Contacts of the helix formed by residues 245 - 257 (chain V) in PDB entry 3EXG
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 ASP 245 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196V GLY 3.5 15.4 + - - +
197V LYS* 3.2 19.7 + - - +
198V ALA* 2.8 43.0 + - + +
238V MET* 5.1 1.8 + - - +
240V THR 4.8 1.6 + - - -
243V PRO 3.5 1.8 + - - -
244V MET* 1.3 67.2 - - - +
246V MET* 1.3 62.4 + - - +
247V GLU* 3.7 7.3 + - - +
248V THR* 2.8 39.3 + - - -
249V ILE* 3.5 19.3 + - - +
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Residues in contact with MET 246 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244V MET* 2.9 21.1 + - + +
245V ASP* 1.3 73.8 + - - +
247V GLU* 1.3 63.2 + - - +
249V ILE* 3.1 21.9 + - + +
250V GLU* 3.1 37.6 + - + +
275V ILE* 3.7 12.1 - - + +
278V ARG* 3.6 63.9 - - + +
279V ILE* 3.6 38.6 - - + +
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Residues in contact with GLU 247 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197V LYS* 5.7 2.8 + - - -
245V ASP* 3.7 6.3 + - - +
246V MET* 1.3 73.7 - - - +
248V THR* 1.3 67.4 + - - +
249V ILE 3.1 0.3 + - - -
250V GLU* 3.1 16.5 + - - +
251V ALA* 2.9 26.5 + - - +
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Residues in contact with THR 248 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197V LYS* 5.3 1.2 - - - +
198V ALA* 3.7 16.6 + - + +
200V ILE* 4.2 26.2 - - + +
236V ILE* 4.3 19.3 - - + -
245V ASP* 2.8 37.6 + - - -
247V GLU* 1.3 77.7 - - - +
249V ILE* 1.3 61.8 + - - +
251V ALA* 3.5 6.2 - - - +
252V SER* 3.2 21.3 + - - -
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Residues in contact with ILE 249 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198V ALA* 5.6 1.3 - - + -
208V THR* 4.7 1.6 - - + -
210V VAL* 3.8 41.5 - - + -
236V ILE* 4.4 17.9 - - + -
238V MET* 5.0 7.4 - - + -
244V MET* 5.3 4.3 - - + -
245V ASP* 3.5 19.7 - - + +
246V MET* 3.1 31.3 + - + +
247V GLU 3.1 0.8 - - - -
248V THR* 1.3 73.2 - - - +
250V GLU* 1.3 69.6 + - - +
252V SER* 3.1 3.6 + - - -
253V VAL* 2.8 34.7 + - + +
259V LEU* 4.5 7.6 - - + -
275V ILE* 4.7 11.4 - - + -
279V ILE* 4.6 2.9 - - + -
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Residues in contact with GLU 250 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246V MET* 3.1 27.8 + - + +
247V GLU* 3.6 19.1 + - - +
249V ILE* 1.3 74.6 - - - +
251V ALA* 1.3 52.7 + - - +
253V VAL* 3.0 4.7 + - - +
254V MET* 2.8 44.0 + - + +
278V ARG 4.0 9.5 - - - +
279V ILE* 4.1 14.7 - - + +
282V GLY* 4.0 7.4 - - - -
283V PRO* 3.2 38.4 - - + +
284V ALA* 4.2 18.0 + - + +
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Residues in contact with ALA 251 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247V GLU 2.9 16.9 + - - +
248V THR* 3.5 7.9 - - - +
250V GLU* 1.3 73.0 - - - +
252V SER* 1.3 64.0 + - - +
254V MET* 3.0 30.8 + - + +
255V LYS* 3.0 13.3 + - - +
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Residues in contact with SER 252 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200V ILE* 5.0 2.0 - - - -
208V THR* 2.9 21.9 + - - +
234V GLU* 3.1 34.9 + - - +
236V ILE* 3.6 19.5 - - - -
248V THR 3.2 5.3 + - - -
249V ILE 3.1 8.8 + - - -
251V ALA* 1.3 78.5 - - - +
253V VAL* 1.3 57.5 + - - +
255V LYS* 3.3 6.0 + - - +
256V THR* 2.8 35.5 + - - +
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Residues in contact with VAL 253 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208V THR* 3.6 16.2 - - + +
249V ILE* 2.8 21.3 + - + +
250V GLU 3.5 7.9 - - - +
252V SER* 1.3 67.9 - - - +
254V MET* 1.3 61.0 + - - +
255V LYS 3.0 1.8 - - - -
256V THR* 4.2 1.8 - - - -
257V ASN* 2.6 34.4 + - - +
258V HIS 4.4 0.7 - - - +
259V LEU* 3.8 32.8 - - + -
279V ILE* 4.4 8.3 - - + -
284V ALA* 4.1 24.0 - - + +
287V PHE* 4.1 2.2 - - + +
288V LEU* 3.7 27.6 - - + -
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Residues in contact with MET 254 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250V GLU* 2.8 20.7 + - + +
251V ALA* 3.0 25.5 + - + +
253V VAL* 1.3 72.4 - - - +
255V LYS* 1.3 58.9 + - - +
257V ASN* 3.6 6.0 + - - -
283V PRO* 4.8 14.4 - - + -
284V ALA* 4.2 15.5 - - - -
287V PHE* 3.5 62.2 - - + -
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Residues in contact with LYS 255 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203V GLN* 3.9 10.5 + - - -
204V GLY 2.8 31.0 + - - +
205V THR* 3.9 24.6 - - + +
234V GLU* 2.8 27.8 + - - -
251V ALA 3.0 10.6 + - - +
252V SER* 3.7 5.8 - - - +
253V VAL 3.0 0.6 - - - -
254V MET* 1.3 81.4 - - - +
256V THR* 1.3 64.2 + - + +
257V ASN* 3.7 5.9 - - - +
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Residues in contact with THR 256 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204V GLY 4.2 9.6 - - - +
205V THR 3.8 9.8 - - - +
206V HIS 3.0 24.7 - - - +
207V ILE 3.5 8.7 - - - +
208V THR* 2.8 25.0 + - - +
234V GLU* 4.6 1.1 - - + -
252V SER* 2.8 20.8 + - - +
253V VAL 4.2 0.3 + - - -
255V LYS* 1.3 92.8 - - + +
257V ASN* 1.3 73.2 + - - +
258V HIS* 2.9 31.1 + - - -
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Residues in contact with ASN 257 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253V VAL* 2.6 25.8 + - - -
254V MET 3.6 14.5 + - - -
255V LYS 4.2 4.9 - - - +
256V THR* 1.3 73.9 + - - +
258V HIS* 1.3 65.2 + - + +
287V PHE* 2.8 33.0 + - - +
288V LEU* 3.3 7.7 - - - +
289V ASP* 2.6 52.3 + - - +
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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