Contacts of the helix formed by residues 68 - 74 (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 THR 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B GLU* 3.4 27.7 + - + +
443B ARG* 4.4 25.8 - - + +
444B ALA* 5.6 5.3 - - + +
66D ALA* 3.7 1.2 - - - +
67D ASP* 1.3 86.8 - - + +
69D PHE* 1.3 60.5 + - - +
70D LEU* 3.6 4.3 + - - +
71D GLU* 3.0 28.2 + - + +
72D HIS* 3.0 26.7 + - - +
433D TYR* 3.4 10.5 + - - -
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Residues in contact with PHE 69 (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* 6.1 10.3 - + - -
396B LEU 6.2 0.4 - - - -
436B GLN* 3.5 30.1 - - - +
440B GLU* 2.9 11.8 + - - +
68D THR* 1.3 69.3 - - - +
70D LEU* 1.3 61.6 + - - +
72D HIS* 3.1 22.3 - + - +
73D LEU* 2.9 63.5 + - + +
433D TYR* 4.0 27.0 - + + -
436D GLN* 4.1 13.6 + - - +
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Residues in contact with LEU 70 (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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358B GLY* 3.9 27.1 - - - +
361B ASN* 4.3 13.2 - - + +
362B LEU* 3.6 31.0 - - + -
397B ASP 6.2 0.2 - - - +
437B LEU* 5.3 8.1 - - + -
440B GLU* 2.9 33.3 + - + +
441B LEU* 3.6 30.3 - - + -
444B ALA* 4.6 2.0 - - + -
68D THR* 3.3 4.9 - - - +
69D PHE* 1.3 74.6 - - - +
71D GLU* 1.3 60.3 + - - +
72D HIS 3.2 0.2 + - - -
73D LEU* 3.2 16.3 + - + +
74D CYS* 2.9 32.7 + - - -
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Residues in contact with GLU 71 (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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362B LEU* 5.5 3.3 - - - +
444B ALA* 6.5 1.1 - - + -
66D ALA* 3.8 9.8 - - + -
67D ASP* 3.0 37.8 + - - +
68D THR* 3.0 20.9 + - - +
70D LEU* 1.3 75.3 - - - +
72D HIS* 1.3 65.9 + - - +
74D CYS* 3.2 15.1 + - + +
75D LEU* 3.3 33.7 + - + +
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Residues in contact with HIS 72 (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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60D GLN 5.7 0.2 - - - -
63D ALA* 2.8 44.3 + - + +
64D ALA 4.7 0.9 - - - -
66D ALA* 3.4 10.5 - - + +
68D THR 3.0 16.1 + - - +
69D PHE* 3.1 34.6 - + - +
71D GLU* 1.3 73.8 - - - +
73D LEU* 1.3 84.1 + - + +
75D LEU* 2.7 17.5 + - - +
76D LEU* 3.4 15.7 + - + +
430D ALA 5.6 0.4 - - - -
431D ALA* 2.9 30.6 + - - -
432D VAL 4.2 2.5 - - - -
433D TYR* 3.4 30.3 + + + +
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Residues in contact with LEU 73 (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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354B LYS* 3.9 39.5 - - + +
355B MET* 3.4 17.3 - - - -
358B GLY* 4.5 6.3 - - - -
397B ASP* 4.6 18.8 - - + +
69D PHE* 2.9 60.7 + - + +
70D LEU* 3.4 21.1 - - + +
72D HIS* 1.3 78.1 - - + +
74D CYS* 1.3 58.9 + - - +
75D LEU 2.8 7.1 + - - -
76D LEU* 3.2 21.2 + - + +
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Residues in contact with CYS 74 (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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355B MET* 3.7 5.8 - - - +
358B GLY* 3.4 10.3 - - - -
359B ARG* 2.7 75.8 + - + +
362B LEU* 4.3 18.2 - - - -
70D LEU* 2.9 24.2 + - - +
71D GLU* 3.5 14.4 - - + +
72D HIS 3.0 0.4 + - - -
73D LEU* 1.3 71.4 - - - +
75D LEU* 1.3 60.9 + - + +
76D LEU 3.7 0.4 - - - -
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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