Contacts of the helix formed by residues 478 - 486 (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 GLY 478 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475C THR* 2.7 22.1 + - - +
476C THR 3.6 0.8 - - - -
477C THR* 1.3 77.9 - - - +
479C ARG* 1.3 59.1 + - - +
481C ALA* 2.9 7.1 + - - +
482C GLN* 2.8 30.3 + - - +
502C ALA* 4.4 2.8 - - - +
506C VAL* 3.7 25.7 - - - +
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Residues in contact with ARG 479 (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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450C ASP* 5.0 6.4 + - - -
452C THR* 5.7 2.2 - - + -
453C GLU* 5.6 2.4 + - - +
475C THR* 3.6 1.0 + - - -
477C THR* 3.3 17.5 + - - +
478C GLY* 1.3 77.5 - - - +
480C SER* 1.3 58.1 + - - +
482C GLN* 3.1 30.7 + - - +
483C LEU* 2.9 63.5 + - + +
580C FBP 4.2 8.5 + - - +
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Residues in contact with SER 480 (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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452C THR* 3.6 21.6 - - - +
456C ALA* 5.3 0.9 - - - +
473C VAL* 4.2 14.4 - - - -
474C LEU 3.9 6.1 + - - -
475C THR* 4.1 0.2 - - - -
478C GLY 3.3 0.6 - - - -
479C ARG* 1.3 75.7 - - - +
481C ALA* 1.3 63.5 + - - +
483C LEU* 4.1 2.8 - - - +
484C LEU* 3.3 26.2 + - - +
555C VAL* 5.4 0.4 - - - -
565C THR* 2.9 29.1 + - - -
580C FBP 2.6 28.6 + - - -
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Residues in contact with ALA 481 (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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473C VAL* 4.2 11.4 - - + +
475C THR* 4.1 11.4 + - + -
478C GLY 2.9 10.9 + - - +
480C SER* 1.3 77.6 + - - +
482C GLN* 1.3 60.8 + - - +
484C LEU* 3.4 5.2 + - - +
485C SER* 3.1 21.3 + - - -
493C VAL* 4.1 5.0 - - + +
495C ALA* 3.9 28.0 - - + -
506C VAL* 4.6 5.2 - - + -
512C VAL* 4.0 19.8 - - + +
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Residues in contact with GLN 482 (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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309C LYS* 4.9 10.6 + - - -
331C ASP 5.1 1.0 + - - -
364C GLY 3.1 26.3 + - - +
365C LYS* 4.4 4.2 - - - +
366C PRO* 4.1 17.3 - - - +
478C GLY 2.8 12.3 + - - +
479C ARG* 3.1 32.8 + - - +
481C ALA* 1.3 75.2 - - - +
483C LEU* 1.3 63.7 + - + +
485C SER* 3.1 4.0 + - - +
486C ARG* 2.8 28.4 + - + +
506C VAL* 5.7 1.0 - - + +
509C CYS* 3.8 30.3 - - - -
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Residues in contact with LEU 483 (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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450C ASP* 4.0 6.5 - - - +
452C THR* 3.6 20.4 - - + +
453C GLU* 3.6 48.0 - - + +
456C ALA* 3.8 14.6 - - + -
479C ARG* 2.9 55.1 + - + +
480C SER* 3.6 4.5 + - - +
481C ALA 3.4 0.2 - - - -
482C GLN* 1.3 78.3 - - + +
484C LEU* 1.3 64.0 + - - +
486C ARG* 3.0 26.6 - - + +
487C TYR* 3.5 13.4 - - + -
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Residues in contact with LEU 484 (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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456C ALA* 3.6 33.2 - - + +
459C ALA* 3.7 18.8 - - + -
460C VAL* 3.9 10.0 - - + +
471C ILE* 3.6 22.7 - - + -
473C VAL* 3.4 40.2 - - + -
480C SER 3.3 13.8 + - - +
481C ALA 3.5 6.1 - - - +
482C GLN 3.2 0.4 - - - -
483C LEU* 1.3 75.7 - - - +
485C SER* 1.3 63.0 + - - +
487C TYR* 2.9 17.0 + - - +
489C PRO* 3.3 15.0 - - + +
493C VAL* 4.0 15.0 - - + -
555C VAL* 4.6 4.5 - - + -
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Residues in contact with SER 485 (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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400C ASP* 4.9 1.7 + - - -
481C ALA 3.1 9.8 + - - -
482C GLN* 3.1 6.7 + - - +
484C LEU* 1.3 79.0 - - - +
486C ARG* 1.3 56.6 + - - +
488C ARG* 2.7 37.6 + - - -
489C PRO* 3.9 9.6 - - - -
493C VAL* 4.8 2.9 - - - -
509C CYS* 3.5 19.8 - - - +
510C ARG 2.9 30.5 + - - +
512C VAL* 4.0 11.0 - - - -
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Residues in contact with ARG 486 (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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361C ASN 3.8 11.5 + - - +
362C LEU* 2.8 33.8 + - - +
363C ALA 3.9 11.3 + - - -
364C GLY* 3.5 28.7 - - - +
441C LEU* 4.0 21.8 + - - +
445C ALA* 3.9 28.7 - - - +
446C PRO* 5.8 2.2 - - - +
453C GLU* 4.4 15.0 + - - -
482C GLN* 2.8 13.4 + - + +
483C LEU* 3.0 28.5 - - + +
485C SER* 1.3 75.1 + - - +
487C TYR* 1.3 78.9 + - - +
488C ARG* 3.3 5.9 + - - +
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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