Contacts of the helix formed by residues 897 - 910 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707B TYR* 3.7 4.0 - - + +
708B SER 3.6 9.1 - - - +
709B ASN* 3.5 35.4 - - + +
711B SER 3.3 24.2 - - - +
712B ILE* 4.4 4.9 - - + -
1077B THR* 4.1 4.7 - - + -
896C ILE* 1.3 86.2 - - + +
898C PHE* 1.3 67.5 + - - +
899C ALA* 3.2 3.4 - - + +
900C MET* 2.8 46.3 + - + +
901C GLN 3.1 8.3 + - - -
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Residues in contact with PHE 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B TYR* 2.8 22.6 + - + +
797C PHE* 3.3 30.3 - - + +
800C PHE* 3.3 40.6 - + + -
802C PHE* 3.3 26.7 - + - -
882C ILE* 3.5 27.8 - - + +
896C ILE 3.2 5.5 + - - -
897C PRO* 1.3 70.5 - - - +
899C ALA* 1.3 64.0 + - - +
901C GLN* 3.0 24.3 + - + +
902C MET* 3.0 25.6 + - + +
1050C MET* 3.7 29.4 - - + -
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Residues in contact with ALA 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B TYR* 4.6 0.4 + - - -
797C PHE 5.1 0.6 + - - -
798C GLY* 4.8 6.8 - - - -
800C PHE* 5.6 3.4 - - + -
897C PRO* 3.1 4.1 + - + +
898C PHE* 1.3 83.4 - - - +
900C MET* 1.3 64.0 + - + +
902C MET* 3.4 3.8 + - - +
903C ALA* 3.1 18.0 + - - +
916C LEU* 3.2 14.8 - - + +
917C TYR* 3.8 12.1 + - + -
920C GLN* 4.0 32.3 - - + +
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Residues in contact with MET 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B ASN 5.8 0.7 - - - +
712B ILE* 4.7 5.8 - - + -
1077B THR* 3.4 41.3 - - + +
1078B ALA 4.6 4.9 - - - +
1079B PRO* 4.2 19.7 - - + -
1094B VAL* 3.6 33.9 - - + -
1107B ARG* 3.9 9.5 + - - +
896C ILE* 4.1 7.9 - - + -
897C PRO* 2.8 25.2 + - + +
899C ALA* 1.3 74.9 - - + +
901C GLN* 1.3 65.3 + - - +
903C ALA* 3.4 2.8 + - - +
904C TYR* 3.1 22.3 + - - +
917C TYR* 3.2 22.4 - - + +
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Residues in contact with GLN 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C THR* 2.7 27.0 + - - +
882C ILE 3.3 15.3 - - - +
885C GLY* 3.2 27.8 + - - -
886C TRP* 4.9 4.3 - - + -
896C ILE* 3.9 26.0 - - + +
897C PRO 3.1 5.9 + - - +
898C PHE* 3.0 15.7 + - + +
900C MET* 1.3 74.5 - - - +
902C MET* 1.3 62.4 + - - +
904C TYR* 3.2 6.2 + - - +
905C ARG* 2.9 59.4 + - + +
1050C MET* 4.4 11.3 - - - +
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Residues in contact with MET 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720C ILE* 5.1 5.8 - - + -
800C PHE* 4.4 25.1 - - + -
898C PHE* 3.0 23.8 + - + +
899C ALA* 3.8 4.9 - - - +
901C GLN* 1.3 78.6 - - - +
903C ALA* 1.3 50.2 + - - +
905C ARG* 3.1 14.8 + - - +
906C PHE* 2.6 43.6 + - + +
916C LEU* 3.5 27.1 - - + -
923C ILE* 5.3 2.5 - - + -
927C PHE* 5.2 0.2 - - + -
1049C LEU* 4.2 26.0 - - + -
1050C MET* 3.4 37.0 - - + +
1065C VAL* 4.8 6.7 - - + -
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Residues in contact with ALA 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107B ARG* 5.0 2.9 - - - +
899C ALA 3.1 2.2 + - - +
900C MET 3.7 4.5 - - - +
901C GLN 3.3 0.2 - - - -
902C MET* 1.3 75.2 - - - +
904C TYR* 1.3 63.4 + - - +
906C PHE* 3.3 6.5 + - - +
907C ASN* 2.9 24.3 + - - +
913C GLN* 3.7 19.8 - - + +
916C LEU* 3.1 21.2 - - + +
917C TYR* 3.5 39.7 - - + +
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Residues in contact with TYR 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910B GLY* 6.0 1.2 - - - -
1107B ARG* 3.3 63.2 - - + +
1108B ASN* 4.8 13.7 + - - -
886C TRP* 4.0 48.9 - + + +
896C ILE* 5.5 1.8 - - + -
900C MET 3.1 7.7 + - - +
901C GLN* 3.4 10.1 - - - +
902C MET 3.2 0.2 - - - -
903C ALA* 1.3 77.4 - - - +
905C ARG* 1.3 57.8 + - - +
907C ASN* 3.1 16.6 + - + +
908C GLY* 2.9 25.6 + - - -
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Residues in contact with ARG 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C THR* 4.0 13.2 + - - -
885C GLY 4.2 9.1 + - - -
886C TRP* 3.3 34.5 - - - +
901C GLN* 2.9 46.3 + - - +
902C MET* 3.5 17.0 - - - +
904C TYR* 1.3 72.9 - - - +
906C PHE* 1.3 65.3 + - - +
908C GLY 3.0 9.2 + - - -
909C ILE* 3.3 12.0 + - - +
1032C CYS 4.7 1.0 + - - -
1033C VAL 4.4 5.9 + - - -
1035C GLY* 3.7 25.7 + - - -
1036C GLN* 3.1 36.4 + - - +
1049C LEU* 2.8 43.5 + - + +
1050C MET* 3.8 16.8 - - - +
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Residues in contact with PHE 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C PHE* 4.1 7.9 - + - -
720C ILE* 4.8 2.0 - - + -
902C MET* 2.6 24.9 + - + +
903C ALA* 3.5 6.3 - - - +
905C ARG* 1.3 72.0 - - - +
907C ASN* 1.3 61.8 + - - +
909C ILE* 3.1 16.1 - - + +
911C VAL* 3.1 35.8 + - + +
913C GLN* 5.2 2.2 - - - -
915C VAL* 5.3 1.8 - - + -
916C LEU* 3.3 36.8 - - + -
923C ILE* 3.5 40.2 - - + -
1049C LEU* 3.4 39.3 - - + -
1067C TYR* 3.6 27.1 - + - -
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Residues in contact with ASN 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091B ARG 4.7 5.5 + - - -
1092B GLU* 4.3 16.2 + - - -
903C ALA 2.9 13.4 + - - +
904C TYR* 3.4 21.8 - - + +
906C PHE* 1.3 75.8 - - - +
908C GLY* 1.3 64.2 + - - +
910C GLY* 3.1 14.6 + - - -
911C VAL 3.2 15.1 + - - +
912C THR* 5.4 1.3 - - - -
913C GLN* 4.0 22.9 + - + +
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Residues in contact with GLY 908 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886C TRP* 5.4 6.5 - - - -
904C TYR* 2.9 15.8 + - - -
905C ARG 3.0 6.7 + - - -
907C ASN* 1.3 77.5 - - - +
909C ILE* 1.3 61.6 + - - +
910C GLY* 4.3 0.3 - - - -
1036C GLN* 3.8 14.1 - - - -
1038C LYS* 4.2 20.7 + - - -
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Residues in contact with ILE 909 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C ARG 3.3 1.1 + - - +
906C PHE* 3.1 13.5 - - + +
908C GLY* 1.3 75.4 - - - +
910C GLY* 1.3 61.8 + - - +
911C VAL* 3.8 17.0 - - + -
1036C GLN* 3.6 14.4 - - - +
1038C LYS* 5.8 2.9 - - - +
1047C TYR* 4.1 31.5 - - + -
1048C HIS 3.6 8.3 - - - +
1049C LEU* 3.6 26.5 - - + -
1067C TYR* 3.6 44.0 - - + -
1108C ASN* 3.6 10.2 + - - +
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Residues in contact with GLY 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906C PHE 3.2 0.2 + - - -
907C ASN* 3.1 14.0 + - - -
908C GLY 4.3 0.2 - - - -
909C ILE* 1.3 79.5 - - - +
911C VAL* 1.3 61.1 + - - +
912C THR* 4.1 1.0 + - - +
1106C GLN* 4.5 11.1 - - - +
1108C ASN* 2.7 26.8 + - - +
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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