Contacts of the helix formed by residues 499 - 506 (chain C) in PDB entry 2VGB
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 499 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476C THR* 3.6 23.3 - - - -
497C THR* 3.4 8.6 + - - +
498C ARG* 1.3 75.0 - - - +
500C ALA* 1.3 63.9 + - - +
501C GLN* 3.6 6.4 + - - +
502C ALA* 2.9 24.8 + - - +
503C ALA* 2.9 19.2 + - - +
516C LEU* 3.9 0.9 - - - -
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Residues in contact with ALA 500 (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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150C PRO* 5.1 0.3 - - - +
498C ARG 3.2 7.5 + - - -
499C SER* 1.3 71.4 - - - +
501C GLN* 1.3 60.8 + - - +
503C ALA* 3.2 15.4 - - - +
504C ARG* 3.2 32.6 + - - +
516C LEU* 3.7 29.1 - - + +
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Residues in contact with GLN 501 (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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279C GLY* 4.1 6.3 + - - -
280C VAL 4.0 12.7 + - - -
281C ASP* 3.4 23.0 + - - +
307C GLY* 4.5 14.0 - - - -
308C ILE* 4.9 3.6 + - - +
499C SER* 3.1 6.1 + - - +
500C ALA* 1.3 74.7 - - - +
502C ALA* 1.3 60.0 + - - +
503C ALA 3.0 0.9 - - - -
504C ARG* 2.7 44.5 + - - +
505C GLN* 2.8 37.7 + - - +
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Residues in contact with ALA 502 (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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475C THR* 6.5 0.2 - - + -
476C THR 3.8 13.5 - - - +
477C THR* 3.9 20.9 - - - +
478C GLY* 4.4 1.6 - - - +
497C THR* 4.3 7.9 - - + +
499C SER* 2.9 27.3 + - - +
501C GLN* 1.3 75.7 - - - +
503C ALA* 1.3 63.3 + - - +
505C GLN* 4.1 12.5 - - - +
506C VAL* 3.1 30.2 + - - +
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Residues in contact with ALA 503 (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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150C PRO* 4.0 21.1 - - + +
497C THR* 3.7 18.0 - - + +
499C SER 2.9 12.7 + - - +
500C ALA* 3.2 15.5 - - - +
501C GLN 3.0 0.2 - - - -
502C ALA* 1.3 76.9 - - - +
504C ARG* 1.3 61.4 + - - +
506C VAL* 4.0 3.2 + - - -
507C HIS* 4.1 0.9 - - - -
514C PRO* 3.1 36.7 - - + +
516C LEU* 4.5 10.5 - - + -
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Residues in contact with ARG 504 (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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135C ARG* 5.7 5.8 - - - +
148C TYR* 5.6 4.0 + - - -
150C PRO* 4.2 6.3 - - + -
151C VAL 3.0 35.7 - - - +
152C ALA* 3.5 15.7 - - - +
153C ILE* 5.7 1.1 - - - -
279C GLY 4.7 4.0 + - - -
281C ASP* 2.5 40.6 + - - +
282C ILE* 5.1 0.3 - - - +
500C ALA* 3.5 29.1 + - - +
501C GLN* 2.7 39.7 + - - +
503C ALA* 1.3 70.2 - - - +
505C GLN* 1.3 64.0 + - - +
506C VAL 3.1 2.9 + - - -
507C HIS* 3.3 29.0 + - - +
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Residues in contact with GLN 505 (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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281C ASP* 2.9 39.4 + - + +
282C ILE* 4.5 9.0 - - + -
307C GLY 2.8 31.8 + - - +
308C ILE* 3.7 0.8 - - - +
309C LYS* 3.5 30.9 - - + +
477C THR 5.0 4.7 - - - +
501C GLN* 2.8 36.1 + - + +
502C ALA* 4.1 11.3 - - - +
504C ARG* 1.3 72.7 - - - +
506C VAL* 1.3 63.2 + - - +
507C HIS 3.1 1.2 + - - -
508C LEU* 3.1 24.5 + - + +
509C CYS* 5.5 0.9 - - - -
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Residues in contact with VAL 506 (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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475C THR* 5.5 0.7 - - + -
477C THR 5.2 0.4 - - - +
478C GLY* 3.7 32.5 - - - +
481C ALA* 4.6 7.0 - - + -
482C GLN* 5.7 0.7 - - + +
495C ALA* 4.8 4.9 - - + -
502C ALA 3.1 18.2 + - - +
503C ALA* 4.1 4.3 - - - +
504C ARG 3.1 0.6 - - - -
505C GLN* 1.3 78.8 - - + +
507C HIS* 1.3 55.8 + - - +
508C LEU 2.9 6.5 + - - -
509C CYS* 3.0 29.1 + - - +
512C VAL* 2.8 41.3 - - + +
514C PRO* 4.2 15.3 - - + -
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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