Contacts of the strand formed by residues 334 - 340 (chain A) in PDB entry 4TMU


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 ALA 334 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  ASN      2.9    10.3    +      -       -      +
    213A  ILE*     4.3     5.6    -      -       +      -
    214A  ARG*     2.8    28.4    +      -       -      +
    305A  VAL      3.9     4.0    -      -       -      +
    306A  ARG*     3.3    15.7    -      -       -      +
    327A  ALA*     3.8    11.0    -      -       +      -
    328A  GLY*     3.6    33.7    -      -       -      +
    332A  LEU      3.2     0.6    +      -       -      +
    333A  PRO*     1.3    75.3    -      -       -      +
    335A  GLU*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  ILE*     5.0     1.6    -      -       -      -
    214A  ARG*     3.5    26.8    +      -       +      +
    216A  MET*     3.3    24.5    -      -       +      +
    230A  TYR*     2.8    38.9    +      -       +      +
    234A  GLN*     4.3     7.8    +      -       -      +
    306A  ARG      2.9     9.8    +      -       -      +
    307A  PHE*     3.2     7.0    -      -       +      +
    308A  VAL*     3.0    23.2    +      -       -      +
    327A  ALA*     4.6     3.4    -      -       -      +
    334A  ALA*     1.3    78.2    -      -       -      +
    336A  ALA*     1.3    68.4    +      -       -      +
    337A  MET*     4.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  ILE*     4.2     7.3    -      -       +      +
    214A  ARG      2.8    11.4    +      -       -      +
    215A  TYR*     4.1    15.0    -      -       +      -
    216A  MET*     2.9    30.8    +      -       -      +
    308A  VAL*     3.3     7.4    -      -       +      +
    320A  TYR*     4.3     3.4    -      -       +      +
    324A  THR*     3.6    39.0    -      -       +      +
    327A  ALA*     6.0     0.2    -      -       +      -
    335A  GLU*     1.3    73.3    -      -       -      +
    337A  MET*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  MET*     3.5    34.3    -      -       +      -
    217A  LEU      4.0     1.3    -      -       -      +
    218A  MET*     3.5    49.1    -      -       +      -
    230A  TYR*     3.7    38.6    -      -       +      +
    308A  VAL      2.9    10.9    +      -       -      +
    309A  VAL*     3.3    11.9    -      -       +      +
    310A  HIS*     2.9    25.8    +      -       -      -
    320A  TYR*     6.1     0.6    -      -       -      -
    324A  THR*     5.7     0.2    -      -       -      +
    335A  GLU*     4.1     3.1    -      -       +      +
    336A  ALA*     1.3    73.3    -      -       -      +
    338A  LEU*     1.3    63.2    +      -       -      +
    339A  PHE*     3.5    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  MET      3.0    14.0    +      -       -      +
    217A  LEU*     3.2    26.3    -      -       +      +
    218A  MET      2.7    33.1    +      -       -      +
    310A  HIS*     3.6    24.7    -      -       +      +
    313A  ILE*     3.8    32.5    -      -       +      -
    314A  PRO*     4.5     2.2    -      -       +      -
    320A  TYR*     4.5    13.9    -      -       +      +
    337A  MET*     1.3    74.2    -      -       -      +
    339A  PHE*     1.3    68.4    +      -       -      +
    340A  TYR*     3.6     1.9    +      -       +      +
    371A  MET*     4.2    24.5    -      -       +      -
    374A  PHE*     4.3    12.1    -      -       +      -
    375A  ALA*     4.6     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  MET*     3.3    22.2    -      -       +      -
    220A  LYS*     4.0    19.7    +      -       +      +
    223A  PRO      4.7     0.7    -      -       -      -
    226A  GLN*     3.7    33.4    -      -       +      -
    227A  LEU*     3.7    24.0    -      -       +      -
    230A  TYR*     4.0    16.8    -      -       +      -
    309A  VAL*     3.5    34.8    -      -       +      -
    310A  HIS      2.9    15.2    +      -       -      +
    311A  PHE*     3.5    36.2    -      +       +      +
    313A  ILE      4.5     4.2    +      -       -      -
    337A  MET*     3.5    20.6    -      -       +      -
    338A  LEU*     1.3    77.9    -      -       -      +
    340A  TYR*     1.3    61.0    +      -       -      +
    341A  ASP      3.8     2.1    +      -       -      -
    344A  ASP*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  LEU*     4.0    27.1    -      -       +      -
    218A  MET      2.8    11.4    +      -       -      +
    219A  GLU*     3.6    13.3    -      -       +      +
    220A  LYS*     2.8    24.4    +      -       -      -
    313A  ILE*     3.7    28.5    -      -       +      -
    338A  LEU*     3.6     5.1    +      -       +      -
    339A  PHE*     1.3    71.2    -      -       -      +
    341A  ASP*     1.3    73.0    +      -       -      +
    342A  PRO*     3.7    25.3    -      -       +      +
    345A  MET*     3.9    17.6    -      -       +      +
    372A  GLY*     4.5     2.1    +      -       -      -
    375A  ALA*     3.7    29.4    -      -       +      -
    376A  GLU*     2.4    40.3    +      -       -      +
    474A  ARG*     4.4     0.2    +      -       -      -
----------------------------------------------------------
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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