Contacts of the strand formed by residues 191 - 201 (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 GLY 191 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F GLU 3.6 1.8 + - - -
190F THR* 1.3 77.9 - - - +
192F TYR* 1.3 66.1 + - - -
193F PHE* 3.5 10.4 - - - -
252F LYS* 3.4 8.9 - - - +
253F LEU 2.9 34.9 + - - +
283F LYS* 4.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 4.0 22.3 + - - -
220A PHE* 4.6 0.2 - + - -
254A GLU* 5.1 1.9 + - - -
172D PHE* 3.4 46.1 - + + -
173D LYS 4.6 2.1 + - - -
174D ARG* 3.4 39.4 - - + +
191F GLY* 1.3 75.9 - - - -
193F PHE* 1.3 62.2 + - - +
250F ILE* 4.3 5.4 - - + -
251F ALA 3.6 2.5 - - - -
252F LYS* 3.8 45.4 + - + +
283F LYS* 3.7 2.6 - - - +
284F LEU* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F ALA* 4.3 4.5 - - + -
178F LEU* 3.7 35.0 - - + -
187F VAL* 4.0 8.1 - - + -
189F GLU 3.4 25.8 - - - -
191F GLY* 3.5 26.5 - - - -
192F TYR* 1.3 77.1 - - - +
194F PHE* 1.3 62.2 + - - +
195F ILE* 3.5 18.7 + - + +
250F ILE* 3.4 5.9 - - - -
251F ALA 2.9 30.9 + - - +
253F LEU* 3.7 29.2 - - + -
281F ALA* 4.7 1.8 - - + -
282F LEU 3.3 5.2 - - - +
283F LYS* 3.5 44.6 - - + -
284F LEU* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D PHE* 3.9 32.3 - + - -
196D TYR* 5.3 3.1 - + - -
246D TYR* 4.5 3.1 - - - -
282D LEU* 5.4 5.4 - - + -
194E PHE* 3.8 26.5 - + - -
193F PHE* 1.3 70.6 - - - +
195F ILE* 1.4 56.2 + - - +
196F TYR* 3.8 23.8 - + + -
246F TYR* 4.0 5.8 - - - -
248F ALA* 3.6 26.9 - - + -
249F GLY* 3.4 20.0 - - - -
250F ILE* 4.2 12.6 - - + -
281F ALA* 3.3 2.3 - - - -
282F LEU* 2.7 62.1 + - + +
284F LEU* 4.3 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F PHE* 3.5 23.1 - - + +
194F PHE* 1.4 75.4 - - - +
196F TYR* 1.3 62.3 + - - +
212F ILE* 3.5 30.1 - - + -
229F LEU* 4.2 9.6 - - + -
230F PHE* 4.3 8.9 - - + -
248F ALA* 3.1 5.1 - - - +
249F GLY 2.8 33.4 + - - +
251F ALA* 3.8 23.6 - - + +
253F LEU* 4.0 19.5 - - + -
259F LEU* 3.8 23.6 - - + -
279F PHE* 4.1 7.4 - - + -
280F GLY 3.6 10.3 - - - +
281F ALA* 4.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E PHE* 5.4 2.0 - + - -
248E ALA 4.5 4.5 - - - -
249E GLY* 4.4 7.4 - - - -
250E ILE* 3.3 34.5 - - + +
147F LEU 4.3 1.4 + - - -
148F GLN* 2.7 41.9 + - - +
194F PHE* 3.8 22.7 - + + -
195F ILE* 1.3 73.0 - - - +
197F GLY* 1.3 58.5 + - - +
212F ILE* 3.8 6.1 - - - -
246F TYR* 3.4 24.5 - - + +
247F SER 3.6 6.5 - - - -
248F ALA* 3.6 6.1 - - + -
278F PHE* 4.2 25.1 - + - -
279F PHE* 3.3 8.1 - - - -
280F GLY* 2.9 60.2 + - - +
281F ALA* 3.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F TYR* 1.3 79.0 - - - +
198F GLN* 1.3 60.3 + - - -
210F HIS* 3.5 11.9 + - - -
212F ILE* 3.7 9.3 - - - +
246F TYR* 3.5 6.4 - - - -
247F SER 3.1 32.8 + - - +
261F LEU* 4.3 6.7 - - - -
278F PHE 3.4 11.9 - - - -
279F PHE* 4.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ARG 2.8 27.9 + - - -
246E TYR 4.0 1.7 - - - +
247E SER* 2.7 29.6 + - - -
197F GLY* 1.3 74.1 - - - +
199F VAL* 1.4 75.5 + - - +
210F HIS* 4.2 0.4 - - - -
244F SER* 4.0 14.7 + - - -
245F CYS 3.2 17.5 - - - +
246F TYR* 3.7 16.6 + - + +
261F LEU* 4.6 0.6 - - - +
276F VAL* 3.0 18.8 + - - +
277F THR* 3.2 2.1 - - - +
278F PHE* 2.9 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F VAL* 4.8 0.4 - - + -
198F GLN* 1.4 80.9 - - - +
200F LEU* 1.3 63.2 + - - +
201F TYR* 3.5 38.1 - - + +
210F HIS* 3.5 18.4 - - + +
244F SER* 3.3 1.8 - - - -
245F CYS 2.9 28.8 + - - -
261F LEU* 3.6 26.9 - - + -
263F ILE* 4.2 6.7 - - + -
270F ILE* 3.8 21.3 - - + -
276F VAL 3.9 3.6 - - - -
277F THR* 3.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ARG* 4.3 4.9 - - - +
233E ILE* 3.6 32.1 - - + -
199F VAL* 1.3 71.2 - - - +
201F TYR* 1.3 66.2 + - - +
202F THR* 4.3 9.9 - - + -
242F ASN* 3.9 10.5 - - + +
243F ASN 3.6 29.8 - - - +
244F SER* 3.7 6.5 - - - +
270F ILE* 3.2 7.3 - - - +
271F SER* 2.9 47.8 + - - +
276F VAL* 3.6 32.7 + - + +
277F THR* 3.3 7.5 + - - -
29K VAL 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F VAL* 3.5 34.4 - - + +
200F LEU* 1.3 73.1 - - - +
202F THR* 1.3 61.2 + - - +
203F ASP 3.5 0.7 - - - -
208F MET* 3.6 37.5 - - + -
209F GLY* 3.0 35.6 - - - -
210F HIS* 2.6 34.1 + - - +
234F GLN* 5.2 2.7 - - + -
236F MET* 3.4 21.5 - - + +
242F ASN* 3.4 5.2 - - - -
243F ASN 2.8 43.8 + - - +
245F CYS* 4.2 12.3 - - + -
263F ILE* 3.9 6.4 - - + +
269F GLN 3.8 1.8 - - - +
270F ILE* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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