    89.3    -      -       -      +
   1339B  PRO*     1.3    63.1    -      -       -      +
   1340B  TYR*     3.5    11.5    -      -       +      -
   1380B  GLY*     4.0    14.8    -      -       -      -
   1381B  GLU      3.6    17.5    -      -       -      +
   1390B  PHE*     4.1    14.1    -      -       +      -
   1391B  TYR*     3.4    34.1    -      -       +      +
   1394B  ILE*     4.6     4.5    -      -       +      -
   1403B  CYS*     4.1    17.0    -      -       +      -
   1404B  ASP      2.8    17.6    +      -       -      +
   1405B  PHE*     3.5    26.7    -      -       +      -
   1406B  LEU*     3.2    17.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO1339 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1337B  VAL*     3.4    18.6    -      -       +      +
   1338B  LEU*     1.3    86.2    -      -       -      +
   1340B  TYR*     1.3    59.0    +      -       -      +
   1341B  ASP      3.0     9.2    +      -       -      +
   1344B  LEU*     3.7    51.4    -      -       +      +
   1347B  PHE*     4.5     9.4    -      -       +      -
   1348B  ALA*     5.2     4.3    -      -       +      +
   1381B  GLU      4.2     8.3    -      -       -      +
   1382B  PRO*     3.2     9.5    -      -       +      +
   1383B  GLY      3.0    16.1    +      -       -      -
   1406B  LEU*     3.4    19.5    -      -       +      +
----------------------------------------------------------
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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