Contacts of the helix formed by residues 478 - 487 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B THR* 2.8 21.7 + - - +
476B THR 3.6 1.4 - - - -
477B THR* 1.3 78.3 - - - +
479B ARG* 1.3 64.6 + - - +
481B ALA* 2.9 6.8 + - - +
482B GLN* 2.8 23.9 + - - +
502B ALA* 4.4 2.8 - - - +
506B VAL* 3.8 26.2 - - - +
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Residues in contact with ARG 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B ASP* 4.9 7.0 + - - -
452B THR* 5.6 2.9 - - + -
453B GLU* 5.6 2.4 + - - +
475B THR* 3.6 0.8 + - - -
477B THR* 3.2 19.4 + - - +
478B GLY* 1.3 76.7 - - - +
480B SER* 1.3 57.6 + - - +
482B GLN* 3.2 30.7 + - - +
483B LEU* 2.9 64.5 + - + +
580B FBP 4.1 8.5 + - - +
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Residues in contact with SER 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B THR* 3.5 23.8 - - - +
456B ALA* 5.3 0.3 - - - +
473B VAL* 4.3 11.2 - - - -
474B LEU 3.8 7.8 + - - -
475B THR* 3.9 0.7 + - - -
478B GLY 3.3 0.8 - - - -
479B ARG* 1.3 74.4 - - - +
481B ALA* 1.3 64.9 + - - +
483B LEU* 4.1 2.7 - - - +
484B LEU* 3.3 26.9 + - - +
555B VAL* 5.4 0.2 - - - -
565B THR* 3.0 29.3 + - - -
580B FBP 2.4 31.4 + - - -
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Residues in contact with ALA 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B VAL* 4.3 11.6 - - + +
475B THR* 4.1 12.0 + - + -
478B GLY 2.9 9.6 + - - +
480B SER* 1.3 77.0 + - - +
482B GLN* 1.3 63.8 - - - +
484B LEU* 3.2 6.5 + - - +
485B SER* 3.1 21.0 + - - -
493B VAL* 4.1 4.3 - - + +
495B ALA* 3.9 28.3 - - + -
506B VAL* 4.5 4.9 - - + -
512B VAL* 4.1 20.7 - - + +
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Residues in contact with GLN 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LYS* 5.0 9.4 + - - -
331B ASP 5.1 1.0 + - - -
364B GLY 3.0 28.5 + - - +
365B LYS* 4.2 4.6 - - - +
366B PRO* 4.1 16.8 - - - +
478B GLY 2.8 11.9 + - - +
479B ARG* 3.3 32.5 + - - +
481B ALA* 1.3 76.7 - - - +
483B LEU* 1.3 61.2 + - + +
485B SER* 3.1 5.4 + - - +
486B ARG* 2.8 28.5 + - + +
506B VAL* 5.6 1.0 - - + +
509B CYS* 4.0 29.3 - - - -
512B VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B ASP* 4.0 6.7 - - - +
452B THR* 3.5 30.5 - - + -
453B GLU* 3.6 39.7 - - + +
456B ALA* 3.9 15.0 - - + -
479B ARG* 2.9 55.2 + - + +
480B SER* 4.1 4.5 - - - +
481B ALA 3.3 0.2 - - - -
482B GLN* 1.3 79.1 - - + +
484B LEU* 1.3 62.3 + - - +
486B ARG* 3.0 26.3 - - + +
487B TYR* 3.6 13.9 - - - -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ALA* 3.6 33.8 - - + +
459B ALA* 3.6 20.0 - - + -
460B VAL* 3.8 13.3 - - + +
471B ILE* 3.7 20.9 - - + -
473B VAL* 3.3 40.8 - - + -
480B SER 3.3 12.7 + - - +
481B ALA 3.2 5.7 + - - +
482B GLN 3.2 0.4 - - - -
483B LEU* 1.3 77.7 - - - +
485B SER* 1.3 65.2 + - - +
487B TYR* 3.0 13.3 + - - -
489B PRO* 3.2 14.9 - - - +
493B VAL* 4.0 13.2 - - + -
555B VAL* 4.5 5.4 - - + -
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ASP* 4.9 1.4 + - - -
481B ALA 3.1 10.0 + - - -
482B GLN* 3.5 6.1 + - - +
484B LEU* 1.3 79.2 - - - +
486B ARG* 1.3 56.8 + - - +
488B ARG* 2.6 39.3 + - - -
489B PRO* 3.8 9.9 - - - -
493B VAL* 4.5 3.7 - - - +
509B CYS* 3.6 18.1 - - - +
510B ARG 2.9 31.3 + - - -
512B VAL* 4.0 11.4 - - - -
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Residues in contact with ARG 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ASN 3.8 11.6 + - - +
362B LEU* 2.8 37.3 + - - +
363B ALA 3.9 10.9 + - - -
364B GLY* 3.4 28.5 - - - +
441B LEU* 3.9 23.1 + - - +
445B ALA* 3.9 28.4 - - - +
446B PRO* 5.9 1.6 - - - +
453B GLU* 4.4 14.7 + - - -
482B GLN* 2.8 13.6 + - + +
483B LEU* 3.0 28.3 - - + +
485B SER* 1.3 76.8 + - - +
487B TYR* 1.3 79.8 + - - -
488B ARG* 3.7 6.0 + - - +
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Residues in contact with TYR 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LYS* 3.3 23.3 + - - -
438B PHE* 4.0 30.7 - + + +
441B LEU* 4.2 17.1 - - + +
442B ARG* 4.6 7.4 - - - -
445B ALA* 4.2 15.0 - - + +
453B GLU* 2.8 31.5 + - - -
456B ALA* 4.6 2.5 - - + -
457B ILE* 3.8 46.2 - - + -
460B VAL* 3.9 19.6 - - + +
483B LEU 3.6 17.3 - - - -
484B LEU 3.0 10.4 + - - +
486B ARG* 1.3 93.9 - - - +
488B ARG* 1.3 74.1 + - - +
489B PRO* 3.4 1.7 - - - -
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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