Contacts of the strand formed by residues 382 - 390 (chain B) in PDB entry 3MA2


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 GLU 382 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320B  ARG*     2.4    48.2    +      -       -      +
    321B  ALA      3.6     4.8    +      -       -      -
    322B  LYS*     3.7    19.3    +      -       -      +
    343B  THR*     2.5    32.9    +      -       -      +
    380B  SER      4.0     6.1    -      -       -      +
    381B  GLU*     1.3    75.0    -      -       -      +
    383B  PHE*     1.3    55.4    +      -       -      +
    404B  PRO*     3.4     8.5    -      -       -      +
    405B  TRP*     2.9    33.3    +      -       +      +
    406B  ASN*     4.6     8.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 383 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320B  ARG*     3.1     7.5    -      -       -      -
    321B  ALA      2.8    34.8    +      -       -      +
    323B  PHE*     3.9    23.1    -      +       +      -
    372B  TYR*     4.7     2.0    -      -       -      -
    374B  HIS*     3.3    35.7    -      +       -      -
    376B  SER*     3.6    21.3    -      -       -      -
    378B  ASN      5.4     0.4    -      -       -      -
    381B  GLU*     3.5    33.7    -      -       +      -
    382B  GLU*     1.3    78.0    -      -       -      +
    384B  LEU*     1.3    61.5    +      -       -      +
    385B  ILE*     3.6     8.6    +      -       +      +
    402B  VAL*     4.3     7.9    -      -       +      -
    403B  ALA*     3.3    25.4    -      -       -      -
    404B  PRO*     3.6    25.8    -      -       +      -
    405B  TRP      4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 384 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  VAL*     3.8    12.8    -      -       +      -
    319B  ILE      3.4    12.6    -      -       -      +
    320B  ARG*     4.4     1.5    -      -       -      +
    346B  TYR*     3.8    30.3    -      -       +      -
    383B  PHE*     1.3    71.8    -      -       -      +
    385B  ILE*     1.3    69.5    +      -       -      +
    386B  ALA*     4.0     4.0    -      -       +      +
    401B  PHE*     4.0    17.0    -      -       +      -
    402B  VAL*     3.2     6.2    -      -       -      +
    403B  ALA      2.8    32.4    +      -       -      +
    405B  TRP*     3.9    22.9    -      -       +      +
    408B  LEU*     4.5     7.9    -      -       +      -
    416B  PHE*     3.7    41.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  LEU      3.8     1.6    -      -       -      +
    318B  VAL*     3.5     2.4    -      -       -      -
    319B  ILE*     2.8    42.8    +      -       +      +
    321B  ALA*     3.7    28.7    -      -       +      -
    323B  PHE*     3.9    26.9    -      -       +      -
    340B  ILE*     4.4    10.3    -      -       +      -
    361B  VAL*     5.0     3.4    -      -       +      -
    383B  PHE*     4.0    12.8    -      -       +      +
    384B  LEU*     1.3    80.3    -      -       -      +
    386B  ALA*     1.3    64.4    +      -       -      +
    394B  LEU*     4.3    15.9    -      -       +      +
    396B  ILE*     3.7    30.1    -      -       +      -
    401B  PHE      4.1     1.6    -      -       -      -
    402B  VAL*     4.4    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311B  ALA*     4.3    18.4    -      -       +      +
    312B  PHE      5.1     0.4    -      -       -      +
    315B  SER*     3.4    18.6    +      -       -      +
    317B  LEU      3.5     5.4    -      -       -      -
    318B  VAL*     4.1    14.1    -      -       +      +
    384B  LEU*     4.1    11.2    -      -       +      -
    385B  ILE*     1.3    77.7    -      -       -      +
    387B  GLY*     1.3    57.2    +      -       -      +
    396B  ILE*     4.6     0.2    -      -       -      -
    400B  SER*     3.6    22.9    +      -       -      -
    401B  PHE*     3.2    19.2    +      -       +      +
    402B  VAL*     4.8     0.2    -      -       -      +
    416B  PHE*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315B  SER*     3.1     4.9    -      -       -      -
    316B  ASP      3.0    21.5    +      -       -      -
    317B  LEU      3.0    14.0    +      -       -      -
    385B  ILE*     4.1     1.4    -      -       -      +
    386B  ALA*     1.3    74.7    -      -       -      +
    388B  LYS*     1.3    66.0    +      -       -      -
    394B  LEU*     3.8    11.6    -      -       -      +
    395B  HIS      3.3    13.2    -      -       -      -
    396B  ILE*     4.0     7.6    -      -       -      +
    400B  SER*     4.7     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 388 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  ASP*     4.3    31.7    +      -       +      +
    195A  GLU      5.6     2.0    +      -       -      -
    196A  GLY      5.6     0.8    -      -       -      -
    197A  GLY*     4.7    11.9    -      -       -      +
    314B  ASN*     3.8    34.0    -      -       -      +
    315B  SER*     4.3     2.7    -      -       -      +
    316B  ASP*     3.4    13.2    -      -       -      +
    387B  GLY*     1.3    78.9    -      -       -      +
    389B  LEU*     1.3    65.4    +      -       -      +
    390B  GLN*     6.3     0.2    -      -       +      -
    393B  LEU      3.4     1.6    -      -       -      +
    394B  LEU*     3.7     5.5    -      -       -      +
    395B  HIS*     2.8    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 389 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316B  ASP*     2.8    29.3    +      -       +      +
    317B  LEU*     3.7    37.5    -      -       +      -
    358B  ILE*     6.3     0.2    -      -       +      -
    388B  LYS*     1.3    74.0    -      -       -      +
    390B  GLN*     1.3    59.2    +      -       -      +
    391B  ASP      4.3     0.4    -      -       -      -
    392B  GLY*     3.9    22.7    -      -       -      +
    393B  LEU      3.3    20.2    -      -       -      +
    394B  LEU*     4.1     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 390 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  PRO*     4.1    27.2    -      -       -      +
    335B  TYR*     4.7     5.5    +      -       -      -
    388B  LYS      3.7     0.6    +      -       -      -
    389B  LEU*     1.3    74.6    -      -       -      +
    391B  ASP*     1.4    80.1    +      -       -      +
    393B  LEU*     2.9    29.9    +      -       -      +
    395B  HIS*     3.2    42.5    +      -       +      +
----------------------------------------------------------
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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