Contacts of the strand formed by residues 243 - 253 (chain C) 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 ASN 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A SO4 3.0 19.0 + - - -
233B ILE 3.4 2.5 - - - -
234B GLN* 3.4 4.3 - - - +
235B ASN* 2.8 42.3 + - - +
200C LEU* 3.6 3.5 - - - +
201C TYR* 2.8 40.6 + - - +
234C GLN* 3.9 17.5 - - + +
235C ASN 2.9 27.5 + - - -
236C MET* 3.5 20.0 - - - +
237C PRO* 4.2 1.4 - - - +
242C ASN* 1.4 73.0 - - - +
244C SER* 1.3 59.9 + - - +
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Residues in contact with SER 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ARG 4.5 1.3 - - - -
232B CYS* 3.3 18.4 - - - -
233B ILE 2.9 33.6 + - - -
234B GLN* 3.5 14.6 - - - +
245B CYS* 3.9 3.1 - - - -
198C GLN* 4.0 20.3 - - - -
199C VAL 3.3 9.9 - - - -
200C LEU* 3.8 14.9 - - - +
234C GLN* 4.2 3.6 + - - +
243C ASN* 1.3 73.9 - - - +
245C CYS* 1.3 61.4 + - - +
276C VAL* 5.0 0.9 - - - -
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Residues in contact with CYS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER* 3.9 12.6 - - - -
198C GLN* 3.2 23.9 - - - -
199C VAL 2.9 9.2 + - - -
201C TYR* 4.2 14.1 - - + -
209C GLY* 5.6 0.2 - - - -
210C HIS* 3.2 10.8 - - + -
232C CYS* 2.0 48.9 - - + -
233C ILE 4.0 2.5 - - - -
234C GLN* 3.7 28.9 - - + -
244C SER* 1.3 76.0 - - - +
246C TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN* 4.0 0.5 - - - +
246A TYR* 3.6 32.6 + + + +
194B PHE* 4.0 4.3 - - - -
246B TYR* 3.4 52.8 + + + +
248B ALA* 3.1 43.9 + - + +
194C PHE* 4.0 9.2 - - - -
196C TYR* 3.4 25.4 - - + +
197C GLY 3.4 13.0 - - - -
198C GLN* 3.7 18.6 - - + +
232C CYS* 3.4 10.0 - - - -
245C CYS* 1.3 76.9 - - - +
247C SER* 1.3 62.2 + - - +
248C ALA* 3.5 20.6 - - + +
278C PHE* 4.3 3.4 - + - -
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 2.7 31.3 + - - -
246A TYR* 4.5 2.2 - - - -
278A PHE* 3.7 8.3 - - - -
196C TYR* 3.6 0.7 - - - -
197C GLY 3.1 31.1 + - - +
210C HIS* 4.8 4.7 + - - -
212C ILE* 3.8 7.7 - - - +
230C PHE* 4.0 14.0 - - - +
231C ARG 4.2 2.5 + - - -
232C CYS* 4.0 16.4 - - - -
246C TYR* 1.3 81.1 - - - +
248C ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 4.5 1.4 - - - -
246A TYR* 3.4 17.9 + - - +
278A PHE* 3.2 23.7 - - - -
194C PHE* 3.7 18.4 - - + -
195C ILE 3.1 15.3 - - - +
196C TYR* 3.7 2.7 - - + -
230C PHE* 4.4 9.2 - - - +
246C TYR* 3.5 27.4 - - + +
247C SER* 1.3 78.7 + - - +
249C GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 249 (chain C).
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* 4.1 4.7 - - - -
196A TYR* 4.5 9.0 - - - -
194C PHE* 3.4 9.3 - - - -
195C ILE* 2.8 31.9 + - - -
230C PHE* 3.3 23.4 - - - -
248C ALA* 1.3 75.7 - - - +
250C ILE* 1.3 65.0 + - - -
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Residues in contact with ILE 250 (chain C).
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* 4.3 18.8 - - + -
148A GLN* 3.2 26.6 + - - +
172A PHE* 3.5 28.4 - - + -
194A PHE* 6.0 0.2 - - + -
196A TYR* 3.4 30.3 - - + +
282A LEU* 4.3 13.7 - - + -
192C TYR* 4.2 11.4 - - + -
193C PHE 3.2 11.2 - - - +
194C PHE* 4.2 12.6 - - + -
230C PHE* 3.7 4.9 - - - -
249C GLY* 1.3 78.8 - - - +
251C ALA* 1.3 67.1 + - - +
284C LEU* 3.8 30.3 - - + -
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 5.2 3.4 - - - -
192C TYR* 4.6 1.8 - - - -
193C PHE* 2.9 31.0 + - - +
195C ILE* 3.9 20.2 - - + -
229C LEU* 4.0 26.7 - - + -
230C PHE* 4.6 2.5 - - + -
250C ILE* 1.3 78.2 - - - +
252C LYS* 1.3 61.3 + - - +
253C LEU* 3.5 13.0 + - + +
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 5.8 2.5 - - + -
190C THR* 4.0 23.6 - - - -
191C GLY* 3.4 17.5 - - - +
192C TYR* 3.7 47.7 + - + -
214C ARG* 3.9 15.6 + - - -
251C ALA* 1.3 71.4 - - - +
253C LEU* 1.3 66.5 + - - +
254C GLU* 5.9 3.6 - - + -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 5.8 0.2 - - + -
187C VAL* 3.9 18.8 - - + -
190C THR* 3.2 5.2 - - - +
191C GLY 2.8 33.8 + - - -
193C PHE* 3.6 29.0 - - + -
195C ILE* 3.8 20.6 - - + -
214C ARG* 3.7 35.2 - - + +
229C LEU* 4.3 2.0 - - + -
251C ALA* 3.9 17.9 - - + +
252C LYS* 1.3 80.4 - - - +
254C GLU* 1.4 61.9 + - - +
257C ASP* 3.8 5.4 - - + +
259C LEU* 3.8 26.2 - - + -
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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