Contacts of the strand formed by residues 317 - 330 (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 LEU 317 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315B  SER*     3.7     0.2    -      -       -      -
    316B  ASP*     1.3    86.1    -      -       +      +
    318B  VAL*     1.3    66.4    +      -       -      +
    319B  ILE*     4.3     9.2    -      -       +      -
    345B  MET*     4.9     2.9    -      -       -      -
    347B  LYS      3.4     4.0    -      -       -      +
    348B  GLY*     3.7    24.7    -      -       -      +
    358B  ILE*     3.5    33.9    -      -       +      -
    385B  ILE      3.8     1.4    -      -       -      +
    386B  ALA*     3.5     0.3    -      -       -      -
    387B  GLY      3.0    30.1    +      -       -      +
    389B  LEU*     3.7    33.9    -      -       +      -
    394B  LEU*     3.5    32.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312B  PHE*     4.1    18.8    -      -       +      -
    315B  SER*     3.9    17.5    -      -       -      -
    317B  LEU*     1.3    79.3    -      -       -      +
    319B  ILE*     1.3    60.7    +      -       -      +
    346B  TYR*     2.7    39.8    +      -       +      -
    347B  LYS*     3.0    32.1    +      -       +      +
    384B  LEU*     3.8    29.2    -      -       +      -
    385B  ILE      3.5     3.4    -      -       -      +
    386B  ALA*     4.1     7.6    -      -       +      -
    416B  PHE*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  LEU*     4.6     8.7    -      -       +      -
    318B  VAL*     1.3    84.0    -      -       -      +
    320B  ARG*     1.3    61.3    +      -       -      +
    321B  ALA*     4.3     4.3    -      -       +      -
    340B  ILE*     3.7    30.1    -      -       +      -
    342B  MET*     3.9    28.5    -      -       +      -
    344B  LYS      3.2    15.9    -      -       -      +
    345B  MET*     4.1    15.5    -      -       +      +
    346B  TYR*     4.3     2.2    -      -       -      +
    358B  ILE*     4.7     7.0    -      -       +      -
    384B  LEU*     3.4    10.7    -      -       -      +
    385B  ILE*     2.8    47.4    +      -       +      +
    394B  LEU*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  ILE*     1.3    74.6    -      -       -      +
    321B  ALA*     1.3    66.4    +      -       -      +
    342B  MET*     3.5     3.3    -      -       -      +
    343B  THR*     2.8    37.6    +      -       -      +
    344B  LYS*     2.9    42.8    +      -       +      +
    346B  TYR*     3.1    26.5    +      -       +      +
    382B  GLU*     2.4    65.0    +      -       +      +
    383B  PHE      3.1    10.3    -      -       -      +
    384B  LEU*     4.4     1.3    -      -       -      +
    405B  TRP*     3.7    40.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  ILE*     4.3     2.9    -      -       +      -
    320B  ARG*     1.3    80.9    -      -       -      +
    322B  LYS*     1.3    64.2    +      -       -      +
    340B  ILE*     4.0    16.8    -      -       +      -
    341B  LYS      3.3    12.8    -      -       -      +
    342B  MET*     4.0     7.2    -      -       -      -
    343B  THR*     4.2     2.2    -      -       -      +
    382B  GLU*     3.6     3.2    -      -       -      -
    383B  PHE*     2.8    37.0    +      -       -      +
    385B  ILE*     3.7    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321B  ALA*     1.3    76.0    -      -       -      +
    323B  PHE*     1.3    66.4    +      -       -      +
    324B  VAL*     3.9     3.2    -      -       +      +
    340B  ILE*     3.3     6.8    -      -       -      +
    341B  LYS*     2.9    60.4    +      -       +      +
    343B  THR*     4.1    10.3    -      -       -      +
    379B  ARG*     3.3    27.8    -      -       +      +
    380B  SER*     3.6    17.0    +      -       -      +
    381B  GLU      3.7    13.7    -      -       -      +
    382B  GLU*     3.7    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  LYS*     1.3    76.7    -      -       -      +
    324B  VAL*     1.3    62.8    +      -       -      +
    325B  GLY      3.8     6.5    +      -       -      +
    338B  TYR*     3.8    43.1    -      +       +      -
    339B  GLU      3.8     2.2    -      -       -      -
    340B  ILE*     4.0     4.5    -      -       +      -
    361B  VAL*     4.1    11.9    -      -       +      -
    372B  TYR*     4.1    18.4    -      +       -      -
    374B  HIS*     3.3    47.1    -      +       +      +
    378B  ASN      5.1     1.3    +      -       -      +
    379B  ARG*     4.0    21.5    +      -       -      +
    381B  GLU      4.5     3.0    +      -       -      -
    383B  PHE*     3.9    20.4    -      +       +      -
    385B  ILE*     3.9    31.6    -      -       +      -
    396B  ILE*     4.7     2.7    -      -       +      -
    402B  VAL*     4.7     3.6    -      -       +      -
    251D  SER*     4.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  LYS*     3.9    10.8    -      -       +      +
    323B  PHE*     1.3    74.6    -      -       -      +
    325B  GLY*     1.3    64.1    +      -       -      +
    326B  THR      4.5     1.9    -      -       -      +
    339B  GLU*     2.8    57.8    +      -       +      +
    340B  ILE      4.2     2.5    -      -       -      -
    341B  LYS*     4.1    21.5    -      -       +      +
    379B  ARG*     3.9    32.5    -      -       +      +
    277D  ARG*     5.5     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  PHE*     3.8     5.9    +      -       -      +
    324B  VAL*     1.3    76.2    +      -       -      +
    326B  THR*     1.3    66.9    +      -       -      -
    327B  PRO*     3.8     2.1    -      -       -      +
    338B  TYR*     4.4    10.6    -      -       -      -
    339B  GLU      5.2     1.4    +      -       -      +
    379B  ARG*     3.2    18.9    -      -       -      +
    251D  SER*     3.7    10.2    +      -       -      -
    274D  ASP*     3.3    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324B  VAL      4.5     1.2    -      -       -      +
    325B  GLY*     1.3    75.8    -      -       -      -
    327B  PRO*     1.3    71.7    -      -       +      +
    338B  TYR*     5.6     0.3    -      -       -      -
    339B  GLU      5.6     0.7    +      -       -      -
    247D  LEU*     6.2     0.2    -      -       +      -
    250D  SER*     6.2     1.6    -      -       -      -
    274D  ASP*     2.7    46.2    +      -       -      +
    277D  ARG*     3.1    28.9    +      -       -      +
    278D  GLY*     3.8    23.6    -      -       -      -
    281D  GLN*     5.7     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  THR*     1.3    92.7    -      -       +      +
    328B  GLU*     1.3    65.9    +      -       -      +
    329B  VAL*     3.9     3.6    +      -       +      +
    336B  GLN*     3.2    33.0    -      -       +      +
    337B  ARG      3.3    19.7    -      -       -      +
    338B  TYR*     3.4    37.5    -      -       +      -
    277D  ARG*     3.4    23.7    -      -       -      +
    281D  GLN*     3.5    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327B  PRO*     1.3    73.3    -      -       -      +
    329B  VAL*     1.3    63.0    +      -       -      +
    330B  ASN      4.1     1.0    +      -       -      +
    335B  TYR      4.2     0.3    -      -       -      +
    336B  GLN*     3.2     2.4    -      -       -      -
    337B  ARG*     2.9    57.4    +      -       +      +
    360B  PHE*     6.3     0.2    -      -       +      -
    276D  ARG*     5.6     3.4    -      -       -      +
    277D  ARG*     3.3    39.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327B  PRO      3.9     5.8    +      -       -      +
    328B  GLU*     1.3    78.3    -      -       -      +
    330B  ASN*     1.3    67.3    +      -       -      +
    331B  GLN*     3.6    31.5    +      -       -      +
    335B  TYR      3.7     5.6    -      -       -      +
    336B  GLN*     3.7    22.4    -      -       +      +
    365B  ALA*     3.7    29.8    -      -       +      +
    277D  ARG*     5.5     0.8    -      -       -      +
    280D  GLN*     5.1     2.7    -      -       +      +
    281D  GLN*     4.2    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328B  GLU*     4.1     1.2    +      -       -      +
    329B  VAL*     1.3    73.2    -      -       -      +
    331B  GLN*     1.3    53.0    +      -       -      +
    332B  THR*     2.7    39.0    +      -       -      +
    333B  THR*     3.3    28.8    +      -       -      +
    334B  LEU*     2.8    34.8    +      -       -      -
    335B  TYR*     2.8    17.3    +      -       +      +
----------------------------------------------------------
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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