Contacts of the helix formed by residues 433 - 445 (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 TYR 433 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443C ARG* 4.7 0.7 + - - -
63D ALA 4.0 7.6 - - - -
64D ALA* 3.8 17.3 - - - +
66D ALA 2.5 33.2 + - - -
67D ASP 3.4 15.1 + - - -
68D THR* 3.8 17.9 - - - -
69D PHE* 4.0 25.8 - + + -
72D HIS* 3.4 36.1 + + + +
431D ALA 3.3 2.6 + - - -
432D VAL* 1.3 73.3 - - - +
434D HIS* 1.3 65.5 + - - +
435D ARG* 3.0 23.4 + - + -
436D GLN* 3.0 44.3 + - + +
437D LEU* 3.1 9.7 + - - +
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Residues in contact with HIS 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 5.6 5.1 - - + +
429D GLU 4.0 5.3 + - - -
432D VAL* 3.1 38.9 + - + +
433D TYR* 1.3 71.3 - - - +
435D ARG* 1.3 59.1 + - - +
437D LEU* 2.7 12.6 + - + +
438D PHE* 2.6 36.0 + - - +
464D PHE* 3.9 27.1 - + + -
488D ARG* 4.0 14.5 + - + -
489D PRO 4.5 4.7 - - - -
490D ARG* 2.9 65.1 + - + +
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Residues in contact with ARG 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ARG* 2.9 64.7 + - + +
64D ALA 4.3 10.2 + - - +
65D MET* 4.3 20.7 + - - +
66D ALA 3.7 13.0 + - - -
67D ASP* 3.6 16.2 + - - -
433D TYR* 3.0 30.4 + - + +
434D HIS* 1.3 81.0 - - - +
436D GLN* 1.3 62.7 + - - +
438D PHE* 4.2 3.2 - - - +
439D GLU* 3.2 38.7 + - + +
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Residues in contact with GLN 436 (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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69B PHE* 3.4 35.4 - - - +
436B GLN* 3.1 28.6 + - - +
440B GLU* 4.8 1.7 - - - +
69D PHE* 4.1 15.5 + - - +
433D TYR* 3.0 32.5 + - + +
435D ARG* 1.3 76.4 - - - +
437D LEU* 1.3 67.1 + - - +
439D GLU* 3.3 6.4 + - + +
440D GLU* 2.9 48.0 + - + +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.5 8.1 - - + -
361D ASN* 4.9 11.7 - - - +
398D GLY* 6.5 1.6 - - - -
432D VAL* 3.5 27.6 - - + -
433D TYR 3.1 11.4 + - - +
434D HIS* 2.7 16.8 + - + +
436D GLN* 1.3 74.4 - - - +
438D PHE* 1.3 64.4 - - - +
440D GLU* 3.1 8.0 + - + +
441D LEU* 2.9 48.3 + - + +
488D ARG* 3.9 29.4 - - + -
510D ARG* 5.4 4.5 - - - +
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Residues in contact with PHE 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ARG* 4.7 11.2 - - - -
434D HIS* 2.6 21.2 + - - +
435D ARG* 4.2 3.1 - - - +
437D LEU* 1.3 73.3 - - - +
439D GLU* 1.3 63.3 + - - +
441D LEU* 3.2 6.4 + - + -
442D ARG* 3.0 58.7 + - + +
457D ILE* 4.3 14.1 - - + -
460D VAL* 3.8 20.0 - - + -
461D GLU* 3.9 28.5 - - - -
464D PHE* 3.6 39.0 - + + -
487D TYR* 4.0 28.3 - + + +
488D ARG 5.7 0.4 - - - +
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Residues in contact with GLU 439 (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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439C GLU* 3.1 36.4 - - - +
442C ARG* 3.9 19.7 + - - +
443C ARG* 3.3 31.5 + - - +
435D ARG* 3.2 28.2 + - + +
436D GLN* 3.3 6.7 + - + +
438D PHE* 1.3 78.6 - - - +
440D GLU* 1.3 60.4 + - + +
442D ARG* 3.7 10.3 - - - +
443D ARG* 2.9 41.1 + - - +
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Residues in contact with GLU 440 (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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68B THR* 3.2 20.4 + - + +
69B PHE* 2.9 29.2 + - - +
70B LEU* 2.8 39.4 + - + +
436B GLN* 4.9 1.0 - - - +
436D GLN* 2.9 44.4 + - + +
437D LEU* 3.7 6.7 - - + +
439D GLU* 1.3 77.3 - - + +
441D LEU* 1.3 59.2 + - - +
443D ARG* 3.5 9.1 - - - +
444D ALA* 2.8 33.1 + - - +
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Residues in contact with LEU 441 (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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70B LEU* 3.7 23.3 - - + -
361D ASN* 3.9 32.1 - - + +
362D LEU* 4.7 1.1 - - - +
437D LEU* 2.9 45.6 + - + +
438D PHE* 3.8 3.6 - - - +
440D GLU* 1.3 72.3 - - - +
442D ARG* 1.3 71.4 + - - +
444D ALA* 2.9 3.3 + - + -
445D ALA* 2.8 25.2 + - - +
486D ARG* 3.9 24.7 - - - +
487D TYR* 4.3 23.8 - - + +
488D ARG* 4.1 12.8 - - + -
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Residues in contact with ARG 442 (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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438C PHE* 4.7 12.7 - - - -
439C GLU* 4.1 19.8 + - - +
442C ARG* 2.7 41.6 - - - +
461C GLU* 3.4 33.1 + - - -
464C PHE* 6.0 1.6 - - - +
465C LYS* 4.8 2.3 + - - +
438D PHE* 3.0 52.0 + - + +
439D GLU* 3.7 9.1 - - - +
441D LEU* 1.3 77.5 - - - +
443D ARG* 1.3 63.5 + - - +
444D ALA 3.0 0.7 + - - -
445D ALA* 3.1 20.3 + - - +
457D ILE* 4.2 10.8 - - + -
487D TYR* 4.7 9.5 - - + -
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Residues in contact with ARG 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.5 21.0 - - + +
67C ASP* 3.3 27.9 + - - +
433C TYR* 4.5 0.8 + - - -
435C ARG* 2.8 61.3 + - + +
439C GLU* 3.1 30.9 + - - +
439D GLU* 2.9 23.6 + - - +
440D GLU* 3.5 8.5 - - - +
442D ARG* 1.3 79.9 - - - +
444D ALA* 1.3 61.6 + - - +
445D ALA 4.3 1.7 - - - +
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Residues in contact with ALA 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 5.9 4.9 - - + +
70B LEU* 4.6 4.0 - - + -
362D LEU* 3.8 32.5 - - + +
440D GLU 2.8 21.1 + - - +
441D LEU* 3.8 1.8 - - - +
443D ARG* 1.3 75.5 - - - +
445D ALA* 1.3 64.5 + - - +
446D PRO* 3.4 6.4 - - - +
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Residues in contact with ALA 445 (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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465C LYS* 3.3 20.8 + - - +
362D LEU* 5.5 3.7 - - - +
441D LEU 2.8 20.6 + - - +
442D ARG 3.1 12.7 - - - +
443D ARG 4.3 2.3 - - - +
444D ALA* 1.3 71.5 - - - +
446D PRO* 1.3 74.5 - - + +
447D LEU* 5.7 0.7 - - - +
486D ARG* 3.8 26.4 - - - +
487D TYR* 4.1 8.5 - - + +
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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