Contacts of the strand formed by residues 243 - 253 (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 ASN 243 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499D SO4 3.2 16.3 + - - -
233E ILE 3.5 2.0 - - - -
234E GLN* 3.4 6.8 - - - +
235E ASN* 2.8 44.9 + - - -
200F LEU* 3.6 3.5 - - - +
201F TYR* 2.8 39.1 + - - +
234F GLN* 3.9 19.1 - - + +
235F ASN 2.9 27.5 + - - -
236F MET* 3.5 20.0 - - - +
237F PRO* 4.2 1.8 - - - +
242F ASN* 1.3 70.1 - - - +
244F SER* 1.3 60.8 + - - +
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Residues in contact with SER 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ARG 4.6 0.9 - - - -
232E CYS* 3.4 17.1 - - - -
233E ILE* 2.9 34.8 + - - -
234E GLN* 3.4 15.6 - - - +
245E CYS* 3.9 2.6 - - - -
198F GLN* 4.0 20.9 + - - -
199F VAL 3.3 10.5 - - - -
200F LEU* 3.7 15.7 - - - +
234F GLN* 4.1 4.0 + - - +
243F ASN* 1.3 74.5 - - - +
245F CYS* 1.3 62.0 + - - +
246F TYR 4.3 0.2 - - - -
276F VAL* 5.0 0.9 - - - -
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Residues in contact with CYS 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D SER* 3.9 12.6 - - - -
198F GLN* 3.2 23.3 - - - -
199F VAL 2.9 9.2 + - - -
201F TYR* 4.2 14.4 - - + -
209F GLY* 5.6 0.2 - - - -
210F HIS* 3.2 11.0 - - + -
232F CYS* 2.0 49.4 - - + -
233F ILE 4.0 1.8 - - - -
234F GLN* 3.7 29.8 - - + +
243F ASN 4.1 0.2 + - - -
244F SER* 1.3 73.9 - - - +
246F TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.9 0.5 - - - +
246D TYR* 3.5 55.2 + + + +
194E PHE* 4.4 2.3 - - - -
246E TYR* 3.6 32.5 + + + +
248E ALA* 3.3 38.9 + - + +
194F PHE* 4.0 9.5 - - - -
196F TYR* 3.4 27.2 - - + +
197F GLY 3.5 10.3 - - - -
198F GLN* 3.7 22.6 + - + +
232F CYS* 3.4 10.1 - - - -
244F SER 4.3 0.6 - - - -
245F CYS* 1.3 77.5 - - - +
247F SER* 1.3 60.2 + - - +
248F ALA* 3.5 23.1 - - + +
278F PHE* 4.2 4.3 - + - -
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Residues in contact with SER 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 2.7 30.6 + - - -
246D TYR* 4.4 1.6 - - - -
278D PHE* 3.7 8.7 - - - -
196F TYR* 3.6 0.7 - - - -
197F GLY 3.1 31.7 + - - +
210F HIS* 5.0 4.5 - - - -
212F ILE* 3.8 8.2 - - - +
230F PHE* 3.8 15.0 - - - +
231F ARG* 4.3 1.0 + - - -
232F CYS* 4.0 17.9 - - - -
246F TYR* 1.3 80.8 - - - +
248F ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TYR* 4.3 1.2 - - - -
246D TYR* 3.3 17.2 + - - +
278D PHE* 3.2 25.9 - - - -
194F PHE* 3.6 14.4 - - + -
195F ILE 3.1 16.2 - - - +
196F TYR* 3.6 5.6 - - + -
212F ILE* 5.2 0.2 - - - -
230F PHE* 4.4 6.7 - - - +
246F TYR* 3.5 27.1 - - + +
247F SER* 1.3 78.4 + - - +
249F GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLN* 3.9 4.9 - - - -
196D TYR* 4.2 10.8 - - - -
278D PHE* 4.7 0.2 - - - -
193F PHE 3.7 0.2 - - - +
194F PHE* 3.4 8.4 - - - -
195F ILE* 2.8 31.4 + - - +
230F PHE* 3.4 22.5 - - - -
248F ALA* 1.3 74.4 - - - +
250F ILE* 1.3 64.9 + - - -
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Residues in contact with ILE 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 4.0 4.0 - - - -
146D CYS* 4.0 24.2 - - + -
147D LEU 5.7 0.2 - - - +
148D GLN* 2.9 29.3 + - - +
172D PHE* 3.4 28.7 - - + -
196D TYR* 3.3 28.7 - - + +
281D ALA 4.9 0.2 - - - +
282D LEU* 4.3 13.2 - - + -
192F TYR* 4.3 11.0 - - + -
193F PHE 3.4 9.4 - - - +
194F PHE* 4.2 13.7 - - + -
230F PHE* 3.7 5.2 - - - -
249F GLY* 1.3 78.1 - - - +
251F ALA* 1.3 65.5 + - - +
284F LEU* 3.8 26.5 - - + -
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Residues in contact with ALA 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.8 10.5 - - + -
192F TYR* 4.4 4.7 - - - -
193F PHE* 2.9 30.8 + - - +
195F ILE* 3.8 19.1 - - + -
229F LEU* 3.9 30.7 - - + -
230F PHE* 4.6 2.0 - - + -
250F ILE* 1.3 77.3 - - - +
252F LYS* 1.4 66.6 + - - +
253F LEU* 3.6 7.8 + - + +
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Residues in contact with LYS 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.6 28.1 - - + -
254A GLU* 4.0 25.5 + - - +
190F THR* 3.8 25.4 - - - -
191F GLY* 3.4 19.7 - - - +
192F TYR* 3.8 43.0 + - + +
214F ARG* 3.8 17.6 + - - +
251F ALA* 1.4 72.7 - - - +
253F LEU* 1.4 65.8 + - - +
254F GLU* 5.3 6.5 - - + -
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Residues in contact with LEU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F VAL* 3.7 28.5 - - + -
190F THR* 3.4 5.0 - - - +
191F GLY 2.9 33.6 + - - +
193F PHE* 3.7 31.6 - - + -
195F ILE* 4.0 5.8 - - + -
214F ARG* 3.5 36.3 - - + +
229F LEU* 4.5 8.7 - - + -
251F ALA* 4.1 6.7 - - + +
252F LYS* 1.4 77.3 - - - +
254F GLU* 1.3 61.2 + - - +
257F ASP* 3.7 5.8 - - + +
259F LEU* 3.7 31.4 - - + -
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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