Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 5VLR
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 HIS 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TRP* 5.9 0.2 - - - -
197A GLU* 5.1 3.1 - - + +
238A ASP* 3.2 36.1 + - + -
239A TYR* 3.8 11.7 - - + +
276A MET 3.9 3.0 + - - -
277A VAL* 1.3 75.9 - - - +
279A SER* 1.4 75.1 + - - +
280A SER* 2.8 34.1 + - - +
281A SER* 3.0 19.3 + - - +
282A ILE* 3.3 10.1 + - - +
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Residues in contact with SER 279 (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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159A TRP* 3.8 39.1 - - - +
238A ASP* 2.7 26.1 + - - -
239A TYR 4.4 1.6 - - - +
278A HIS* 1.4 81.1 + - - +
280A SER* 1.3 55.4 + - - +
282A ILE* 3.3 9.2 + - - +
283A LEU* 3.0 39.6 + - - +
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Residues in contact with SER 280 (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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278A HIS* 2.8 34.0 + - - +
279A SER* 1.3 76.3 - - - +
281A SER* 1.3 57.1 + - - -
283A LEU* 3.6 11.0 + - - +
284A ALA* 3.2 25.3 + - - +
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Residues in contact with SER 281 (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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197A GLU* 4.7 12.3 - - - +
277A VAL* 4.5 11.5 - - - +
278A HIS* 3.0 22.5 + - - -
280A SER* 1.3 78.5 + - - +
282A ILE* 1.4 62.4 + - - +
284A ALA* 3.4 9.3 - - - +
285A MET* 3.3 25.9 + - - +
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Residues in contact with ILE 282 (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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159A TRP* 4.4 22.9 - - + +
162A TRP* 4.5 7.6 - - + -
163A LEU* 5.5 11.4 - - + -
277A VAL* 5.8 1.5 - - + +
278A HIS 3.3 7.1 + - - +
279A SER* 3.3 12.2 + - - +
281A SER* 1.4 76.4 - - - +
283A LEU* 1.4 53.1 + - - +
285A MET* 3.0 17.2 + - - +
286A ARG* 2.8 32.7 + - - +
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Residues in contact with LEU 283 (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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158A GLY* 5.2 1.6 - - - -
159A TRP* 4.5 19.1 - - + +
279A SER* 3.0 25.6 + - - +
280A SER* 3.9 9.0 - - - +
281A SER 3.5 0.2 - - - -
282A ILE* 1.4 74.8 - - - +
284A ALA* 1.3 56.3 + - - +
286A ARG* 3.4 42.5 - - - +
287A ASP* 3.0 35.0 + - - +
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Residues in contact with ALA 284 (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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280A SER 3.2 15.1 + - - +
281A SER* 3.4 14.6 - - - +
282A ILE 3.2 0.2 - - - -
283A LEU* 1.3 76.3 - - - +
285A MET* 1.4 60.1 + - - +
287A ASP* 3.4 19.0 - - - -
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Residues in contact with MET 285 (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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162A TRP* 3.9 16.1 - - + -
167A PHE* 4.2 21.5 - - + -
247A HIS* 5.4 5.8 - - - -
249A TYR* 3.7 23.8 - - - -
281A SER* 3.3 13.2 + - - +
282A ILE* 3.0 15.3 + - - +
284A ALA* 1.4 74.1 - - - +
286A ARG* 1.4 61.3 + - - +
287A ASP 3.0 10.2 + - - +
677A HIS* 3.5 14.2 + - - -
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Residues in contact with ARG 286 (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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155A GLN* 3.0 52.6 + - - +
156A GLN 3.8 5.7 + - - -
157A LEU 3.0 29.2 + - - -
158A GLY* 4.4 2.0 - - - -
159A TRP* 5.1 2.0 - - - +
162A TRP* 3.6 45.3 - - + -
282A ILE 2.8 15.6 + - - +
283A LEU* 3.4 38.3 - - - +
285A MET* 1.4 70.8 - - - +
287A ASP* 1.4 83.2 + - - +
677A HIS* 3.2 15.9 - - - -
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Residues in contact with ASP 287 (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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155A GLN* 4.3 11.6 + - - +
283A LEU* 3.0 15.2 + - - +
284A ALA* 3.4 17.0 - - - +
285A MET 3.1 6.3 - - - +
286A ARG* 1.4 119.9 + - - +
677A HIS* 4.5 6.9 + - - -
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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