Contacts of the helix formed by residues 478 - 486 (chain A) 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 GLY 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A THR* 2.8 19.5 + - - +
476A THR 3.6 0.8 - - - -
477A THR* 1.3 76.5 - - - +
479A ARG* 1.3 64.9 + - - +
480A SER 3.3 2.2 - - - -
481A ALA* 2.9 7.1 + - - +
482A GLN* 2.9 23.1 + - - +
502A ALA* 4.3 4.1 - - - +
506A VAL* 3.8 26.0 - - - +
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ASP* 5.0 6.6 + - - -
452A THR* 5.6 2.2 - - + -
453A GLU* 5.6 2.0 + - - +
475A THR* 3.7 0.6 + - - -
477A THR* 3.2 19.1 + - - +
478A GLY* 1.3 76.7 - - - +
480A SER* 1.3 58.0 + - - +
482A GLN* 3.1 31.1 + - - +
483A LEU* 2.9 64.3 + - + +
580A FBP 4.1 8.7 - - - +
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A THR* 3.6 22.5 - - - +
456A ALA* 5.3 1.0 - - - +
473A VAL* 4.2 13.9 - - - -
474A LEU 3.8 6.1 + - - -
475A THR* 3.9 0.9 + - - -
479A ARG* 1.3 73.5 - - - +
481A ALA* 1.3 65.6 + - - +
483A LEU* 3.5 3.1 + - - +
484A LEU* 3.3 24.9 + - - +
555A VAL* 5.4 0.2 - - - -
565A THR* 3.0 27.9 + - - -
580A FBP 2.3 34.5 + - - -
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A VAL* 4.3 6.0 - - + +
475A THR* 4.2 12.0 + - + -
478A GLY 2.9 11.2 + - - +
480A SER* 1.3 75.9 + - - +
482A GLN* 1.3 62.8 + - - +
484A LEU* 3.1 6.5 + - - +
485A SER* 3.1 20.8 + - - -
493A VAL* 4.2 10.4 - - + +
495A ALA* 4.0 27.1 - - + -
506A VAL* 4.4 5.2 - - + -
512A VAL* 4.0 21.4 - - + +
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Residues in contact with GLN 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LYS* 5.0 9.5 + - - -
331A ASP 5.1 1.0 + - - -
364A GLY 3.2 26.5 + - - +
365A LYS* 4.4 3.4 - - - +
366A PRO* 4.0 19.4 - - - +
478A GLY 2.9 11.6 + - - +
479A ARG* 3.4 32.8 + - - +
481A ALA* 1.3 77.1 - - - +
483A LEU* 1.3 67.0 + - + +
485A SER* 3.0 4.9 + - - +
486A ARG* 2.8 24.1 + - + +
506A VAL* 5.6 1.0 - - + +
509A CYS* 3.9 28.9 - - - -
512A VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ASP* 4.0 6.1 - - - +
452A THR* 3.5 31.4 - - + +
453A GLU* 3.6 39.9 - - + +
456A ALA* 3.9 14.4 - - + -
479A ARG* 2.9 56.3 + - + +
480A SER* 4.2 3.6 - - - +
481A ALA 3.3 0.4 - - - -
482A GLN* 1.3 77.8 - - + +
484A LEU* 1.3 62.2 + - - +
486A ARG* 3.1 26.0 - - + +
487A TYR* 3.5 14.7 - - - -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ALA* 3.6 33.0 - - + +
459A ALA* 3.7 19.5 - - + -
460A VAL* 3.8 12.6 - - + +
471A ILE* 3.7 21.1 - - + -
473A VAL* 3.3 40.8 - - + -
480A SER 3.3 13.4 + - - +
481A ALA 3.1 6.6 + - - +
482A GLN 3.1 0.6 - - - -
483A LEU* 1.3 76.8 - - - +
485A SER* 1.3 63.8 + - - +
487A TYR* 3.0 14.0 + - - -
489A PRO* 3.3 15.2 - - + +
493A VAL* 4.0 14.4 - - + -
555A VAL* 4.5 5.2 - - + -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ASP* 4.8 2.4 + - - -
481A ALA 3.1 4.6 + - - -
482A GLN* 3.0 7.2 + - - +
484A LEU* 1.3 76.2 - - - +
486A ARG* 1.3 57.1 + - - +
488A ARG* 2.5 39.1 + - - -
489A PRO* 3.8 10.1 - - - -
493A VAL* 4.5 4.4 - - - +
509A CYS* 3.5 19.6 - - - +
510A ARG 2.8 31.6 + - - -
512A VAL* 4.0 16.6 - - - -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ASN 3.8 9.0 + - - +
362A LEU* 2.7 34.3 + - - +
363A ALA 3.7 12.9 + - - -
364A GLY* 3.6 28.7 - - - +
441A LEU* 3.9 25.7 + - - +
445A ALA* 3.9 26.8 - - - +
446A PRO* 6.0 1.6 - - - +
453A GLU* 4.3 14.4 + - - -
482A GLN* 2.8 13.0 + - + +
483A LEU* 3.1 28.7 - - + +
485A SER* 1.3 76.3 + - - +
487A TYR* 1.3 82.1 + - - -
488A ARG* 3.6 6.9 + - - +
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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