Contacts of the helix formed by residues 433 - 445 (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 TYR 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA 4.0 3.6 - - - -
64A ALA* 4.1 11.2 - - - +
66A ALA 2.4 30.9 + - - -
67A ASP 3.2 5.2 + - - -
68A THR* 3.2 20.5 + - - -
69A PHE* 3.9 37.4 - + + -
72A HIS* 3.4 42.4 - + + +
431A ALA 3.3 3.2 + - - -
432A VAL* 1.3 71.7 - - - +
434A HIS* 1.3 65.2 + - - +
435A ARG* 3.1 22.7 + - + -
436A GLN* 3.2 37.0 + - + +
437A LEU* 3.1 16.8 + - - +
443B ARG* 4.9 0.7 + - - -
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Residues in contact with HIS 434 (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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64A ALA* 5.5 5.6 - - + +
429A GLU 3.9 6.3 + - - -
432A VAL* 3.1 40.6 + - + +
433A TYR* 1.3 68.6 - - - +
435A ARG* 1.3 62.9 + - - +
437A LEU* 2.7 13.6 + - + +
438A PHE* 2.5 36.5 + - - +
464A PHE* 4.0 27.1 - + + -
488A ARG* 4.0 15.1 + - + +
489A PRO 4.5 4.3 - - - -
490A ARG* 3.0 62.4 + - + +
510A ARG* 6.3 0.2 - - - -
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Residues in contact with ARG 435 (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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64A ALA* 4.3 11.6 + - - +
65A MET* 4.1 20.2 + - - +
66A ALA 3.6 13.1 + - - -
67A ASP* 3.4 20.8 + - - +
433A TYR* 3.1 31.3 + - + +
434A HIS* 1.3 80.0 - - - +
436A GLN* 1.3 62.4 + - - +
438A PHE* 4.0 2.8 - - - +
439A GLU* 3.1 38.0 + - + +
443B ARG* 3.3 57.0 + - + +
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Residues in contact with GLN 436 (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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69A PHE* 4.2 13.9 + - - +
433A TYR* 3.2 32.2 + - + +
435A ARG* 1.3 79.4 - - - +
437A LEU* 1.3 65.1 + - - +
439A GLU* 3.2 7.4 + - - +
440A GLU* 2.8 49.0 + - + +
69C PHE* 3.5 34.8 - - - +
436C GLN* 2.9 30.8 + - - +
440C GLU* 5.1 0.5 - - - +
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Residues in contact with LEU 437 (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* 4.8 13.7 - - - +
398A GLY* 6.4 1.6 - - - -
432A VAL* 3.6 25.8 - - + -
433A TYR 3.1 13.0 + - - +
434A HIS* 2.7 17.2 + - - +
436A GLN* 1.3 72.9 - - - +
438A PHE* 1.3 62.5 + - - +
440A GLU* 3.3 6.9 + - + +
441A LEU* 3.0 48.2 + - + +
488A ARG* 3.9 30.1 - - + -
510A ARG* 5.3 4.0 - - - +
70C LEU* 5.3 9.9 - - + -
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Residues in contact with PHE 438 (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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434A HIS* 2.5 20.8 + - + +
435A ARG* 4.0 3.1 - - - +
437A LEU* 1.3 71.2 - - - +
439A GLU* 1.3 66.5 + - - +
441A LEU* 3.1 6.4 + - + -
442A ARG* 3.0 58.5 + - + +
457A ILE* 4.3 11.7 - - + -
460A VAL* 3.8 21.1 - - + -
461A GLU* 3.8 29.4 - - - -
464A PHE* 3.6 36.8 - + + -
487A TYR* 3.9 32.5 - + + +
488A ARG 5.7 0.2 - - - +
442B ARG* 4.7 9.9 - - - -
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Residues in contact with GLU 439 (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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435A ARG* 3.1 27.4 + - + +
436A GLN* 3.5 6.5 - - - +
438A PHE* 1.3 78.9 - - + +
440A GLU* 1.3 60.8 + - + +
442A ARG* 3.4 12.4 + - - +
443A ARG* 2.9 40.3 + - - +
439B GLU* 3.2 34.2 - - - +
442B ARG* 3.8 21.2 + - - +
443B ARG* 3.2 35.6 + - - +
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Residues in contact with GLU 440 (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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436A GLN* 2.8 44.6 + - + +
437A LEU* 3.8 6.8 - - + +
439A GLU* 1.3 76.9 - - + +
441A LEU* 1.3 51.7 + - - +
443A ARG* 3.4 9.6 - - - +
444A ALA* 2.8 38.3 + - - +
68C THR* 3.1 25.4 - - + +
69C PHE* 3.0 23.6 + - - +
70C LEU* 2.9 39.5 + - + +
436C GLN* 5.1 0.5 - - - +
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Residues in contact with LEU 441 (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 30.7 - - + +
362A LEU* 4.7 1.1 - - - +
437A LEU* 3.0 44.3 + - + +
438A PHE* 3.1 3.8 + - - +
440A GLU* 1.3 71.8 - - - +
442A ARG* 1.3 71.7 + - - +
444A ALA* 3.0 2.8 + - - -
445A ALA* 2.8 25.6 + - - +
486A ARG* 3.9 27.9 + - - +
487A TYR* 4.3 23.6 - - + +
488A ARG* 4.2 11.9 - - + -
70C LEU* 3.7 23.6 - - + -
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Residues in contact with ARG 442 (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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438A PHE* 3.0 51.4 + - + +
439A GLU* 3.6 9.8 - - - +
441A LEU* 1.3 78.6 - - - +
443A ARG* 1.3 64.1 + - - +
444A ALA 3.0 0.3 + - - -
445A ALA* 3.1 19.2 + - - +
457A ILE* 4.2 10.1 - - + -
487A TYR* 4.7 9.3 - - - -
438B PHE* 4.5 12.7 - - - -
439B GLU* 4.0 20.6 + - - +
442B ARG* 2.4 46.3 - - - +
461B GLU* 3.4 30.7 + - - -
464B PHE* 6.2 1.2 - - - +
465B LYS* 5.1 1.4 + - - +
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Residues in contact with ARG 443 (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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439A GLU* 2.9 25.0 + - - +
440A GLU* 3.4 8.5 - - - +
442A ARG* 1.3 76.6 - - - +
444A ALA* 1.3 61.4 + - - +
445A ALA 4.2 2.4 - - - +
67B ASP* 3.3 28.5 + - - +
433B TYR* 4.6 0.6 + - - -
435B ARG* 3.2 58.9 + - + +
439B GLU* 2.9 35.6 + - - +
68C THR* 4.7 20.0 - - + +
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Residues in contact with ALA 444 (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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362A LEU* 4.0 30.9 - - + +
440A GLU 2.8 20.9 + - - +
441A LEU* 3.8 2.9 - - - +
443A ARG* 1.3 76.8 - - - +
445A ALA* 1.3 63.2 + - - +
446A PRO* 3.4 6.4 - - - +
68C THR* 6.0 4.0 - - + +
70C LEU* 4.8 2.7 - - + -
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Residues in contact with ALA 445 (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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362A LEU* 5.8 2.2 - - - +
441A LEU 2.8 21.7 + - - +
442A ARG 3.2 11.7 - - - +
443A ARG 4.2 2.1 - - - +
444A ALA* 1.3 72.5 - - - +
446A PRO* 1.4 73.8 - - + +
447A LEU* 3.8 0.5 + - - +
453A GLU* 5.8 0.2 - - - +
486A ARG* 3.9 26.4 - - - +
487A TYR* 4.2 7.0 - - + +
465B LYS* 3.4 22.3 + - - +
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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