Contacts of the strand formed by residues 258 - 263 (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 GLU 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181F LYS* 5.4 6.7 - - - +
184F LYS* 3.4 34.2 - - + +
185F ILE 3.2 8.5 - - - +
186F LEU* 3.8 25.1 - - + +
214F ARG* 3.5 4.2 - - - +
215F LYS* 2.7 55.0 + - + +
256F GLY 4.3 4.6 - - - +
257F ASP* 1.3 78.8 - - - +
259F LEU* 1.3 62.7 + - - +
260F GLN* 4.3 0.8 + - - +
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Residues in contact with LEU 259 (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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178F LEU* 5.4 0.4 - - + -
184F LYS* 3.4 10.2 - - - +
185F ILE* 2.7 48.6 + - + +
187F VAL* 4.7 4.0 - - + -
195F ILE* 3.8 26.0 - - + -
212F ILE* 5.0 3.1 - - + -
213F GLN 3.3 12.1 - - - +
214F ARG* 4.2 3.4 - - + -
229F LEU* 4.0 17.0 - - + -
253F LEU* 3.7 44.0 - - + -
258F GLU* 1.3 78.4 - - - +
260F GLN* 1.3 61.6 + - - +
279F PHE* 3.8 15.0 - - + -
281F ALA* 4.2 14.6 - - + -
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Residues in contact with GLN 260 (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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165F PHE* 3.9 30.8 - - + -
183F ASN 5.3 3.4 - - - +
184F LYS* 4.2 24.8 - - + +
211F LEU 3.3 1.6 - - - +
212F ILE* 3.5 2.4 - - - -
213F GLN* 2.7 70.5 + - + +
215F LYS* 5.6 3.9 - - + +
226F LEU* 4.0 20.7 - - + +
258F GLU 5.6 1.3 - - - +
259F LEU* 1.3 76.0 - - - +
261F LEU* 1.3 60.5 + - - +
279F PHE* 3.8 9.7 - - - -
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Residues in contact with LEU 261 (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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164F THR 4.6 0.2 - - - +
165F PHE* 3.4 22.0 - - - -
166F VAL* 4.4 18.3 + - + -
168F TRP* 4.1 28.6 + - + +
197F GLY* 4.3 11.0 - - - -
199F VAL* 3.6 28.7 - - + -
210F HIS* 3.7 39.3 - - + +
211F LEU 3.3 4.5 - - - +
212F ILE* 4.6 3.4 - - + +
260F GLN* 1.3 73.3 - - - +
262F ALA* 1.3 58.6 + - - +
263F ILE* 4.4 5.8 - - + -
278F PHE 4.4 1.6 - - - +
279F PHE* 3.8 28.5 - - + -
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Residues in contact with ALA 262 (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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163F TYR* 3.9 15.3 - - + -
164F THR 4.1 0.4 - - - -
165F PHE* 3.5 28.9 - - + -
210F HIS* 3.3 2.8 - - - -
211F LEU* 2.8 38.6 + - + +
213F GLN* 3.6 24.0 - - - +
260F GLN* 4.0 0.9 - - - +
261F LEU* 1.3 73.8 - - - +
263F ILE* 1.4 61.8 + - - +
264F PRO* 3.6 4.1 - - - +
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Residues in contact with ILE 263 (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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163F TYR* 3.2 3.9 - - - -
164F THR* 2.9 49.1 + - + +
166F VAL* 4.1 24.5 - - + -
199F VAL* 4.2 8.1 - - + -
201F TYR* 3.9 15.0 - - + +
208F MET* 4.1 7.2 - - + -
209F GLY 3.5 13.0 - - - +
210F HIS* 3.9 6.1 - - + -
261F LEU* 4.4 3.4 - - + -
262F ALA* 1.4 73.7 - - - +
264F PRO* 1.4 54.7 - - - +
265F ARG* 2.7 28.3 + - + -
268F ALA* 3.7 24.7 - - + -
270F ILE* 4.0 26.7 - - + -
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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