Contacts of the strand formed by residues 191 - 201 (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 GLY 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C THR* 1.3 77.8 - - - +
192C TYR* 1.4 68.7 + - - -
193C PHE* 3.3 11.6 - - - -
252C LYS* 3.4 8.6 - - - +
253C LEU 2.8 32.1 + - - -
283C LYS* 4.1 9.9 - - - -
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Residues in contact with TYR 192 (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* 4.8 0.2 - - - -
172A PHE* 3.4 50.2 - + + +
173A LYS 4.7 3.6 + - - -
174A ARG* 3.3 46.8 - - + +
191C GLY* 1.4 76.3 - - - -
193C PHE* 1.3 59.9 + - - +
250C ILE* 4.2 5.2 - - + -
251C ALA 3.8 1.6 - - - -
252C LYS* 3.7 45.0 + - + +
283C LYS* 3.6 5.0 - - - +
284C LEU* 2.8 50.6 + - + +
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Residues in contact with PHE 193 (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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177C ALA* 4.3 4.5 - - + -
178C LEU* 4.0 30.1 - - + -
187C VAL* 4.0 7.9 - - + -
189C GLU 3.3 26.7 - - - -
191C GLY 3.3 26.7 - - - -
192C TYR* 1.3 74.7 - - - +
194C PHE* 1.4 60.5 + - - +
195C ILE* 3.9 10.5 + - + +
249C GLY 3.8 0.2 - - - +
250C ILE* 3.2 7.9 - - - +
251C ALA 2.9 35.0 + - - +
253C LEU* 3.6 37.9 - - + -
281C ALA* 4.9 1.3 - - + -
282C LEU 3.1 7.9 - - - +
283C LYS* 3.6 45.8 - - + -
284C LEU* 4.4 1.1 - - - -
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Residues in contact with PHE 194 (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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194A PHE* 3.8 27.8 - + - -
196A TYR* 5.5 2.2 - + - -
246A TYR* 4.5 3.4 - - - -
282A LEU* 5.5 4.3 - - + -
194B PHE* 3.6 37.7 - + - -
193C PHE* 1.4 68.9 - - - +
195C ILE* 1.3 58.4 + - - +
196C TYR* 4.0 20.8 - + + -
246C TYR* 4.0 2.0 - - - -
248C ALA* 3.7 26.9 - - + -
249C GLY* 3.4 19.5 - - - -
250C ILE* 4.2 13.0 - - + +
281C ALA* 3.3 2.1 - - - -
282C LEU* 2.7 56.6 + - + +
284C LEU* 4.1 18.4 - - + +
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Residues in contact with ILE 195 (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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193C PHE* 4.0 15.3 - - + +
194C PHE* 1.3 76.2 - - - +
196C TYR* 1.3 62.1 + - - +
212C ILE* 3.6 29.8 - - + -
229C LEU* 4.3 9.2 - - + -
230C PHE* 4.3 8.8 - - + -
248C ALA* 3.1 5.6 - - - +
249C GLY 2.8 32.8 + - - +
251C ALA* 3.9 24.0 - - + +
253C LEU* 3.8 24.2 - - + -
259C LEU* 3.8 22.9 - - + -
279C PHE* 4.1 7.9 - - + -
280C GLY 3.6 11.7 - - - +
281C ALA* 4.2 3.6 - - + -
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Residues in contact with TYR 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 5.2 1.1 - + - -
248B ALA 4.4 4.9 - - - -
249B GLY* 4.1 9.2 - - - -
250B ILE* 3.4 36.7 - - + +
147C LEU 4.2 0.9 + - - -
148C GLN* 2.7 42.1 + - - +
194C PHE* 4.0 21.3 - + + -
195C ILE* 1.3 73.9 - - - +
197C GLY* 1.3 60.7 + - - +
212C ILE* 3.9 6.1 - - - -
246C TYR* 3.4 24.9 - - + +
247C SER 3.6 5.8 - - - -
248C ALA* 3.7 4.5 - - + -
278C PHE* 4.2 22.0 - + - -
279C PHE* 3.4 6.8 - - - -
280C GLY* 2.9 62.7 + - - +
281C ALA* 3.7 4.3 - - - -
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Residues in contact with GLY 197 (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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196C TYR* 1.3 79.5 - - - +
198C GLN* 1.3 60.1 + - - -
210C HIS* 3.5 11.9 + - - -
212C ILE* 3.7 9.4 - - - +
246C TYR* 3.4 6.1 - - - -
247C SER 3.1 33.2 + - - +
261C LEU* 4.3 7.0 - - - -
278C PHE* 3.4 10.8 - - - -
279C PHE* 4.2 2.7 - - - -
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Residues in contact with GLN 198 (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 2.9 27.5 + - - -
246B TYR 4.0 2.1 - - - +
247B SER* 2.6 29.8 + - - -
168C TRP* 4.9 0.2 - - - -
197C GLY* 1.3 73.7 - - - +
199C VAL* 1.3 75.3 + - - +
210C HIS* 4.2 0.4 - - - -
244C SER* 4.0 14.5 + - - -
245C CYS 3.2 16.4 - - - +
246C TYR* 3.7 15.9 - - + +
261C LEU* 4.6 0.6 - - - +
276C VAL 3.0 18.9 + - - +
277C THR* 3.2 1.7 - - - +
278C PHE* 2.9 59.5 + - + +
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Residues in contact with VAL 199 (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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166C VAL* 4.8 0.2 - - + -
198C GLN* 1.3 79.9 - - - +
200C LEU* 1.3 63.4 + - - +
201C TYR* 3.5 38.5 - - + +
210C HIS* 3.5 17.2 - - + +
244C SER* 3.3 2.1 - - - -
245C CYS 2.9 28.2 + - - -
261C LEU* 3.6 27.4 - - + -
263C ILE* 4.2 6.5 - - + -
270C ILE* 3.8 21.3 - - + -
276C VAL 3.9 3.6 - - - -
277C THR* 3.7 19.5 - - + +
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Residues in contact with LEU 200 (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* 4.2 5.2 - - - +
233B ILE* 3.8 25.6 - - + -
199C VAL* 1.3 71.3 - - - +
201C TYR* 1.3 64.8 - - - +
202C THR* 4.3 9.4 - - + -
242C ASN* 3.9 12.1 - - + +
243C ASN 3.6 28.7 - - - +
244C SER* 3.8 7.2 - - - +
270C ILE* 3.3 7.3 - - - +
271C SER* 2.9 49.1 + - - +
276C VAL* 3.6 39.0 + - + -
277C THR* 3.3 7.7 + - - -
29H VAL 5.9 1.3 - - - +
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Residues in contact with TYR 201 (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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199C VAL* 3.5 33.5 - - + +
200C LEU* 1.3 71.4 - - - +
202C THR* 1.3 61.2 - - - +
203C ASP 3.5 1.1 - - - +
208C MET* 3.6 36.1 - - + -
209C GLY* 2.9 35.9 + - - -
210C HIS* 2.6 33.7 + - - +
234C GLN* 5.2 2.5 - - + -
236C MET* 3.3 20.9 - - + +
242C ASN* 3.4 5.4 - - - -
243C ASN 2.8 45.0 + - - +
245C CYS* 4.2 12.8 - - + -
263C ILE* 4.0 6.1 - - + +
269C GLN 3.8 2.0 - - - +
270C ILE* 3.5 18.8 - - + -
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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