Contacts of the helix formed by residues 884 - 893 (chain C) in PDB entry 6V3O
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 ASP 884 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C GLY 4.5 6.1 - - - +
136C SER* 4.0 25.2 + - - -
651C PRO* 6.0 0.9 - - - +
881C LEU* 3.0 27.6 + - + +
883C GLY* 1.3 78.8 - - - +
885C PRO* 1.3 64.4 - - - +
886C PHE* 3.6 9.0 + - - +
887C LEU* 2.9 43.0 + - + +
888C LYS* 3.0 21.5 + - - +
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Residues in contact with PRO 885 (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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28C VAL* 3.7 16.7 - - + +
881C LEU 3.9 2.0 - - - +
882C GLU 4.3 7.9 - - - +
883C GLY 3.6 8.3 - - - +
884C ASP* 1.3 89.1 - - - +
886C PHE* 1.3 73.0 + - + +
888C LYS* 3.7 11.5 - - + +
889C GLN* 2.9 30.7 + - - +
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Residues in contact with PHE 886 (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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28C VAL* 3.7 48.2 - - + -
29C SER* 4.2 14.1 - - - -
120C ARG* 4.2 23.3 - - - +
126C LEU* 3.8 30.5 - - + -
136C SER* 5.0 1.1 - - - +
138C THR* 3.5 39.3 - - + -
884C ASP* 3.2 7.1 - - - +
885C PRO* 1.3 87.5 - - + +
887C LEU* 1.3 66.4 + - - +
889C GLN* 3.3 5.0 + - - +
890C GLY* 3.0 19.4 + - - -
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Residues in contact with LEU 887 (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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113C GLU* 5.9 2.0 - - - +
647C ARG* 4.4 3.8 - - - +
651C PRO* 6.0 1.1 - - + -
831C MET* 4.0 13.5 - - + -
881C LEU* 3.8 30.1 - - + -
884C ASP* 2.9 30.4 + - - +
886C PHE* 1.3 75.6 - - - +
888C LYS* 1.3 63.2 + - - +
890C GLY* 3.1 2.5 + - - -
891C LEU* 3.0 50.6 + - + +
1003C FLC 3.7 40.8 - - - +
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Residues in contact with LYS 888 (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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834C ALA* 6.0 2.2 - - + -
879C ASP* 4.2 12.2 - - - +
880C ILE* 2.7 37.2 + - - +
881C LEU* 4.1 22.4 - - + +
882C GLU* 5.5 1.7 - - - +
884C ASP 3.0 17.7 + - - +
885C PRO* 3.7 10.3 - - + +
887C LEU* 1.3 78.1 - - - +
889C GLN* 1.3 61.3 + - - +
891C LEU* 3.4 2.7 + - - +
892C VAL* 3.1 27.9 + - + +
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Residues in contact with GLN 889 (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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24C VAL* 3.6 37.0 - - + +
26C GLY 3.8 4.8 + - - -
28C VAL* 3.4 28.6 - - + +
32C ASP* 3.0 30.4 + - - +
34C LEU* 3.7 17.5 - - + +
35C ILE* 5.0 4.8 - - - +
116C GLN* 6.0 0.5 - - - +
885C PRO 2.9 18.2 + - - +
886C PHE* 3.7 4.3 - - - +
888C LYS* 1.3 75.4 - - - +
890C GLY* 1.3 62.1 + - - +
891C LEU 3.3 0.2 + - - -
892C VAL* 3.3 20.1 + - - +
893C LEU* 3.5 24.4 + - + +
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Residues in contact with GLY 890 (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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34C LEU* 4.6 11.6 - - - +
113C GLU* 3.9 26.4 - - - +
886C PHE 3.0 14.9 + - - -
887C LEU* 3.1 5.5 + - - -
889C GLN* 1.3 77.4 + - - +
891C LEU* 1.3 62.5 + - - +
893C LEU* 4.1 2.3 + - - +
894C ARG* 3.5 23.9 + - - +
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Residues in contact with LEU 891 (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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831C MET* 4.2 5.6 - - + +
834C ALA* 4.0 25.6 - - + +
835C LYS* 3.8 32.1 - - + -
881C LEU* 4.3 2.5 - - + -
887C LEU* 3.0 41.5 + - + +
888C LYS* 4.1 3.4 - - - +
890C GLY* 1.3 78.3 - - - +
892C VAL* 1.3 64.5 + - - +
893C LEU 3.2 0.7 - - - -
894C ARG* 3.1 53.1 + - - +
895C ASN* 3.5 12.9 - - - +
1003C FLC 3.6 13.7 - - - +
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Residues in contact with VAL 892 (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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23C LEU* 3.8 35.6 - - + +
24C VAL* 4.5 6.5 - - + -
72C GLU* 4.2 23.3 - - + +
888C LYS* 3.1 18.1 + - + +
889C GLN* 3.3 18.2 - - - +
891C LEU* 1.3 78.4 - - - +
893C LEU* 1.3 75.4 + - + +
895C ASN* 3.3 18.5 + - - +
896C PRO* 3.5 8.8 - - - +
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Residues in contact with LEU 893 (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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20C LEU* 3.5 48.2 - - + +
23C LEU* 4.5 4.7 - - + -
24C VAL* 4.2 9.4 - - + -
34C LEU* 4.0 26.7 - - + -
35C ILE* 4.2 15.0 - - + +
38C ASP* 3.9 20.6 - - - +
109C ALA* 4.9 2.2 - - - +
889C GLN* 3.5 27.4 + - + +
890C GLY 4.1 3.6 + - - +
891C LEU 3.2 0.6 - - - -
892C VAL* 1.3 79.9 - - + +
894C ARG* 1.3 63.2 + - - +
895C ASN 3.4 0.2 - - - -
896C PRO* 3.7 7.2 - - - +
897C TYR* 3.3 20.6 + - - -
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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