Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 3V56
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 PHE 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 5.0 5.8 - - + -
149A LEU 3.3 14.1 - - - +
150A ILE* 3.9 12.8 - - + -
168A TRP* 3.6 6.1 - - - -
196A TYR* 4.2 22.7 - + - -
197A GLY* 3.4 1.0 - - - -
198A GLN* 2.9 70.5 + - + +
246A TYR* 4.2 4.5 - + - -
261A LEU* 4.3 0.5 - - - +
274A GLY 3.8 11.4 - - - -
275A ASP 3.8 11.7 - - - -
276A VAL 4.0 0.2 - - - -
277A THR* 1.3 82.3 - - - +
279A PHE* 1.3 63.9 + - - +
230C PHE* 4.0 20.4 - + - -
247C SER* 3.7 13.7 - - - -
248C ALA 3.2 27.6 - - - -
249C GLY* 4.9 0.2 - - - -
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Residues in contact with PHE 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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148A GLN* 3.6 0.6 - - - -
149A LEU* 2.6 54.7 + - + +
168A TRP* 3.7 31.2 - + + -
183A ASN 5.5 0.4 - - - -
184A LYS* 5.4 1.1 - - - -
185A ILE* 3.8 24.6 - - + +
195A ILE* 4.1 13.7 - - + -
196A TYR* 3.3 23.1 - - - -
197A GLY* 4.2 0.4 - - - -
212A ILE* 4.1 19.3 - - + -
259A LEU* 3.8 26.2 - - + -
260A GLN* 3.8 30.7 - - - -
261A LEU* 3.9 16.8 - - + -
278A PHE* 1.3 76.6 - - - +
280A GLY* 1.3 55.8 + - - +
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Residues in contact with GLY 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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147A LEU 3.2 11.9 - - - -
148A GLN* 4.1 0.4 - - - -
185A ILE* 4.0 6.7 - - - -
195A ILE* 3.6 6.6 - - - +
196A TYR* 2.9 58.0 + - - +
279A PHE* 1.3 76.8 - - - +
281A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 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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146A CYS* 3.3 4.9 - - - +
147A LEU 3.0 31.5 + - - +
178A LEU* 3.5 22.8 - - + +
185A ILE* 4.2 6.3 - - + +
193A PHE* 4.6 4.3 - - + -
194A PHE 3.3 8.7 - - - +
195A ILE* 4.2 16.2 - - + -
196A TYR* 3.7 4.3 - - - -
259A LEU* 4.2 14.4 - - + -
280A GLY* 1.3 74.1 - - - +
282A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 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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144A GLN* 3.7 40.8 - - + +
145A ASP 3.6 9.2 - - - +
146A CYS* 3.9 12.3 - - + -
193A PHE* 3.2 6.0 - - - -
194A PHE* 2.8 62.8 + - + +
196A TYR* 5.1 0.2 - - + -
281A ALA* 1.3 75.5 - - - +
283A LYS* 1.3 63.2 + - - +
284A LEU* 3.5 4.7 + - + +
194C PHE* 5.5 5.4 - - + -
250C ILE* 4.3 15.0 - - + -
284C LEU* 4.1 28.7 - - + -
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Residues in contact with LYS 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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144A GLN* 3.4 28.4 + - - +
145A ASP* 2.8 31.4 + - + +
177A ALA* 3.6 21.3 - - + -
178A LEU* 4.7 0.2 - - - +
189A GLU* 3.5 23.0 + - - +
190A THR 3.4 28.5 + - - -
191A GLY* 4.0 10.3 - - - -
192A TYR 4.0 3.8 - - - +
193A PHE* 3.6 25.8 - - + -
282A LEU* 1.3 70.8 - - - +
284A LEU* 1.3 73.5 + - - +
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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