Contacts of the strand formed by residues 62 - 70 (chain M) 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 M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  THR*     3.9    24.0    -      -       +      -
     94I  THR*     4.2     2.9    -      -       +      -
     96I  GLN*     3.2    22.0    -      -       +      -
     29M  GLN      3.7    10.6    +      -       -      -
     30M  PHE*     3.3    36.6    +      -       +      +
     31M  HIS*     3.2    39.0    -      +       -      -
     33M  PRO*     3.3    28.5    -      -       +      -
     54M  MET*     3.2    43.3    -      -       +      -
     56M  PHE*     3.7    19.7    -      +       +      -
     60M  TRP      3.9     0.2    -      -       -      -
     61M  SER*     1.3    76.9    +      -       -      +
     63M  TYR*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 63 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27I  TYR*     4.5     8.0    +      -       -      -
     26M  TYR*     3.9    24.5    -      +       +      -
     27M  VAL      3.4     5.4    -      -       -      -
     28M  THR*     3.6    26.0    -      -       +      -
     30M  PHE*     4.2     1.6    -      -       -      -
     53M  ASP      5.1     0.5    -      -       -      +
     54M  MET*     3.2     6.2    -      -       -      +
     55M  SER*     3.0    45.9    +      -       -      +
     56M  PHE      3.4     4.4    +      -       -      -
     57M  SER*     3.2    42.0    -      -       -      -
     61M  SER*     4.1     2.9    -      -       -      +
     62M  PHE*     1.3    79.3    -      -       -      +
     64M  ILE*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 64 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25M  CYS      4.1     0.5    -      -       -      +
     26M  TYR*     4.0     3.6    -      -       -      -
     27M  VAL*     3.1    32.6    +      -       +      +
     30M  PHE*     4.4    13.4    -      -       +      -
     35M  ILE*     4.2    16.4    -      -       +      -
     37M  ILE*     4.2    18.4    -      -       +      -
     51M  MET*     3.0    33.7    -      -       +      -
     52M  SER*     3.7     8.7    -      -       -      +
     53M  ASP      2.8    30.7    -      -       -      +
     54M  MET*     4.0    15.9    -      -       +      -
     63M  TYR*     1.3    76.8    -      -       -      +
     65M  LEU*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235I  PRO*     3.8    25.4    -      -       +      +
    236I  ALA      4.6     2.7    -      -       -      +
    237I  GLY*     4.9     7.4    -      -       -      -
     10M  TYR*     4.0     2.2    -      -       -      +
     24M  ASN*     3.0    31.9    -      -       -      +
     25M  CYS      3.0    36.6    -      -       -      +
     26M  TYR*     3.4    25.1    -      -       +      +
     37M  ILE*     5.3     0.9    -      -       -      -
     51M  MET*     3.2    22.6    -      -       -      +
     52M  SER*     3.4    19.1    +      -       -      +
     64M  ILE*     1.3    80.8    -      -       -      +
     66M  ALA*     1.3    61.4    +      -       -      +
     67M  HIS*     4.7     7.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 66 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24M  ASN*     3.4     3.8    -      -       -      +
     25M  CYS*     2.8    54.0    +      -       +      +
     37M  ILE*     4.2    26.2    -      -       +      +
     38M  GLN*     6.0     0.4    -      -       -      +
     39M  MET*     3.4    14.6    -      -       +      +
     49M  VAL*     4.9     5.6    -      -       +      +
     50M  GLU      4.1     5.2    -      -       -      +
     51M  MET*     4.1     6.1    -      -       -      -
     65M  LEU*     1.3    76.1    -      -       -      +
     67M  HIS*     1.3    60.5    +      -       -      +
     80M  CYS*     5.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 67 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237I  GLY*     5.9     5.8    +      -       -      -
     12M  ARG*     5.5     4.0    -      -       -      -
     22M  ILE*     4.1    18.8    -      -       +      -
     23M  LEU      3.2    16.8    -      -       -      +
     24M  ASN*     3.7    14.8    +      -       -      +
     39M  MET*     3.3     3.8    -      -       -      -
     49M  VAL      4.7     0.2    +      -       -      -
     50M  GLU*     3.0    53.3    +      -       +      +
     51M  MET*     3.8    19.6    -      -       -      -
     52M  SER      4.7     1.8    +      -       -      -
     65M  LEU*     4.7     6.6    +      -       +      +
     66M  ALA*     1.3    76.8    -      -       -      +
     68M  THR*     1.3    59.7    +      -       -      +
     69M  GLU      4.4     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22M  ILE*     4.8     2.7    -      -       -      -
     23M  LEU*     3.1    28.4    +      -       -      +
     39M  MET*     2.9    35.0    -      -       +      +
     46M  ILE*     3.7    20.9    -      -       +      +
     48M  LYS      2.9    26.9    -      -       -      +
     49M  VAL*     3.3    26.5    -      -       +      -
     67M  HIS*     1.3    73.8    -      -       -      +
     69M  GLU*     1.3    72.2    +      -       -      +
     70M  PHE*     5.3     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 69 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20M  PRO*     5.4     5.0    -      -       -      +
     21M  ASN      3.0    25.7    -      -       -      +
     22M  ILE*     3.6    16.7    -      -       +      +
     46M  ILE*     4.9     4.3    -      -       -      +
     48M  LYS      5.1     1.2    +      -       -      -
     50M  GLU*     5.9     2.7    -      -       -      +
     67M  HIS*     4.4     0.8    +      -       -      -
     68M  THR*     1.3    82.3    -      -       -      +
     70M  PHE*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11M  SER*     4.3    12.1    -      -       -      -
     20M  PRO*     3.2     3.5    -      -       -      +
     21M  ASN*     2.5    52.5    +      -       +      -
     22M  ILE      3.0    25.1    -      -       -      -
     23M  LEU*     3.0    48.2    -      -       +      -
     46M  ILE*     5.6     2.0    -      -       +      -
     68M  THR*     4.0     2.5    -      -       -      +
     69M  GLU*     1.3    78.9    +      -       -      +
     71M  THR*     1.3    56.8    +      -       -      +
     72M  PRO*     4.3    20.6    -      -       +      -
     78M  TYR*     3.4    44.0    -      +       +      +
     95M  TRP*     4.6     8.1    -      +       -      -
----------------------------------------------------------
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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