Contacts of the helix formed by residues 311 - 318 (chain B) in PDB entry 2Q41


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 ASN 311 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309B  PHE      3.5     1.8    +      -       -      -
    310B  TYR*     1.3    85.4    -      -       -      +
    312B  ALA*     1.3    59.1    +      -       -      +
    313B  GLU*     3.2    19.3    -      -       -      +
    314B  ILE*     2.8    36.1    +      -       -      +
    315B  HIS*     2.9    28.4    +      -       -      +
    321C  LEU      3.3    13.6    +      -       -      +
    323C  SER*     3.0    39.1    +      -       -      +
    326C  LYS*     3.6    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292B  PRO*     4.6    16.9    -      -       +      +
    295B  PRO*     5.5     8.3    -      -       +      -
    310B  TYR*     4.7     2.5    -      -       -      -
    311B  ASN*     1.3    74.1    -      -       -      +
    313B  GLU*     1.3    77.2    +      -       -      +
    315B  HIS*     3.2    21.0    +      -       -      +
    316B  SER*     3.3     8.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311B  ASN*     3.2    15.5    -      -       -      +
    312B  ALA*     1.3    87.2    +      -       -      +
    314B  ILE*     1.3    58.5    +      -       +      +
    316B  SER*     3.0     9.7    +      -       -      -
    317B  ALA*     2.9    28.2    +      -       -      +
    320C  CYS*     4.0    27.4    -      -       +      -
    321C  LEU      5.7     0.7    -      -       -      +
    326C  LYS*     3.4    28.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  MSE      3.6    30.9    -      -       +      +
    309B  PHE*     4.0    13.0    -      -       +      +
    310B  TYR*     4.1     8.7    -      -       -      -
    311B  ASN*     2.8    25.8    +      -       -      +
    313B  GLU*     1.3    76.6    -      -       -      +
    315B  HIS*     1.3    63.6    +      -       -      +
    317B  ALA*     3.3     8.2    +      -       +      +
    318B  ALA*     3.1    23.7    +      -       -      +
    264C  TRP*     4.6     8.5    -      -       +      +
    320C  CYS*     3.3    26.2    -      -       +      +
    321C  LEU      3.5    15.9    -      -       -      +
    322C  PRO*     3.7    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  MSE      4.9     3.6    -      -       -      -
    112B  HIS      3.7     6.3    -      -       -      -
    113B  LEU*     3.5    35.1    -      -       +      +
    116B  CYS*     4.2     0.7    -      -       +      -
    117B  SER*     3.9     3.9    +      -       -      -
    289B  PHE      2.9    25.2    +      -       -      -
    290B  LYS      4.4     0.2    -      -       -      -
    292B  PRO*     3.1    35.0    -      -       +      +
    310B  TYR*     2.7    38.7    +      -       +      +
    311B  ASN      2.9    14.2    +      -       -      +
    312B  ALA*     3.2    14.1    -      -       -      +
    313B  GLU      3.1     0.2    -      -       -      -
    314B  ILE*     1.3    80.1    -      -       -      +
    316B  SER*     1.3    62.5    +      -       -      +
    318B  ALA*     3.6     6.1    +      -       -      +
    319B  PHE*     3.3    18.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290B  LYS*     3.2    27.7    -      -       -      +
    291B  HIS*     5.1     5.6    -      -       -      -
    292B  PRO*     5.4     1.8    -      -       -      -
    312B  ALA      3.3     6.7    +      -       -      -
    313B  GLU*     3.0    15.8    +      -       -      -
    315B  HIS*     1.3    76.6    -      -       -      +
    317B  ALA*     1.3    65.2    +      -       -      +
    318B  ALA      3.1     2.5    -      -       -      -
    319B  PHE*     3.0    22.8    +      -       -      +
    320B  CYS*     3.9     8.6    -      -       -      -
    320C  CYS*     5.4     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  TRP*     4.8     2.6    +      -       -      -
    313B  GLU      2.9    18.7    +      -       -      +
    314B  ILE*     3.4    12.6    -      -       +      +
    316B  SER*     1.3    78.8    +      -       -      +
    318B  ALA*     1.3    56.5    +      -       -      +
    319B  PHE      3.0     5.4    +      -       -      -
    320B  CYS*     3.1    23.7    +      -       -      +
    317C  ALA*     3.9    21.4    -      -       +      +
    320C  CYS*     3.9    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  MSE      3.6    30.1    -      -       +      -
    113B  LEU*     4.8     2.2    -      -       +      -
    262B  TYR      3.7     0.2    -      -       -      +
    263B  ALA*     2.9    38.3    -      -       +      -
    264B  TRP*     3.0    30.3    +      -       -      +
    314B  ILE      3.1     7.9    +      -       -      +
    315B  HIS      3.7     8.1    -      -       -      +
    316B  SER      3.1     1.0    -      -       -      -
    317B  ALA*     1.3    75.1    -      -       -      +
    319B  PHE*     1.3    60.6    +      -       +      +
    320B  CYS      3.4     0.7    -      -       -      -
    321B  LEU*     4.1     0.3    -      -       -      +
----------------------------------------------------------
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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