Contacts of the strand formed by residues 191 - 201 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B GLU 3.7 2.2 + - - -
190B THR* 1.3 77.6 - - - +
192B TYR* 1.3 70.3 + - - -
193B PHE* 3.7 8.9 - - - -
252B LYS* 3.4 5.2 - - - +
253B LEU 2.9 33.4 + - - +
283B LYS* 4.7 8.7 - - - -
174C ARG* 6.3 0.2 - - - -
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLY* 1.3 78.2 - - - -
193B PHE* 1.3 66.0 + - - +
250B ILE* 4.3 3.8 - - + -
251B ALA 3.8 2.2 - - - -
252B LYS* 3.9 26.1 - - + +
283B LYS* 3.7 3.2 - - - +
284B LEU* 2.9 49.6 + - + +
146C CYS* 4.1 6.5 - - - -
172C PHE* 3.6 41.2 - + - +
173C LYS 4.3 6.6 + - - -
174C ARG* 3.3 52.7 - - + +
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ALA* 4.3 4.9 - - + -
178B LEU* 3.7 33.0 - - + -
187B VAL* 3.8 9.0 - - + -
189B GLU 3.3 27.1 - - - -
191B GLY 3.7 23.3 - - - -
192B TYR* 1.3 77.8 - - - +
194B PHE* 1.3 60.8 + - - +
195B ILE* 3.5 12.0 + - + +
250B ILE* 3.2 8.3 - - - +
251B ALA 2.9 33.3 + - - +
253B LEU* 3.7 38.4 - - + -
281B ALA* 4.7 1.1 - - + -
282B LEU 3.3 8.7 - - - +
283B LYS* 3.5 39.9 - - + -
284B LEU* 4.5 0.7 - - - -
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Residues in contact with PHE 194 (chain B).
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 26.0 - + - -
193B PHE* 1.3 71.0 - - - +
195B ILE* 1.3 57.8 + - - +
196B TYR* 3.9 20.4 + + + -
246B TYR* 4.0 7.6 - - - -
248B ALA* 3.6 28.0 - - + -
249B GLY* 3.5 19.1 - - - -
250B ILE* 4.3 12.1 - - + +
280B GLY 4.3 0.2 - - - +
281B ALA* 3.3 2.8 - - - -
282B LEU* 2.8 53.2 + - + +
284B LEU* 4.3 17.6 - - + +
194C PHE* 3.6 37.7 - + - -
196C TYR* 5.2 2.0 - + - -
246C TYR* 4.0 4.5 - - - -
282C LEU* 5.5 2.9 - - + -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B PHE* 3.7 22.4 - - + +
194B PHE* 1.3 75.6 - - - +
196B TYR* 1.3 63.0 + - - +
212B ILE* 3.6 28.7 - - + -
229B LEU* 4.3 9.4 - - + -
230B PHE* 4.3 8.4 - - + -
248B ALA* 3.1 5.5 - - - +
249B GLY 2.9 32.8 + - - +
251B ALA* 3.8 24.5 - - + +
253B LEU* 3.9 18.8 - - + -
259B LEU* 3.8 23.3 - - + -
279B PHE* 4.1 8.5 - - + -
280B GLY 3.5 10.8 - - - +
281B ALA* 4.2 2.9 - - + -
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 5.2 2.7 - + - -
248A ALA 4.3 4.5 - - - -
249A GLY* 4.2 6.3 - - - -
250A ILE* 3.3 33.6 - - + +
147B LEU 4.3 0.5 + - - -
148B GLN* 2.7 40.3 + - - +
194B PHE* 3.9 23.8 - + + -
195B ILE* 1.3 73.7 - - - +
197B GLY* 1.3 59.5 + - - +
212B ILE* 3.8 6.1 - - - -
246B TYR* 3.4 23.1 - - + +
247B SER 3.6 6.1 - - - -
248B ALA* 3.7 5.6 - - + -
278B PHE* 4.2 25.1 - + - -
279B PHE* 3.3 8.0 - - - -
280B GLY* 2.9 60.5 + - - +
281B ALA* 3.8 6.3 - - - -
282B LEU 5.0 0.2 - - - -
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B TYR* 1.3 79.7 - - - +
198B GLN* 1.3 59.5 + - - -
210B HIS* 3.5 11.3 + - - -
212B ILE* 3.7 9.3 - - - +
246B TYR* 3.4 6.5 - - - -
247B SER 3.1 32.1 + - - +
261B LEU* 4.3 7.4 - - - -
278B PHE* 3.4 12.1 - - - -
279B PHE* 4.2 1.8 - - - -
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ARG 2.9 28.1 + - - -
232A CYS* 4.7 0.2 - - - -
246A TYR 4.0 1.9 - - - +
247A SER* 2.7 30.0 + - - -
197B GLY* 1.3 73.5 - - - +
199B VAL* 1.3 74.7 + - - +
210B HIS* 4.3 0.2 - - - -
244B SER* 4.0 15.8 + - - -
245B CYS 3.2 16.6 - - - +
246B TYR* 3.7 17.1 + - + +
261B LEU* 4.7 0.6 - - - +
276B VAL 3.0 18.9 + - - +
277B THR* 3.2 2.1 - - - +
278B PHE* 2.9 57.1 + - + +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 4.7 0.7 - - + -
198B GLN* 1.3 79.5 - - - +
200B LEU* 1.3 63.2 + - - +
201B TYR* 3.5 38.9 - - + +
210B HIS* 3.5 17.9 - - + +
244B SER* 3.3 1.0 - - - -
245B CYS 2.9 28.2 + - - -
261B LEU* 3.6 27.4 - - + -
263B ILE* 4.1 7.0 - - + -
270B ILE* 3.8 21.8 - - + -
276B VAL 3.9 3.6 - - - -
277B THR* 3.6 19.5 - - + +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ARG* 4.5 5.2 - - - +
233A ILE* 3.8 24.9 - - + -
199B VAL* 1.3 70.8 - - - +
201B TYR* 1.3 62.0 + - - +
202B THR* 4.3 9.9 - - + -
242B ASN* 3.9 11.0 - - + +
243B ASN 3.6 33.7 - - - +
244B SER* 3.8 7.4 - - - +
270B ILE* 3.2 7.6 - - - +
271B SER* 2.9 48.8 + - - +
276B VAL* 3.6 39.0 + - + +
277B THR* 3.2 7.7 + - - -
29G VAL 6.0 0.9 - - - +
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.5 33.7 - - + +
200B LEU* 1.3 71.4 - - - +
202B THR* 1.3 61.6 + - - +
203B ASP 3.5 0.7 - - - -
208B MET* 3.6 37.0 - - + -
209B GLY* 3.0 35.8 - - - -
210B HIS* 2.6 33.8 + - - +
234B GLN* 5.2 2.0 - - + -
236B MET* 3.3 20.8 - - + +
242B ASN* 3.4 5.4 - - - -
243B ASN 2.8 43.4 + - - +
245B CYS* 4.2 13.0 - - + -
263B ILE* 4.0 6.6 - - + +
269B GLN 3.8 1.8 - - - +
270B ILE* 3.5 18.4 - - + -
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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