Contacts of the helix formed by residues 803 - 817 (chain C) in PDB entry 2VGO
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 SER 803 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798C ILE* 3.7 19.5 + - - +
799C PRO 3.3 11.0 + - - -
800C ALA* 3.1 17.4 + - - -
802C ALA* 1.3 77.4 - - - +
804C GLY* 1.3 67.3 + - - +
805C ASN* 3.3 2.5 - - - -
806C LEU* 3.0 11.3 + - - -
807C LEU* 2.8 22.1 + - - -
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Residues in contact with GLY 804 (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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798C ILE* 5.0 1.2 - - - +
802C ALA 3.6 3.4 + - - -
803C SER* 1.3 69.2 - - - +
805C ASN* 1.3 62.4 + - - +
807C LEU* 3.5 8.5 + - - +
808C THR* 2.8 32.1 + - - -
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Residues in contact with ASN 805 (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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803C SER* 3.0 3.2 + - - -
804C GLY* 1.3 72.6 - - - +
806C LEU* 1.3 73.8 + - + +
808C THR* 3.7 5.3 + - - -
809C GLN* 3.5 24.9 + - - +
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Residues in contact with LEU 806 (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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800C ALA* 3.3 41.1 - - + +
801C TRP* 4.2 9.2 - - - +
803C SER* 3.0 8.2 + - - +
805C ASN* 1.3 82.4 - - + +
807C LEU* 1.3 64.9 + - - +
809C GLN* 3.4 8.4 + - + +
810C ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 807 (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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97B ARG* 3.9 14.4 - - - +
109B LEU* 3.8 34.3 - - + -
118B ILE* 4.0 18.8 - - + -
172B PHE* 5.0 9.4 - - + -
801C TRP* 3.7 16.3 + - + +
802C ALA* 4.0 9.4 - - - +
803C SER 2.8 15.8 + - - +
804C GLY* 3.7 7.4 - - - +
806C LEU* 1.3 78.1 - - - +
808C THR* 1.3 57.1 + - - +
810C ALA* 3.2 3.6 + - - +
811C ILE* 2.9 54.6 + - + +
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Residues in contact with THR 808 (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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226B TYR* 4.8 12.2 - - + +
804C GLY 2.8 23.0 + - - -
805C ASN* 3.9 8.0 + - - -
807C LEU* 1.3 76.4 - - - +
809C GLN* 1.3 64.1 + - + +
811C ILE* 3.5 5.8 + - - +
812C ARG* 3.1 24.8 + - + +
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Residues in contact with GLN 809 (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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805C ASN 3.5 15.5 - - - +
806C LEU* 3.4 8.5 + - - +
807C LEU 3.3 0.4 - - - -
808C THR* 1.3 78.9 - - + +
810C ALA* 1.3 58.7 + - - +
812C ARG* 3.4 11.2 + - - +
813C GLN* 3.1 40.8 + - - +
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Residues in contact with ALA 810 (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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118B ILE* 3.7 22.4 - - + -
801C TRP 5.4 2.5 - - - +
806C LEU 3.1 16.8 + - - +
807C LEU* 3.2 5.4 + - - +
809C GLN* 1.3 76.0 - - - +
811C ILE* 1.3 60.2 + - - +
813C GLN* 3.4 9.3 + - - +
814C GLN* 3.0 30.0 + - - +
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Residues in contact with ILE 811 (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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118B ILE* 3.7 28.9 - - + -
172B PHE* 3.6 31.2 - - + -
174B PRO* 3.6 29.2 - - + -
226B TYR* 3.7 18.4 - - + -
807C LEU* 2.9 32.1 + - + +
808C THR* 3.8 5.8 - - - +
810C ALA* 1.3 74.8 - - - +
812C ARG* 1.3 57.6 + - - +
814C GLN* 3.2 13.0 + - - +
815C TYR* 2.9 28.1 + - + +
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Residues in contact with ARG 812 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B TYR* 3.3 33.5 + - - +
808C THR* 3.1 18.1 + - + +
809C GLN* 3.6 10.8 - - - +
811C ILE* 1.3 77.6 - - - +
813C GLN* 1.3 63.2 + - + +
815C TYR* 3.3 2.3 + - - +
816C TYR* 3.1 62.3 + - + +
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Residues in contact with GLN 813 (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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809C GLN* 3.1 28.6 + - - +
810C ALA* 3.7 8.0 - - - +
812C ARG* 1.3 77.6 - - + +
814C GLN* 1.3 55.1 + - - +
816C TYR* 5.1 2.0 - - - -
817C LYS* 2.7 69.1 + - + +
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Residues in contact with GLN 814 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B LYS 4.3 2.8 - - - +
117B PHE* 3.4 41.5 - - + -
118B ILE* 2.9 57.5 + - - +
172B PHE* 5.9 1.0 - - - +
810C ALA 3.0 15.9 + - - +
811C ILE* 3.4 13.4 - - - +
813C GLN* 1.3 78.0 - - - +
815C TYR* 1.3 60.0 + - - +
817C LYS 4.3 4.9 - - - +
818C PRO* 3.5 24.0 - - + +
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Residues in contact with TYR 815 (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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226B TYR* 3.6 39.5 - + + -
227B LYS* 3.6 26.8 - - + +
229B GLU* 2.7 32.5 + - - -
350B VAL* 4.5 3.6 - - - +
351B LEU 4.3 2.9 + - - -
352B PRO* 3.7 12.3 - - + +
353B PRO* 3.4 50.0 - - + +
811C ILE* 2.9 16.6 + - + +
812C ARG 3.5 4.0 - - - +
813C GLN 3.3 0.2 - - - -
814C GLN* 1.3 78.6 - - - +
816C TYR* 1.3 76.8 + + - +
818C PRO* 3.8 7.3 - - - +
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Residues in contact with TYR 816 (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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226B TYR* 4.0 6.3 - + - -
227B LYS* 2.7 34.5 + - - -
353B PRO* 3.9 21.3 - - + +
356B GLN* 3.4 20.4 - - - +
812C ARG* 3.1 68.3 + - + +
813C GLN* 4.4 2.7 - - - +
815C TYR* 1.3 96.7 - + - +
817C LYS* 1.3 66.1 + - + +
818C PRO* 3.3 10.3 - - - +
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Residues in contact with LYS 817 (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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356B GLN* 4.9 11.0 - - + +
357B SER* 5.2 10.5 - - - +
813C GLN* 2.7 49.0 + - + +
814C GLN* 3.6 9.9 - - - +
816C TYR* 1.3 84.0 - - + +
818C PRO* 1.4 66.2 - - - +
819C ILE* 3.7 6.4 + - - +
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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
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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