Contacts of the strand formed by residues 377 - 384 (chain A) in PDB entry 4TZ1


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 LYS 377 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  ARG*     3.7    38.8    -      -       -      +
    267A  PRO*     4.2    24.0    -      -       +      -
    280A  VAL*     3.6    34.3    -      -       +      +
    281A  PRO      5.4     0.2    -      -       -      -
    348A  ASN*     2.9    24.4    +      -       -      +
    349A  THR      2.9    10.8    +      -       -      +
    350A  VAL*     3.5    15.3    -      -       +      +
    351A  ALA      2.9    28.5    +      -       -      +
    375A  GLY*     2.9    23.1    +      -       -      +
    376A  VAL*     1.3    74.3    -      -       -      +
    378A  VAL*     1.3    61.9    +      -       -      +
    379A  ALA*     3.9     1.5    +      -       -      +
    408A  ASN*     4.3     3.8    -      -       -      +
    411A  SER*     3.7     8.3    -      -       -      +
    413A  GLN*     5.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  ILE*     4.8     5.8    -      -       +      -
    351A  ALA*     3.6     6.3    -      -       +      +
    368A  LEU*     3.8    25.1    -      -       +      -
    370A  VAL*     4.3     7.2    -      -       +      -
    376A  VAL*     4.0    17.9    -      -       +      -
    377A  LYS*     1.3    72.9    -      -       -      +
    379A  ALA*     1.3    64.3    +      -       -      +
    381A  LEU*     3.6    25.1    -      -       +      -
    410A  THR*     5.2     1.1    -      -       +      -
    411A  SER      3.0     7.4    +      -       -      +
    412A  LEU*     3.4    28.4    -      -       +      -
    413A  GLN*     2.9    26.4    +      -       -      +
    415A  VAL*     3.7    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  LYS*     3.6    32.3    -      -       +      -
    267A  PRO*     4.5    10.1    -      -       +      -
    350A  VAL*     6.1     0.7    -      -       +      -
    351A  ALA      3.0    12.5    +      -       -      +
    352A  LEU*     3.4    16.3    -      -       +      +
    353A  GLY      2.8    24.8    +      -       -      -
    377A  LYS      4.8     2.5    -      -       -      +
    378A  VAL*     1.3    79.2    -      -       -      +
    380A  GLY*     1.3    60.0    +      -       -      +
    381A  LEU*     3.7     2.2    -      -       -      +
    413A  GLN*     3.1     9.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  LYS*     5.5     2.0    -      -       -      -
    353A  GLY*     3.5    26.5    -      -       -      +
    356A  LEU*     4.5     7.5    +      -       -      -
    357A  ALA      4.1    10.7    +      -       -      +
    379A  ALA*     1.3    73.3    -      -       -      +
    381A  LEU*     1.3    60.3    +      -       -      +
    382A  LEU      4.4     0.2    +      -       -      -
    413A  GLN      3.0    12.9    +      -       -      -
    414A  ASP*     3.1    17.7    +      -       -      +
    415A  VAL*     4.6     0.2    -      -       -      +
    416A  PHE*     5.6     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  PHE*     4.0    32.8    -      -       +      -
    351A  ALA*     4.5    11.4    -      -       +      +
    353A  GLY*     4.6     2.7    -      -       -      +
    356A  LEU*     5.7     0.2    -      -       -      -
    357A  ALA*     3.5    16.8    -      -       +      +
    359A  ILE*     3.9    29.8    -      -       +      -
    368A  LEU*     5.1     6.7    -      -       +      -
    378A  VAL*     3.6    28.5    -      -       +      -
    379A  ALA      4.7     4.7    -      -       -      +
    380A  GLY*     1.3    81.7    -      -       -      +
    382A  LEU*     1.3    60.1    +      -       -      +
    383A  VAL*     4.9     5.4    -      -       +      -
    414A  ASP      3.2     3.7    +      -       -      -
    415A  VAL*     3.3    16.8    -      -       +      +
    416A  PHE*     2.9    27.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  TYR*     4.0    25.1    -      -       +      -
    153A  TRP*     4.0    20.2    -      -       +      +
    356A  LEU*     4.5     9.0    +      -       +      +
    357A  ALA      3.0     7.1    +      -       -      +
    358A  THR*     3.0    30.6    -      -       +      +
    359A  ILE*     2.9    25.6    +      -       -      +
    380A  GLY      4.3     0.4    +      -       -      -
    381A  LEU*     1.3    72.0    -      -       -      +
    383A  VAL*     1.3    68.4    +      -       -      +
    384A  ASP*     4.7     1.3    -      -       +      -
    416A  PHE*     3.2    38.8    -      -       +      +
    417A  VAL      4.2     0.2    -      -       -      -
    418A  ARG*     4.0    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     3.4    14.6    -      -       +      +
    361A  PRO*     4.8     1.1    -      -       +      -
    367A  ALA*     3.7    30.5    -      -       +      -
    368A  LEU*     5.5     5.2    -      -       +      -
    381A  LEU*     4.7     8.1    -      -       +      +
    382A  LEU*     1.3    73.9    -      -       -      +
    384A  ASP*     1.3    59.9    +      -       -      +
    385A  ALA      4.1     0.2    +      -       -      -
    393A  LEU*     4.1    27.1    -      -       +      -
    394A  VAL*     4.0    18.8    -      -       +      -
    415A  VAL*     4.4    13.5    -      -       +      -
    416A  PHE      2.7    13.5    +      -       -      +
    417A  VAL*     3.3    11.8    -      -       +      +
    418A  ARG      3.0    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ARG*     5.6     0.2    +      -       -      -
    358A  THR*     3.7    22.0    -      -       +      +
    359A  ILE      3.0     6.9    +      -       -      -
    360A  ILE*     3.4    26.0    -      -       +      +
    361A  PRO*     3.3    17.0    -      -       -      +
    382A  LEU*     3.9     3.8    +      -       +      -
    383A  VAL*     1.3    70.5    -      -       -      +
    385A  ALA*     1.3    75.2    +      -       -      +
    418A  ARG*     2.9    54.5    +      -       -      +
    420A  GLY      4.5     3.8    +      -       -      +
    422A  ALA*     4.7     8.8    -      -       -      +
----------------------------------------------------------
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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