Contacts of the helix formed by residues 270 - 282 (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 GLY 270 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134V ALA* 3.8 12.6 - - - -
263V GLU* 3.8 9.4 - - - -
266V TRP 4.1 5.6 - - - -
267V PRO 3.3 12.8 + - - -
268V GLN 3.1 2.8 - - - -
269V PHE* 1.3 82.0 - - - +
271V VAL* 1.3 66.2 + - - +
272V GLY 3.3 2.7 - - - -
273V ALA* 3.2 18.4 - - - +
274V GLU 3.5 2.1 + - - -
138X HIS* 4.1 3.8 - - - -
269X PHE* 3.8 5.1 - - - -
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Residues in contact with VAL 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131V CYS* 6.2 0.2 - - - -
133V ALA* 4.1 19.3 - - + -
134V ALA* 4.0 8.3 - - + +
212V HIS* 4.0 20.2 - - + +
238V MET* 3.8 32.8 - - + -
241V ILE* 4.4 8.7 - - + -
244V MET* 4.9 4.0 - - + -
263V GLU* 3.1 18.8 + - + +
270V GLY* 1.3 68.9 - - - -
272V GLY* 1.3 65.3 + - - +
274V GLU* 3.0 13.9 + - - +
275V ILE* 3.0 20.6 + - + +
269X PHE* 3.6 21.3 - - + -
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Residues in contact with GLY 272 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261V THR* 3.8 23.8 - - - -
263V GLU* 2.8 22.8 + - - +
271V VAL* 1.3 69.8 - - - +
273V ALA* 1.3 68.2 + - - +
275V ILE* 2.6 21.1 + - - +
276V CYS* 2.7 12.7 + - - +
294V ARG* 3.7 10.1 - - - -
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Residues in contact with ALA 273 (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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269V PHE* 4.4 2.2 - - - -
270V GLY 3.2 18.5 + - - +
272V GLY* 1.3 71.8 - - - +
274V GLU* 1.3 52.5 + - - +
276V CYS* 3.0 2.8 + - - +
277V ALA* 2.7 37.1 + - - +
294V ARG* 3.2 15.4 - - - +
269X PHE* 5.7 0.2 - - - -
273X ALA* 4.0 24.3 - - + +
274X GLU* 3.9 22.4 - - - +
277X ALA* 3.7 15.5 - - - -
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Residues in contact with GLU 274 (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* 3.5 24.0 - - + -
270V GLY 3.5 0.6 + - - -
271V VAL 3.0 9.7 + - - +
272V GLY 2.7 4.9 + - - -
273V ALA* 1.3 78.1 - - - +
275V ILE* 1.3 57.4 + - - +
277V ALA* 3.2 1.3 + - - +
278V ARG* 2.7 61.5 + - - +
268X GLN* 3.3 15.7 - - + +
269X PHE* 3.0 38.6 + - + +
273X ALA* 4.2 3.8 - - - -
294X ARG* 2.9 31.5 + - - -
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Residues in contact with ILE 275 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210V VAL* 3.8 26.0 - - + -
238V MET* 4.1 8.7 - - + -
244V MET* 4.4 13.9 - - - -
246V MET* 4.4 14.1 - - + -
249V ILE* 4.7 12.6 - - + -
259V LEU* 4.5 11.0 - - + -
261V THR* 3.8 24.9 - - + -
271V VAL* 3.2 33.0 - - + +
272V GLY* 2.6 11.8 + - - +
274V GLU* 1.3 72.2 - - - +
276V CYS* 1.3 61.2 + - - +
278V ARG* 3.5 6.0 + - - +
279V ILE* 3.0 24.5 + - - +
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Residues in contact with CYS 276 (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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259V LEU* 5.5 1.1 - - - -
261V THR* 4.9 7.4 - - - -
272V GLY 2.7 16.9 + - - -
273V ALA 3.4 7.0 - - - +
275V ILE* 1.3 73.8 - - - +
277V ALA* 1.3 67.8 + - - +
279V ILE* 3.0 5.8 + - - +
280V MET* 2.9 25.3 + - - +
292V ALA* 3.9 27.4 - - - -
293V VAL 5.4 0.4 - - - -
294V ARG* 4.3 21.1 - - - -
277X ALA* 4.0 16.4 - - + -
280X MET* 3.5 20.4 - - + +
281X GLU* 6.0 1.8 - - - -
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Residues in contact with ALA 277 (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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273V ALA 2.7 20.4 + - - +
274V GLU 3.7 1.8 - - - +
276V CYS* 1.3 74.1 - - - +
278V ARG* 1.3 58.7 + - - +
280V MET* 3.3 3.8 + - - +
281V GLU* 2.8 35.0 + - - +
273X ALA* 3.9 11.4 - - - -
276X CYS* 4.3 17.7 - - + +
294X ARG* 3.5 37.2 - - - +
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Residues in contact with ARG 278 (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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349U ARG* 5.4 3.4 - - - +
244V MET* 4.3 21.4 + - - +
246V MET* 3.6 49.3 - - + +
250V GLU* 4.0 5.9 - - - +
274V GLU* 2.7 49.2 + - + +
275V ILE 3.7 0.4 - - - +
277V ALA* 1.3 78.3 - - - +
279V ILE* 1.3 61.2 + - - +
281V GLU* 3.8 15.6 - - - +
282V GLY* 3.1 21.3 + - - -
268X GLN* 3.8 18.2 + - - +
294X ARG* 4.4 3.1 - - - +
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Residues in contact with ILE 279 (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* 3.6 18.2 - - + -
249V ILE* 4.6 2.2 - - + -
250V GLU* 4.1 15.7 - - + +
253V VAL* 4.4 9.6 - - + -
259V LEU* 3.6 27.8 - - + -
275V ILE 3.0 19.3 + - - +
276V CYS* 3.0 6.0 + - - +
278V ARG* 1.3 75.9 - - - +
280V MET* 1.3 67.9 + - + +
282V GLY* 3.2 16.8 + - - +
284V ALA* 3.6 27.7 - - + +
285V PHE* 3.6 10.5 + - - -
288V LEU* 4.0 30.1 - - + -
292V ALA* 5.4 3.1 - - + -
280X MET* 5.4 1.6 - - + -
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Residues in contact with MET 280 (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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276V CYS 2.9 14.0 + - - +
277V ALA 3.7 2.9 - - - +
279V ILE* 1.3 80.5 - - - +
281V GLU* 1.3 60.0 + - - +
282V GLY 3.3 1.4 + - - +
285V PHE* 3.4 47.9 - - + +
276X CYS* 3.6 39.5 - - + +
279X ILE* 4.9 3.4 - - + -
280X MET* 4.6 18.4 - - + +
285X PHE* 4.9 1.8 - - - -
288X LEU* 4.6 10.5 - - - -
291X PRO* 3.4 13.8 - - + +
292X ALA* 3.5 48.9 - - + +
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Residues in contact with GLU 281 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349U ARG* 2.7 45.0 + - - -
353U GLN* 3.0 40.1 + - + +
277V ALA* 2.8 18.1 + - + +
278V ARG* 3.8 11.8 - - - +
279V ILE 3.2 0.4 - - - -
280V MET* 1.3 77.6 - - - +
282V GLY* 1.3 60.0 + - - +
276X CYS* 6.1 1.1 - - - -
291X PRO* 5.1 3.7 - - - +
292X ALA 4.1 16.6 - - - +
293X VAL* 5.5 1.1 - - - -
294X ARG* 3.0 44.9 + - + +
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Residues in contact with GLY 282 (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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250V GLU* 4.0 2.0 - - - -
278V ARG 3.1 14.1 + - - -
279V ILE 3.2 2.2 + - - +
280V MET 3.1 1.3 - - - +
281V GLU* 1.3 84.0 - - - +
283V PRO* 1.4 75.6 - - - +
284V ALA 3.2 3.3 + - - -
285V PHE* 3.3 16.6 + - - +
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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