Contacts of the strand formed by residues 315 - 322 (chain A) in PDB entry 4X4U


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 PRO 315 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  PHE*     3.5    54.0    -      -       +      +
    308A  LEU*     3.8    12.8    -      -       +      -
    309A  GLU*     3.7    26.2    -      -       +      +
    313A  PHE      3.6     0.8    -      -       -      -
    314A  MET*     1.3    92.2    -      -       -      +
    316A  LEU*     1.3    61.5    +      -       -      +
    317A  ARG      5.4     0.7    -      -       -      +
    331A  PHE*     5.7     0.7    -      -       +      -
    332A  GLU      3.3     9.6    -      -       -      +
    333A  CYS*     3.7    16.8    -      -       -      -
    334A  GLN*     4.5     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ARG*     4.3     6.7    -      -       -      +
    276A  THR*     3.9    15.9    -      -       +      -
    305A  PHE*     3.9     9.3    -      -       -      -
    315A  PRO*     1.3    75.6    -      -       -      +
    317A  ARG*     1.3    71.7    +      -       +      +
    332A  GLU*     2.8    50.7    +      -       +      +
    334A  GLN*     3.4    39.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ARG*     5.0    12.5    -      -       -      +
    305A  PHE*     4.0    10.1    -      -       -      -
    315A  PRO*     5.4     0.2    -      -       -      +
    316A  LEU*     1.3    88.1    -      -       +      +
    318A  SER*     1.3    68.2    +      -       -      +
    331A  PHE*     3.9     0.7    -      -       -      +
    332A  GLU*     3.3    27.2    +      -       -      +
    431A  GLU*     3.5    18.8    +      -       -      +
    432A  MET*     3.2    56.1    +      -       +      +
    434A  GLY*     5.1     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  SER*     2.9    24.9    +      -       -      -
    302A  ARG*     5.8     0.2    -      -       -      -
    305A  PHE*     4.0    14.2    -      -       -      +
    317A  ARG*     1.3    80.5    +      -       -      +
    319A  ALA*     1.3    65.9    +      -       -      +
    330A  LEU      3.3    15.3    -      -       -      -
    331A  PHE*     3.7    17.5    -      -       -      -
    432A  MET*     4.1     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  SER*     4.6     3.2    +      -       -      -
    318A  SER*     1.3    80.8    -      -       -      +
    320A  PHE*     1.3    68.2    +      -       -      +
    329A  LEU*     3.6     1.6    -      -       -      +
    330A  LEU*     2.7    42.4    +      -       +      +
    428A  GLU*     4.7    10.1    -      -       +      +
    432A  MET*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  TYR*     3.5    35.1    -      +       -      -
    297A  LEU*     3.8    33.9    -      -       +      -
    298A  GLU*     3.6    40.2    -      -       +      -
    301A  SER*     4.2     9.6    -      -       -      -
    318A  SER*     5.9     0.2    -      -       -      -
    319A  ALA*     1.3    81.4    -      -       -      +
    321A  LYS*     1.3    63.0    +      -       -      +
    328A  TYR      3.1    14.4    -      -       -      +
    329A  LEU*     3.8    14.4    -      -       +      -
    330A  LEU*     4.6     2.0    -      -       -      +
    428A  GLU*     4.2    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  TYR*     6.1     0.7    -      -       -      -
    297A  LEU*     5.1     1.2    -      -       -      +
    320A  PHE*     1.3    78.1    -      -       -      +
    322A  ALA*     1.3    75.5    +      -       -      +
    323A  SER*     5.1     7.9    -      -       -      +
    327A  CYS*     3.4     4.0    -      -       -      +
    328A  TYR*     2.8    39.2    +      -       +      +
    330A  LEU*     5.4     1.0    -      -       +      +
    424A  PRO*     3.0    34.1    -      -       +      +
    425A  VAL*     4.4    13.5    -      -       +      -
    427A  ALA*     5.8     1.8    -      -       -      +
    428A  GLU*     3.2    37.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  LYS*     4.7     2.2    -      -       +      -
    293A  LEU*     4.1    18.2    -      -       +      -
    294A  TYR*     3.8    25.3    +      -       +      +
    297A  LEU*     4.2     7.8    -      -       +      +
    321A  LYS*     1.3    85.8    +      -       -      +
    323A  SER*     1.3    65.8    +      -       -      +
    326A  PHE      3.9     4.3    -      -       -      -
    327A  CYS*     4.1    16.6    -      -       -      -
----------------------------------------------------------
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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