Contacts of the helix formed by residues 499 - 506 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476D THR* 3.6 24.1 + - - -
497D THR* 3.4 7.0 + - - +
498D ARG* 1.3 75.0 - - - +
500D ALA* 1.3 64.6 + - - +
501D GLN* 3.7 7.3 + - - +
502D ALA* 3.0 21.5 + - - +
503D ALA 2.9 18.4 + - - -
516D LEU* 4.0 1.3 - - - -
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Residues in contact with ALA 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D PRO* 5.3 0.3 - - - +
498D ARG 3.2 7.4 + - - +
499D SER* 1.3 69.9 - - - +
501D GLN* 1.3 62.1 + - - +
503D ALA* 3.3 6.0 - - - +
504D ARG* 3.2 43.2 + - - +
516D LEU* 3.8 29.2 - - + -
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Residues in contact with GLN 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D GLY* 4.1 6.7 + - - -
280D VAL 3.7 19.4 + - - -
281D ASP* 3.7 16.7 + - - +
307D GLY* 4.4 15.3 - - - -
308D ILE* 4.8 3.7 + - - +
499D SER* 3.1 6.2 + - - +
500D ALA* 1.3 75.6 - - - +
502D ALA* 1.3 68.1 + - - +
504D ARG* 2.8 36.8 + - - +
505D GLN* 2.8 37.9 + - - +
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Residues in contact with ALA 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D THR* 6.4 0.2 - - + -
476D THR 3.7 18.2 - - - +
477D THR* 3.9 21.5 - - - +
478D GLY* 4.3 1.8 - - - +
497D THR* 4.4 7.0 - - + +
499D SER* 3.0 19.8 + - - +
501D GLN* 1.3 78.8 - - - +
503D ALA* 1.3 62.6 + - - +
505D GLN* 4.0 12.5 - - - +
506D VAL* 3.0 30.4 + - - +
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Residues in contact with ALA 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D PRO* 4.1 16.1 - - + +
497D THR* 3.7 18.2 - - + +
499D SER 2.9 12.9 + - - +
500D ALA* 3.3 15.0 - - - +
502D ALA* 1.3 76.8 - - - +
504D ARG* 1.3 59.8 + - - +
506D VAL* 3.9 4.1 + - - +
507D HIS* 4.2 1.4 - - - -
514D PRO* 3.1 41.4 - - + +
516D LEU* 4.7 11.4 - - + -
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Residues in contact with ARG 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ARG* 5.7 5.2 - - - +
148D TYR* 5.6 3.2 + - - -
150D PRO* 4.3 5.8 - - + -
151D VAL 3.1 33.2 - - - +
152D ALA* 3.4 24.5 - - - +
153D ILE* 4.9 2.0 - - - +
279D GLY 4.7 4.4 + - - -
281D ASP* 2.5 46.5 + - - +
282D ILE* 4.9 0.3 - - - +
500D ALA* 3.2 34.7 + - - +
501D GLN* 2.8 36.5 + - - +
503D ALA* 1.3 70.2 - - - +
505D GLN* 1.3 62.0 + - - +
506D VAL 3.1 3.1 + - - -
507D HIS* 3.3 22.0 + - - +
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Residues in contact with GLN 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ASP* 2.7 41.7 + - + +
282D ILE* 4.5 8.7 - - + -
307D GLY 2.8 30.5 + - - +
308D ILE* 3.5 3.0 - - - +
309D LYS* 3.3 31.3 - - + +
477D THR 5.1 3.3 - - - +
501D GLN* 2.8 37.4 + - - +
502D ALA* 3.1 11.9 + - - +
504D ARG* 1.3 72.6 - - - +
506D VAL* 1.3 63.3 + - + +
507D HIS 3.2 0.2 - - - -
508D LEU* 3.2 26.4 + - - +
509D CYS* 5.3 1.0 - - - -
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Residues in contact with VAL 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D THR* 5.5 1.1 - - + -
478D GLY* 3.7 33.2 - - - +
481D ALA* 4.5 6.3 - - + -
482D GLN* 5.6 0.4 - - + +
495D ALA* 4.8 4.0 - - + -
502D ALA 3.0 18.2 + - - +
503D ALA 4.1 4.5 - - - +
504D ARG 3.1 0.6 - - - -
505D GLN* 1.3 75.4 - - + +
507D HIS* 1.3 54.9 + - - +
508D LEU 3.0 11.1 + - - -
509D CYS* 3.0 29.5 + - - +
512D VAL* 2.7 43.1 - - + +
514D PRO* 4.4 13.9 - - + -
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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