Contacts of the strand formed by residues 522 - 533 (chain A) in PDB entry 2E3M


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 LYS 522 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506A  SER*     3.4    28.0    +      -       -      +
    507A  VAL*     5.4     2.3    +      -       -      +
    508A  ASP*     4.5    15.4    +      -       -      -
    514A  LEU*     6.5     0.4    -      -       -      -
    520A  ARG*     3.9    17.9    +      -       +      +
    521A  ALA*     1.3    80.0    -      -       -      +
    523A  ILE*     1.3    60.4    +      -       -      +
    556A  ASN      3.8     1.6    -      -       -      +
    557A  VAL*     3.5     1.4    -      -       -      -
    558A  ASN*     2.7    49.6    +      -       +      +
    560A  GLY*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 523 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467A  GLN*     6.1     0.4    -      -       -      +
    480A  VAL*     3.8    21.8    -      -       +      -
    482A  TYR*     3.9    28.7    -      -       +      -
    504A  ASN*     4.0    20.9    -      -       +      +
    505A  PHE*     3.3     2.4    -      -       -      +
    506A  SER*     2.8    48.1    +      -       -      +
    521A  ALA*     4.7     4.9    -      -       +      -
    522A  LYS*     1.3    76.2    -      -       -      +
    524A  ASN*     1.3    62.6    +      -       -      +
    525A  VAL*     4.6    10.5    -      -       +      -
    556A  ASN      3.4     4.3    -      -       -      -
    557A  VAL*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  MET*     3.1    30.8    -      -       +      +
    378A  HIS*     2.8    33.7    +      -       -      -
    503A  CYS*     6.1     0.3    -      -       -      +
    504A  ASN      3.5     4.4    -      -       -      +
    505A  PHE*     4.3     2.5    -      -       +      +
    523A  ILE*     1.3    76.4    -      -       -      +
    525A  VAL*     1.3    61.0    +      -       -      +
    554A  VAL      4.6     0.2    -      -       -      -
    555A  ALA*     3.8     0.3    -      -       -      -
    556A  ASN*     2.7    52.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  HIS*     4.3     0.6    +      -       -      -
    436A  PHE*     4.4     7.4    -      -       +      -
    502A  VAL      3.8     0.2    -      -       -      +
    503A  CYS*     3.5     3.1    -      -       -      +
    504A  ASN*     2.7    59.8    +      -       +      +
    523A  ILE*     4.6    11.7    -      -       +      -
    524A  ASN*     1.3    81.7    +      -       -      +
    526A  ALA*     1.3    65.6    +      -       -      +
    553A  TYR*     3.8    26.5    -      -       +      +
    554A  VAL      3.3     7.6    -      -       -      +
    555A  ALA*     3.9    23.8    -      -       +      -
    557A  VAL*     4.5    13.7    -      -       +      -
    576A  TYR*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  HIS*     3.6    25.6    -      -       +      +
    501A  ILE*     4.2     4.3    -      -       +      -
    502A  VAL      3.2     9.2    -      -       -      +
    503A  CYS*     4.7     0.4    -      -       -      -
    525A  VAL*     1.3    79.5    -      -       -      +
    527A  MET*     1.3    60.0    +      -       -      +
    528A  ILE*     4.0    12.6    -      -       +      -
    552A  THR      4.5     0.2    -      -       -      -
    553A  TYR*     3.3     5.0    -      -       -      -
    554A  VAL*     2.8    53.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 527 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432A  VAL*     4.3    12.8    -      -       +      -
    433A  CYS*     3.9     7.0    -      -       -      -
    436A  PHE*     3.3    62.1    -      -       +      -
    500A  TRP      3.9     0.7    -      -       -      +
    501A  ILE*     3.3     5.0    -      -       -      -
    502A  VAL*     3.1    28.4    +      -       +      +
    526A  ALA*     1.3    71.5    -      -       -      +
    528A  ILE*     1.3    59.3    +      -       -      +
    529A  CYS*     4.2    11.2    -      -       -      -
    551A  ILE*     3.9    26.2    -      -       -      -
    552A  THR      3.7     2.5    -      -       -      -
    553A  TYR*     4.0    11.2    -      -       +      +
    579A  PHE*     3.8    14.8    -      -       +      -
    580A  LEU*     4.8     3.6    -      -       +      -
    583A  PHE*     3.7    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 528 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  HIS*     4.2    14.6    -      -       +      +
    379A  MET*     4.4     7.0    -      -       -      +
    382A  SER*     3.8    25.4    -      -       -      -
    383A  LEU*     3.7    36.3    -      -       +      -
    499A  THR*     3.4    30.1    -      -       +      -
    500A  TRP      3.6     2.7    -      -       -      +
    501A  ILE*     3.8    16.8    -      -       +      +
    526A  ALA*     4.0     9.2    -      -       +      -
    527A  MET*     1.3    77.3    -      -       -      +
    529A  CYS*     1.3    60.6    +      -       -      +
    530A  GLN*     5.6     1.3    -      -       +      +
    550A  LYS      3.5     1.2    -      -       -      +
    551A  ILE*     3.4     3.5    -      -       -      -
    552A  THR*     2.6    50.2    +      -       +      +
    554A  VAL*     4.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 529 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  GLY*     3.4    25.4    -      -       -      +
    432A  VAL*     3.5    33.0    -      -       -      -
    433A  CYS*     3.8    13.5    -      -       -      -
    498A  GLU      3.9     0.5    -      -       -      +
    499A  THR*     3.5     4.2    -      -       -      -
    500A  TRP*     2.8    39.9    +      -       -      +
    527A  MET*     4.2     7.4    -      -       -      -
    528A  ILE*     1.3    81.6    -      -       -      +
    530A  GLN*     1.3    64.1    +      -       -      +
    549A  CYS*     3.6     5.4    -      -       -      -
    550A  LYS      3.3     2.7    -      -       -      -
    551A  ILE*     4.0    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 530 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379A  MET*     4.7     1.6    -      -       -      +
    383A  LEU*     4.4    18.6    -      -       -      +
    429A  GLY*     5.3     0.2    -      -       -      -
    497A  PRO*     3.7    30.8    +      -       +      +
    498A  GLU      3.5    13.7    -      -       -      +
    499A  THR*     2.5    34.1    +      -       +      +
    528A  ILE*     5.6     1.6    -      -       +      -
    529A  CYS*     1.3    75.2    -      -       -      +
    531A  THR*     1.3    61.4    +      -       -      +
    532A  LEU*     4.0     5.6    +      -       +      +
    548A  LEU      3.9     0.3    -      -       -      +
    549A  CYS*     3.5     2.1    -      -       -      -
    550A  LYS*     2.7    48.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 531 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427A  VAL      4.4     2.9    -      -       -      +
    428A  THR*     3.3    26.6    -      -       +      -
    429A  GLY*     2.5    33.8    +      -       -      -
    430A  HIS      4.6     0.2    +      -       -      -
    497A  PRO*     4.1    12.5    -      -       -      +
    498A  GLU      4.3     5.5    +      -       -      -
    500A  TRP*     5.8     0.9    -      -       -      -
    530A  GLN*     1.3    71.7    -      -       -      +
    532A  LEU*     1.3    69.0    +      -       -      +
    533A  VAL*     3.9    24.8    +      -       +      +
    547A  ILE*     4.5     2.7    -      -       +      -
    548A  LEU      3.6     6.7    -      -       -      +
    549A  CYS*     4.5     0.8    -      -       -      +
    598A  PHE*     4.7     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 532 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  PRO*     4.9     9.9    -      -       +      -
    530A  GLN*     4.4     9.4    -      -       +      +
    531A  THR*     1.3    77.9    -      -       -      +
    533A  VAL*     1.3    63.2    +      -       -      +
    546A  ASN      3.8     0.9    -      -       -      +
    547A  ILE*     3.4     2.9    -      -       -      +
    548A  LEU*     2.9    50.7    +      -       +      +
    550A  LYS*     3.8    40.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 533 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  THR*     3.9    13.1    +      -       +      +
    532A  LEU*     1.3    78.1    -      -       -      +
    534A  SER*     1.3    73.2    +      -       -      +
    542A  ILE*     3.9    36.6    -      -       +      -
    546A  ASN      3.3     6.3    -      -       -      +
    547A  ILE*     3.6     9.0    -      -       +      -
    598A  PHE*     3.5    29.2    -      -       +      -
----------------------------------------------------------
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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