Contacts of the helix formed by residues 897 - 910 (chain A) in PDB entry 6VSB
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.
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 PRO 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A ILE* 1.3 89.3 - - + +
898A PHE* 1.3 66.7 + - - +
899A ALA* 4.8 2.0 - - + +
900A MET* 3.1 37.4 + - + +
901A GLN* 3.1 16.6 + - - +
707C TYR* 3.8 1.3 - - + +
708C SER 3.6 12.0 - - - +
709C ASN* 3.7 31.6 - - + +
711C SER 3.3 24.2 - - - +
712C ILE* 4.5 1.8 - - + -
1077C THR* 3.8 9.0 - - - +
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Residues in contact with PHE 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A PHE* 3.1 31.6 - - + +
798A GLY* 4.8 0.2 - - - -
800A PHE* 3.2 42.6 - + + -
802A PHE* 3.3 32.1 - + - -
882A ILE* 3.6 26.0 - - + +
896A ILE 3.3 4.2 + - - -
897A PRO* 1.3 71.1 - - - +
899A ALA* 1.3 67.6 + - - +
901A GLN* 2.9 24.4 + - - +
902A MET* 2.9 24.7 + - + -
1050A MET* 3.9 24.0 - - + -
707C TYR* 3.1 21.6 + - - +
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Residues in contact with ALA 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A GLY* 4.8 7.6 - - - -
800A PHE* 5.9 2.2 - - + -
897A PRO* 3.4 2.1 - - + +
898A PHE* 1.3 84.6 - - - +
900A MET* 1.3 59.3 + - + +
902A MET* 3.3 4.8 + - - +
903A ALA* 2.9 29.6 + - - +
916A LEU* 3.6 7.6 - - + +
917A TYR* 4.3 10.5 - - + -
920A GLN* 3.4 36.8 - - + +
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Residues in contact with MET 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A ILE* 4.1 11.9 - - + -
897A PRO* 3.1 35.9 + - + +
899A ALA* 1.3 79.2 - - + +
901A GLN* 1.3 62.0 + - - +
903A ALA* 3.2 3.3 + - - +
904A TYR* 3.1 22.0 + - - +
917A TYR* 3.3 23.5 + - + +
712C ILE* 5.2 1.3 - - + -
1077C THR* 3.7 26.0 - - + -
1078C ALA 4.4 7.4 - - - +
1079C PRO* 4.3 21.3 - - + +
1094C VAL* 3.6 39.0 - - + -
1095C PHE 5.2 0.2 - - - +
1107C ARG* 4.0 4.0 + - - +
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Residues in contact with GLN 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A THR* 3.0 20.8 + - - -
882A ILE 3.4 19.4 - - - +
884A SER 3.8 3.0 - - - -
885A GLY* 3.2 21.0 + - - -
886A TRP* 3.9 14.8 - - + -
896A ILE* 3.9 22.0 - - + +
897A PRO 3.1 10.2 + - - +
898A PHE* 2.9 15.0 + - + +
900A MET* 1.3 76.3 - - - +
902A MET* 1.3 62.4 + - - +
904A TYR* 3.2 5.2 + - - +
905A ARG* 3.0 59.8 + - - +
1050A MET* 4.8 6.7 - - - +
1107C ARG* 4.4 2.7 - - - +
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Residues in contact with MET 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A ILE* 4.0 23.8 - - + -
800A PHE* 3.9 29.6 - - + -
898A PHE* 2.9 24.8 + - + +
899A ALA* 3.7 8.7 - - - +
901A GLN* 1.3 76.6 - - - +
903A ALA* 1.3 64.5 + - - +
905A ARG* 3.0 19.4 + - - +
906A PHE* 2.9 23.3 + - + +
916A LEU* 3.5 23.4 - - + +
923A ILE* 5.0 1.6 - - + -
1049A LEU* 4.5 11.0 - - + -
1050A MET* 3.4 38.6 - - + +
1065A VAL* 4.7 1.8 - - + -
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Residues in contact with ALA 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A ALA 2.9 10.6 + - - +
900A MET 3.2 2.9 + - - +
902A MET* 1.3 74.9 - - - +
904A TYR* 1.3 62.9 + - - +
906A PHE* 3.2 6.2 + - - +
907A ASN 3.1 15.1 + - - -
913A GLN* 3.9 19.7 - - + +
916A LEU* 3.5 22.4 - - + +
917A TYR* 3.3 43.1 - - + +
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Residues in contact with TYR 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886A TRP* 3.2 38.8 + + + -
900A MET 3.1 6.3 + - - -
901A GLN 3.5 7.0 - - - +
902A MET 3.2 0.2 - - - -
903A ALA* 1.3 77.7 - - - +
905A ARG* 1.3 62.1 + - + +
907A ASN* 2.7 33.6 + - + +
908A GLY* 2.8 20.2 + - - -
913A GLN* 4.4 12.9 - - - +
1036A GLN* 5.5 2.5 - - - -
1107C ARG* 3.1 50.9 - - - +
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Residues in contact with ARG 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A THR* 3.9 10.3 + - - -
885A GLY* 3.3 18.6 - - - -
886A TRP* 3.5 21.0 - - + +
901A GLN* 3.0 49.0 + - - +
902A MET* 3.0 21.1 + - - +
904A TYR* 1.3 77.9 - - + +
906A PHE* 1.3 62.4 + - - +
908A GLY 3.2 7.3 + - - +
909A ILE* 3.5 8.8 + - - +
1033A VAL 5.0 1.2 + - - -
1035A GLY 3.5 23.8 + - - -
1036A GLN* 3.1 43.7 + - - +
1049A LEU* 2.9 39.6 + - + +
1050A MET* 4.3 15.3 - - - +
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Residues in contact with PHE 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A PHE* 4.1 13.5 - + - -
720A ILE* 5.2 2.9 - - + -
902A MET* 2.9 11.7 + - + +
903A ALA* 3.4 10.1 - - - +
904A TYR 3.1 0.2 - - - -
905A ARG* 1.3 76.8 - - - +
907A ASN* 1.3 60.6 + - - +
909A ILE* 2.9 29.2 - - + +
910A GLY 3.3 3.1 + - - -
911A VAL* 3.3 19.1 + - + +
912A THR 5.2 2.5 - - - +
913A GLN* 5.3 0.2 - - - -
915A VAL* 5.0 6.7 - - + -
916A LEU* 3.3 37.0 - - + -
923A ILE* 3.5 36.8 - - + -
1049A LEU* 3.5 37.5 - - + -
1067A TYR* 3.5 29.2 - + - -
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Residues in contact with ASN 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A ALA 3.1 1.8 + - - -
904A TYR* 2.7 27.4 + - + +
906A PHE* 1.3 76.1 - - - +
908A GLY* 1.3 59.9 + - - +
909A ILE 3.1 1.4 + - - -
910A GLY* 3.3 11.6 + - - -
911A VAL 3.4 12.2 + - - +
912A THR* 5.3 1.6 - - - +
913A GLN* 3.3 43.5 - - + +
1091C ARG 4.7 7.7 + - - -
1121C PHE* 6.3 0.2 - - - -
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Residues in contact with GLY 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A TYR* 2.8 26.1 + - - -
905A ARG* 3.2 6.2 + - - -
906A PHE 3.1 1.4 - - - -
907A ASN* 1.3 71.8 - - - +
909A ILE* 1.3 57.4 + - - +
1036A GLN* 3.6 17.3 + - - -
1038A LYS* 3.4 29.6 + - - -
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Residues in contact with ILE 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905A ARG 3.5 14.1 - - - +
906A PHE* 2.9 22.0 + - + +
908A GLY* 1.3 80.3 - - - +
910A GLY* 1.3 57.0 + - - +
911A VAL* 3.7 18.4 - - + -
1036A GLN* 4.0 2.0 - - - +
1038A LYS* 5.5 1.8 - - - +
1047A TYR* 4.2 25.0 - - + -
1048A HIS 3.8 14.6 - - - +
1049A LEU* 3.7 16.4 - - + -
1067A TYR* 3.5 44.0 - - + -
1108A ASN* 3.9 11.4 + - - +
904B TYR* 5.5 2.4 + - - -
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Residues in contact with GLY 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A ASN 3.3 10.5 + - - -
909A ILE* 1.3 79.3 - - - +
911A VAL* 1.3 67.1 + - - +
912A THR* 4.2 1.1 + - - +
1106A GLN* 4.3 13.7 - - - +
1107A ARG 5.3 0.5 + - - -
1108A ASN* 4.0 15.4 + - - +
904B TYR* 6.1 1.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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