Contacts of the strand formed by residues 62 - 70 (chain L) in PDB entry 1MWA


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 PHE 62 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  THR*     3.8    25.6    -      -       +      -
     94H  THR*     4.2     2.9    -      -       +      -
     96H  GLN*     3.3    24.2    -      -       +      -
     29L  GLN      3.5    17.7    +      -       -      -
     30L  PHE*     2.9    38.0    +      -       +      +
     31L  HIS*     3.2    33.2    -      +       -      -
     33L  PRO*     3.8    32.5    -      -       +      -
     54L  MET*     3.8    27.4    -      -       +      -
     55L  SER      3.2    17.0    -      -       -      +
     56L  PHE*     3.6    10.5    -      +       +      +
     60L  TRP      3.8     0.9    -      -       -      -
     61L  SER*     1.3    73.7    -      -       -      +
     63L  TYR*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 63 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  TYR*     4.3    12.8    +      -       -      -
     26L  TYR*     4.1    21.5    -      +       +      -
     27L  VAL      3.3    12.3    -      -       -      +
     28L  THR*     3.9    16.4    -      -       +      -
     30L  PHE*     4.1     0.7    -      -       -      -
     53L  ASP      4.6     0.3    -      -       -      +
     54L  MET*     3.1    14.3    -      -       -      +
     55L  SER*     2.9    50.8    +      -       -      -
     56L  PHE*     3.7    13.2    +      -       -      -
     57L  SER*     3.3    27.6    -      -       -      -
     62L  PHE*     1.3    76.9    -      -       -      +
     64L  ILE*     1.3    72.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 64 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25L  CYS      4.0     1.4    -      -       -      +
     26L  TYR*     3.7     7.8    -      -       -      -
     27L  VAL*     3.1    29.6    +      -       +      +
     30L  PHE*     3.6    28.3    -      -       +      -
     35L  ILE*     4.9     2.2    -      -       +      -
     37L  ILE*     3.9    16.4    -      -       +      -
     51L  MET*     3.5    28.9    -      -       +      -
     52L  SER*     3.9    25.8    -      -       -      +
     53L  ASP      4.5     2.0    -      -       -      +
     54L  MET*     3.9    24.7    -      -       +      -
     63L  TYR*     1.3    85.7    -      -       -      +
     65L  LEU*     1.3    70.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235H  PRO*     4.1    13.5    -      -       +      +
    237H  GLY*     4.2    25.4    -      -       -      -
     10L  TYR*     4.0    11.0    -      -       -      +
     24L  ASN*     4.3    12.8    -      -       -      +
     25L  CYS      4.1     2.2    -      -       -      +
     26L  TYR*     3.9    36.6    -      -       +      +
     50L  GLU      3.8     0.5    -      -       -      +
     51L  MET*     3.4     2.4    -      -       -      -
     52L  SER*     2.8    50.3    +      -       -      +
     64L  ILE*     1.3    77.1    -      -       -      +
     66L  ALA*     1.3    72.6    +      -       -      +
     67L  HIS*     4.9    12.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24L  ASN*     3.5     1.9    -      -       -      +
     25L  CYS*     2.7    41.6    +      -       +      +
     37L  ILE*     3.9    18.6    -      -       +      -
     39L  MET*     3.9     7.3    -      -       -      +
     49L  VAL*     3.8    10.8    -      -       +      -
     50L  GLU      3.2     5.2    -      -       -      -
     51L  MET*     3.4    26.2    -      -       +      -
     65L  LEU*     1.3    73.8    -      -       -      +
     67L  HIS*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 67 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237H  GLY*     6.3     0.2    -      -       -      -
     12L  ARG*     4.9    12.2    +      -       -      -
     22L  ILE*     3.7    20.9    -      -       +      +
     23L  LEU      3.1     7.6    -      -       -      +
     24L  ASN*     3.0    27.6    -      -       -      +
     39L  MET*     4.0     1.1    -      -       -      -
     49L  VAL*     3.7     0.8    -      -       -      +
     50L  GLU*     2.8    76.8    +      -       +      +
     52L  SER*     5.6     3.6    -      -       -      -
     65L  LEU*     4.9    13.9    -      -       +      -
     66L  ALA*     1.3    72.7    -      -       -      +
     68L  THR*     1.3    70.1    +      -       -      +
     69L  GLU      5.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22L  ILE*     3.3     6.9    -      -       -      -
     23L  LEU*     2.7    45.8    +      -       -      +
     39L  MET*     3.9     4.6    -      -       -      +
     46L  ILE*     3.6    30.5    -      -       +      +
     48L  LYS      3.8     7.0    -      -       -      +
     49L  VAL*     3.3    37.7    -      -       +      -
     50L  GLU*     4.8     4.3    -      -       -      -
     67L  HIS*     1.3    84.0    -      -       -      +
     69L  GLU*     1.3    66.9    +      -       -      +
     70L  PHE*     4.8     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 69 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21L  ASN      3.4     7.4    -      -       -      +
     22L  ILE*     4.0    14.4    -      -       +      +
     46L  ILE*     5.8     1.4    -      -       -      +
     48L  LYS*     5.2    12.6    -      -       -      -
     50L  GLU*     5.3     6.0    +      -       -      +
     67L  HIS*     5.2     0.2    +      -       -      -
     68L  THR*     1.3    77.3    -      -       -      +
     70L  PHE*     1.3    63.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11L  SER*     4.0    11.7    -      -       -      -
     20L  PRO*     3.4     1.1    -      -       -      +
     21L  ASN*     2.5    77.6    +      -       +      +
     22L  ILE      3.5    14.8    -      -       -      -
     23L  LEU*     3.5    33.0    -      -       +      -
     46L  ILE*     6.0     0.9    -      -       +      -
     68L  THR*     4.6     3.8    -      -       -      +
     69L  GLU*     1.3    76.3    -      -       -      +
     71L  THR*     1.3    59.5    +      -       -      +
     72L  PRO*     4.0    23.8    -      -       +      -
     78L  TYR*     3.4    47.8    -      +       +      +
     95L  TRP*     4.4    16.2    -      +       -      -
----------------------------------------------------------
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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