Contacts of the strand formed by residues 278 - 283 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E PHE* 3.9 20.6 - + - -
247E SER* 3.7 12.8 - - - -
248E ALA 3.1 28.5 - - - -
249E GLY* 4.7 0.2 - - - -
148F GLN* 5.0 6.1 - - + -
149F LEU 3.3 14.4 - - - +
150F ILE* 3.9 13.5 - - + -
168F TRP* 3.6 6.6 - - - -
196F TYR* 4.2 19.1 - + - -
197F GLY* 3.4 1.4 - - - -
198F GLN* 2.9 70.8 + - + +
246F TYR* 4.2 8.3 - + - -
261F LEU* 4.4 0.7 - - - +
274F GLY 3.9 11.2 - - - -
275F ASP 3.7 11.7 - - - -
276F VAL 4.0 0.2 - - - -
277F THR* 1.3 81.9 - - - +
279F PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F GLN* 4.6 0.2 - - - -
149F LEU* 2.7 49.6 + - + +
168F TRP* 3.6 37.7 - + + -
183F ASN 5.5 0.4 - - - -
184F LYS* 5.4 1.1 - - - -
185F ILE* 3.8 23.1 - - + -
195F ILE* 4.1 8.3 - - + -
196F TYR* 3.3 23.8 - - - -
197F GLY* 4.2 0.4 - - - -
212F ILE* 4.1 24.7 - - + -
259F LEU* 3.8 26.7 - - + -
260F GLN* 3.8 23.1 - - - -
261F LEU* 3.8 25.1 - - + -
278F PHE* 1.3 76.8 - - - +
280F GLY* 1.3 55.3 + - - +
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Residues in contact with GLY 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU 3.2 12.6 - - - -
148F GLN* 4.1 0.2 - - - -
185F ILE* 4.0 7.2 - - - -
195F ILE* 3.6 6.4 - - - +
196F TYR* 2.9 56.4 + - - +
279F PHE* 1.3 77.7 - - - +
281F ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ILE* 5.0 0.2 - - - +
146F CYS* 3.3 4.7 - - - +
147F LEU 3.0 30.4 + - - +
178F LEU* 3.4 23.8 - - + +
185F ILE* 4.3 6.3 - - + +
193F PHE* 4.7 3.8 - - + -
194F PHE 3.3 9.0 - - - +
195F ILE* 4.2 15.9 - - + -
196F TYR* 3.8 4.0 - - - -
259F LEU* 4.2 15.0 - - + -
280F GLY* 1.3 74.3 - - - +
282F LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E PHE* 5.6 4.9 - - + -
250E ILE* 4.1 15.7 - - + -
284E LEU* 3.9 25.4 - - + -
144F GLN* 3.7 39.5 - - + +
145F ASP 3.7 2.9 - - - +
146F CYS* 3.7 24.0 - - + -
193F PHE* 3.3 3.3 - - - -
194F PHE* 2.7 61.3 + - + +
196F TYR* 5.0 0.2 - - + -
281F ALA* 1.3 76.8 - - - +
283F LYS* 1.3 63.3 + - - +
284F LEU* 3.5 4.9 + - + +
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Residues in contact with LYS 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLN* 3.4 27.9 + - - +
145F ASP* 2.8 28.4 + - + +
177F ALA* 3.6 20.2 - - + -
178F LEU* 4.7 0.2 - - - +
189F GLU* 3.1 33.7 + - - +
190F THR 3.8 19.5 + - - -
191F GLY* 4.4 4.7 - - - -
192F TYR 4.0 4.5 - - - +
193F PHE* 3.5 30.9 - - + -
282F LEU* 1.3 73.1 - - - +
284F LEU* 1.3 72.2 + - - +
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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