Contacts of the helix formed by residues 428 - 433 (chain E) in PDB entry 6V3O
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 ASP 428 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E MET* 4.8 5.0 - - - +
334E ARG* 5.1 4.9 + - - +
423E LEU* 2.7 40.1 + - + +
424E CYS 4.1 0.2 + - - -
426E CYS* 3.6 10.2 - - - +
427E GLY* 1.3 70.1 - - - +
429E LYS* 1.3 64.5 + - - +
430E ALA 3.1 2.7 - - - -
431E ILE* 2.9 24.8 + - + +
432E ALA* 3.1 10.9 + - - +
222F GLN* 2.9 24.8 + - - +
226F ARG* 3.0 43.1 + - - +
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Residues in contact with LYS 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ARG* 5.2 7.1 - - - +
420E TYR* 3.6 17.3 + - - -
423E LEU 3.5 2.4 + - - -
424E CYS* 3.7 34.9 - - + +
427E GLY 3.5 3.3 - - - -
428E ASP* 1.3 76.5 - - - +
430E ALA* 1.3 63.9 + - - +
432E ALA* 3.0 3.6 + - - +
433E ASP* 2.8 51.4 + - - +
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Residues in contact with ALA 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E GLY 5.2 0.2 + - - -
428E ASP 3.1 1.0 - - - -
429E LYS* 1.3 79.3 - - - +
431E ILE* 1.3 61.7 + - - +
433E ASP* 3.3 9.9 + - - +
218F GLN* 6.1 0.7 - - + -
219F ARG* 3.0 37.1 + - + +
222F GLN* 3.4 27.1 - - - +
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Residues in contact with ILE 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU* 4.0 15.0 - - + +
332E MET* 4.0 34.5 - - + -
423E LEU* 4.3 5.3 - - + +
428E ASP* 2.9 34.0 + - + +
430E ALA* 1.3 72.7 - - - +
432E ALA* 1.3 67.3 + - - +
434E GLY* 2.9 16.8 + - - -
435E SER 4.5 1.4 + - - -
436E LEU* 4.9 2.3 + - - +
219F ARG* 3.9 12.9 - - + +
222F GLN* 4.1 12.6 - - + +
223F ALA* 3.7 41.5 - - + +
226F ARG* 4.8 1.6 - - + -
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Residues in contact with ALA 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E TYR* 3.6 31.8 - - + +
423E LEU* 3.7 34.3 - - + +
424E CYS* 4.4 0.4 - - - -
428E ASP 3.1 6.5 + - - +
429E LYS* 3.0 13.6 + - - +
431E ILE* 1.3 77.3 - - - +
433E ASP* 1.3 57.1 + - - +
434E GLY 3.1 1.1 + - - -
436E LEU* 3.5 7.6 - - - +
437E LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E ARG* 2.9 28.6 + - - -
275E ARG* 3.7 30.4 + - - +
420E TYR* 2.7 29.5 + - - -
429E LYS* 2.8 42.3 + - - +
430E ALA* 3.8 11.3 - - - +
431E ILE 3.1 1.0 - - - -
432E ALA* 1.3 73.3 - - - +
434E GLY* 1.3 59.7 + - - +
437E LEU* 3.7 14.0 - - + +
219F ARG* 3.7 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