Contacts of the strand formed by residues 38 - 48 (chain G) in PDB entry 5M64


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 ILE 38 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  HIS*     3.8     9.3    -      -       -      -
     31D  VAL*     3.5    18.0    -      -       -      +
     32D  SER      4.8     3.1    -      -       -      +
     33D  THR*     6.2     3.6    -      -       +      -
     36D  VAL*     5.5     8.7    -      -       +      -
     96D  PHE*     5.6     3.1    -      -       +      -
     35G  SER      5.3     1.1    -      -       -      +
     36G  ASN*     3.6     3.3    -      -       -      +
     37G  CYS*     1.3    86.3    -      -       -      +
     39G  VAL*     1.3    65.4    +      -       -      +
     40G  ARG*     4.8    20.4    -      -       -      +
     82G  LEU*     4.3    21.1    -      -       +      -
    123G  TYR*     5.5     0.9    -      -       +      -
    124G  VAL      3.9     7.6    -      -       -      +
    125G  TRP*     3.6    25.6    -      -       +      +
    150G  HIS*     4.2    25.1    -      -       +      +
    153G  PHE*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 39 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  PRO*     4.4    14.6    -      -       +      +
     29D  GLN      4.0     5.4    -      -       -      +
     30D  HIS*     3.7    38.8    -      -       +      +
     31D  VAL*     4.6     1.1    -      -       -      -
     24G  VAL*     5.2     7.2    -      -       +      -
     26G  ASN*     4.9     1.8    -      -       -      +
     37G  CYS      3.6     1.6    +      -       -      +
     38G  ILE*     1.3    74.3    -      -       -      +
     40G  ARG*     1.3    74.0    +      -       -      +
     41G  VAL*     3.6    22.7    -      -       +      -
    123G  TYR*     3.8     1.4    -      -       -      +
    124G  VAL*     2.7    33.7    +      -       +      +
    126G  GLN*     3.3    34.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 40 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  GLN      4.0    16.4    +      -       -      +
     31D  VAL*     3.3    44.0    -      -       +      +
     32D  SER      4.6     3.6    +      -       -      -
     35D  GLU*     4.0     4.6    -      -       -      +
     36D  VAL*     3.7    33.9    -      -       -      +
     39D  PHE*     3.3    34.2    -      -       -      -
     38G  ILE*     4.8    12.4    -      -       -      +
     39G  VAL*     1.3    82.7    -      -       -      +
     41G  VAL*     1.3    62.9    +      -       -      +
     42G  PRO*     3.6     8.0    -      -       -      +
    121G  ASN*     3.5    14.6    +      -       -      +
    122G  LEU      3.7     5.4    -      -       -      -
    123G  TYR*     3.2    56.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 41 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  ALA*     4.4    10.3    -      -       +      -
     26D  GLN      4.8     1.1    -      -       -      +
     28D  PRO*     3.6    37.7    -      -       +      -
     39G  VAL*     3.6    21.3    +      -       +      -
     40G  ARG*     1.3    70.3    -      -       -      +
     42G  PRO*     1.3    77.6    -      -       +      +
     43G  ILE*     3.6    11.1    +      -       +      +
     77G  VAL*     3.8    24.5    -      -       +      -
    121G  ASN*     3.2     3.6    -      -       -      -
    122G  LEU*     2.9    32.6    +      -       -      +
    124G  VAL*     3.7    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 42 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25D  THR*     2.8    31.8    +      -       +      +
     26D  GLN*     3.8    37.3    +      -       +      +
     27D  LEU      4.8     0.7    -      -       -      +
     28D  PRO*     4.6    10.8    -      -       +      -
     29D  GLN      5.2     1.3    -      -       -      +
     40G  ARG      3.6     8.5    -      -       -      +
     41G  VAL*     1.3    90.6    -      -       +      +
     43G  ILE*     1.3    60.9    +      -       -      +
    119G  HIS*     6.3     2.9    -      -       +      -
    120G  VAL      4.7     0.9    -      -       -      +
    121G  ASN*     3.7    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 43 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  ILE*     3.7    27.4    -      -       +      -
     23D  HIS      3.7     2.9    -      -       -      +
     24D  ALA*     3.8    18.2    -      -       +      +
     25D  THR*     3.2     6.6    +      -       -      -
     41G  VAL*     4.2    14.8    -      -       +      +
     42G  PRO*     1.3    78.8    -      -       -      +
     44G  ALA*     1.3    58.8    +      -       -      +
     45G  LEU*     4.3     9.2    -      -       +      -
     76G  LYS*     6.4     1.6    -      -       +      -
     77G  VAL*     5.1    11.9    -      -       +      -
    119G  HIS*     3.4     1.2    -      -       -      +
    120G  VAL*     2.8    56.9    +      -       +      +
    122G  LEU*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  ILE*     3.2     6.7    -      -       -      +
     23D  HIS      2.7    33.8    +      -       -      +
     25D  THR*     3.3     6.4    +      -       +      +
     58F  PHE*     3.5    32.8    -      -       +      -
     43G  ILE*     1.3    70.9    -      -       -      +
     45G  LEU*     1.3    59.3    +      -       -      +
     46G  TYR*     3.6    16.9    -      -       +      +
    118G  CYS      5.0     0.9    -      -       -      +
    119G  HIS*     4.0    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  PRO*     3.8    26.2    -      -       +      -
     22D  ILE*     3.9    16.8    -      -       +      -
     43G  ILE*     3.8    14.5    +      -       +      -
     44G  ALA*     1.3    72.3    -      -       -      +
     46G  TYR*     1.3    61.3    +      -       -      +
     47G  VAL*     3.5    35.3    +      -       +      -
     61G  VAL*     4.8     6.7    -      -       +      -
     65G  HIS*     5.3     8.7    -      -       +      +
     66G  LEU*     6.0     5.6    -      -       +      -
     69G  LEU*     5.7     7.9    -      -       +      -
    117G  TRP      3.9     0.2    -      -       -      -
    118G  CYS*     2.8    51.0    +      -       -      +
    120G  VAL*     4.5     9.9    -      -       +      -
    122G  LEU*     6.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 46 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1202B  PRO*     3.9    15.7    -      -       +      -
   1203B  LYS*     3.5    21.1    +      -       -      -
     19D  PRO*     3.3    17.9    -      -       -      +
     20D  VAL*     3.5    15.7    +      -       +      +
     21D  VAL*     3.0    45.0    +      -       +      +
     23D  HIS*     4.7     4.9    -      +       -      -
     58F  PHE*     3.2    29.3    -      +       -      -
     62F  GLU*     4.8     3.5    +      -       -      -
     65F  ARG*     5.4     3.4    +      -       -      -
     44G  ALA*     3.6    25.9    -      -       +      +
     45G  LEU*     1.3    70.7    -      -       -      +
     47G  VAL*     1.3    59.6    +      -       -      +
    116G  THR      3.9     4.0    -      -       -      -
    117G  TRP*     3.3    54.1    -      +       +      +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  PRO*     4.3     8.5    -      -       +      -
     20D  VAL*     5.4     2.7    -      -       -      +
     45G  LEU*     3.5    19.5    +      -       +      -
     46G  TYR*     1.3    74.1    -      -       -      +
     48G  SER*     1.3    77.0    +      -       -      +
     61G  VAL*     3.6    19.1    -      -       +      -
     65G  HIS*     3.3    48.7    -      -       +      +
    115G  PHE*     3.8     4.4    -      -       -      +
    116G  THR*     2.8    50.3    +      -       +      +
    117G  TRP*     4.9     0.5    -      -       -      -
    118G  CYS*     4.8     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 48 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PRO*     6.1     0.7    -      -       -      +
      8A  GLY*     6.1     0.3    -      -       -      -
     15D  THR*     4.5    15.4    +      -       -      -
     16D  LEU*     6.3     1.3    -      -       -      -
     20D  VAL*     6.0     2.1    -      -       -      +
     47G  VAL*     1.3    95.7    -      -       -      +
     49G  LEU*     1.3    75.2    +      -       -      +
     61G  VAL*     4.6     2.4    -      -       -      +
     65G  HIS*     4.6    11.3    -      -       -      -
    113G  PHE*     4.3    12.3    -      -       -      -
    114G  GLY      3.1    13.2    -      -       -      -
    115G  PHE*     3.2    27.4    -      -       -      -
----------------------------------------------------------
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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