Contacts of the strand formed by residues 191 - 201 (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 GLY 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLU 3.6 2.2 + - - -
190A THR* 1.3 78.8 - - - +
192A TYR* 1.4 67.0 + - - -
193A PHE* 3.6 10.0 - - - -
252A LYS* 3.4 8.0 - - - +
253A LEU 2.9 35.2 + - - +
283A LYS* 4.0 7.6 - - - -
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Residues in contact with TYR 192 (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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191A GLY* 1.4 76.6 - - - -
193A PHE* 1.3 63.5 + - - +
250A ILE* 4.3 2.7 - - + -
251A ALA 3.5 1.8 - - - -
252A LYS* 3.7 47.7 + - + +
283A LYS* 3.8 2.6 - - - +
284A LEU* 2.9 49.9 + - + +
172B PHE* 3.3 46.8 - + + -
173B LYS 4.8 1.2 + - - -
174B ARG* 3.8 35.6 - - + +
218F HIS* 3.8 24.4 + - - -
220F PHE* 4.4 0.2 - + - -
254F GLU* 5.0 2.1 + - - -
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Residues in contact with PHE 193 (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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177A ALA* 4.4 3.8 - - + -
178A LEU* 3.7 33.4 - - + -
187A VAL* 4.0 15.9 - - + -
189A GLU 3.4 25.4 - - - -
191A GLY* 3.6 25.4 - - - -
192A TYR* 1.3 75.0 - - - +
194A PHE* 1.3 62.9 + - - +
195A ILE* 3.4 24.1 + - + +
250A ILE* 3.4 6.8 - - - +
251A ALA 2.9 32.2 + - - +
253A LEU* 3.8 17.5 - - + -
281A ALA* 4.6 2.2 - - + -
282A LEU 3.2 7.0 - - - +
283A LYS* 3.6 44.9 - - + -
284A LEU* 4.6 0.2 - - - -
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Residues in contact with PHE 194 (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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193A PHE* 1.3 69.9 - - - +
195A ILE* 1.3 57.4 + - - +
196A TYR* 3.9 24.2 - + + -
246A TYR* 4.0 5.2 - - - -
248A ALA* 3.6 26.7 - - + -
249A GLY* 3.4 20.2 - - - -
250A ILE* 4.3 12.6 - - + +
281A ALA* 3.3 2.3 - - - -
282A LEU* 2.8 58.9 + - + +
284A LEU* 4.2 18.4 - - + +
194B PHE* 3.8 36.3 - + - -
196B TYR* 5.2 2.9 - + - -
246B TYR* 4.4 2.9 - - - -
282B LEU* 5.4 4.7 - - + -
194C PHE* 3.8 24.0 - + - -
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Residues in contact with ILE 195 (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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193A PHE* 3.4 24.2 - - + +
194A PHE* 1.3 76.4 - - - +
196A TYR* 1.3 62.9 + - - +
212A ILE* 3.6 30.3 - - + -
229A LEU* 4.3 9.6 - - + -
230A PHE* 4.3 8.8 - - + -
248A ALA* 3.1 5.2 - - - +
249A GLY 2.8 33.2 + - - +
251A ALA* 4.0 20.2 - - + +
253A LEU* 4.0 22.2 - - + -
259A LEU* 3.9 23.6 - - + -
279A PHE* 4.1 7.9 - - + -
280A GLY 3.6 10.3 - - - +
281A ALA* 4.2 3.1 - - + -
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Residues in contact with TYR 196 (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 4.3 1.2 + - - -
148A GLN* 2.6 42.6 + - - +
194A PHE* 3.9 22.9 - + + -
195A ILE* 1.3 73.9 - - - +
197A GLY* 1.3 59.4 + - - +
212A ILE* 3.8 5.8 - - - -
246A TYR* 3.4 24.0 - - + +
247A SER 3.6 6.3 - - - -
248A ALA* 3.7 5.6 - - + -
278A PHE* 4.2 24.7 - + - -
279A PHE* 3.3 7.4 - - - -
280A GLY* 2.9 60.1 + - - +
281A ALA* 3.7 6.3 - - - -
282A LEU 4.9 0.2 - - - -
194C PHE* 5.5 2.2 - + - -
248C ALA 4.5 5.4 - - - -
249C GLY* 4.5 7.0 - - - -
250C ILE* 3.4 33.1 - - + +
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Residues in contact with GLY 197 (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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196A TYR* 1.3 78.2 - - - +
198A GLN* 1.3 59.7 + - - -
210A HIS* 3.5 11.3 + - - -
212A ILE* 3.7 9.3 - - - +
246A TYR* 3.4 6.1 - - - -
247A SER 3.1 33.1 + - - +
261A LEU* 4.3 7.4 - - - -
278A PHE* 3.4 11.7 - - - -
279A PHE* 4.2 2.5 - - - -
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Residues in contact with GLN 198 (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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197A GLY* 1.3 74.6 - - - +
199A VAL* 1.3 76.8 + - - +
210A HIS* 4.2 0.4 - - - -
244A SER* 4.0 15.3 + - - -
245A CYS 3.2 17.0 - - - +
246A TYR* 3.7 17.3 + - + +
261A LEU* 4.6 0.6 - - - +
276A VAL* 3.0 19.2 + - - +
277A THR* 3.2 1.7 - - - +
278A PHE* 2.9 58.0 + - + +
231C ARG 2.8 28.1 + - - +
246C TYR 4.0 1.7 - - - +
247C SER* 2.7 29.5 + - - -
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Residues in contact with VAL 199 (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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166A VAL* 4.7 0.7 - - + -
198A GLN* 1.3 81.6 - - - +
200A LEU* 1.3 62.4 + - - +
201A TYR* 3.5 38.9 - - + +
210A HIS* 3.5 17.7 - - + +
244A SER* 3.3 1.2 - - - -
245A CYS 2.9 28.6 + - - -
261A LEU* 3.6 26.5 - - + -
263A ILE* 4.2 6.5 - - + -
270A ILE* 3.7 21.5 - - + -
276A VAL 3.9 3.4 - - - -
277A THR* 3.6 19.3 - - + +
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Residues in contact with LEU 200 (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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199A VAL* 1.3 70.6 - - - +
201A TYR* 1.3 65.8 + - - +
202A THR* 4.3 10.1 - - + -
242A ASN* 3.9 11.0 - - - +
243A ASN 3.6 29.4 - - - +
244A SER* 3.8 8.1 - - - +
270A ILE* 3.2 7.1 - - - +
271A SER* 2.9 48.7 + - - +
276A VAL* 3.6 38.9 + - + -
277A THR* 3.3 7.5 + - - -
231C ARG* 4.3 5.4 - - - +
233C ILE* 3.8 25.4 - - + -
29I VAL 5.6 1.6 - - - +
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Residues in contact with TYR 201 (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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199A VAL* 3.5 35.1 - - + +
200A LEU* 1.3 72.6 - - - +
202A THR* 1.3 61.4 + - - +
203A ASP 3.5 0.9 - - - +
208A MET* 3.6 36.6 - - + -
209A GLY* 3.0 36.1 - - - -
210A HIS* 2.6 34.0 + - - +
234A GLN* 5.2 2.7 - - + -
236A MET* 3.3 21.1 - - + +
242A ASN* 3.4 5.4 - - - -
243A ASN 2.8 44.7 + - - +
245A CYS* 4.2 12.6 - - + -
263A ILE* 3.9 6.1 - - + +
269A GLN 3.8 1.6 - - - +
270A ILE* 3.5 18.2 - - + -
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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