Contacts of the helix formed by residues 270 - 282 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134R ALA* 4.2 2.5 - - - -
263R GLU* 3.5 9.6 - - - -
266R TRP 4.0 5.8 - - - -
267R PRO 3.2 14.1 + - - -
268R GLN 3.0 5.7 - - - -
269R PHE* 1.3 79.0 - - - +
271R VAL* 1.3 65.7 + - - +
272R GLY 3.3 2.7 - - - -
273R ALA* 3.1 19.0 + - - +
274R GLU 3.3 3.6 + - - -
138T HIS* 4.2 6.7 - - - -
269T PHE* 3.7 8.5 - - - -
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Residues in contact with VAL 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R CYS* 6.2 0.4 - - - -
133R ALA* 3.8 29.2 - - + -
134R ALA* 4.3 7.1 - - + +
212R HIS* 4.1 10.3 - - + +
238R MET* 3.8 34.5 - - + -
241R ILE* 4.4 7.4 - - + -
244R MET* 4.6 5.4 - - + -
263R GLU* 3.2 19.9 + - + +
270R GLY* 1.3 69.7 - - - -
272R GLY* 1.3 65.0 + - - +
274R GLU* 3.0 13.2 + - - +
275R ILE* 3.1 15.9 + - + +
269T PHE* 3.5 24.8 - - + -
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Residues in contact with GLY 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261R THR* 3.3 29.6 - - - -
263R GLU* 2.6 24.3 + - - +
271R VAL* 1.3 72.7 - - - +
273R ALA* 1.3 63.3 + - - -
275R ILE* 3.0 5.6 + - - +
276R CYS* 3.0 24.6 + - - -
294R ARG* 3.7 10.5 - - - -
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Residues in contact with ALA 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263R GLU* 4.2 0.4 + - - -
269R PHE* 4.2 4.0 - - - -
270R GLY 3.1 22.6 + - - +
272R GLY* 1.3 73.9 - - - +
274R GLU* 1.3 62.9 + - - +
276R CYS* 3.2 2.1 + - - +
277R ALA* 3.0 19.4 + - - +
294R ARG* 3.5 23.7 - - - +
269T PHE* 5.8 0.2 - - - -
273T ALA* 3.7 23.0 - - + +
274T GLU* 3.8 11.9 - - - +
277T ALA* 3.8 12.8 - - + -
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Residues in contact with GLU 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244R MET* 3.9 24.5 - - + -
270R GLY 3.3 1.8 + - - -
271R VAL 3.0 9.8 + - - +
273R ALA* 1.3 76.9 - - - +
275R ILE* 1.3 65.1 - - - +
276R CYS 3.1 0.5 + - - -
277R ALA* 3.1 2.3 + - - -
278R ARG* 2.9 54.0 + - + +
267T PRO 3.7 4.0 - - - +
268T GLN* 3.1 21.7 - - - +
269T PHE* 2.7 48.5 + - + +
273T ALA* 3.8 5.4 - - - +
294T ARG* 3.7 16.5 + - - -
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Residues in contact with ILE 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210R VAL* 3.9 19.7 - - + -
238R MET* 3.8 31.9 - - + -
244R MET* 4.0 17.9 - - + -
246R MET* 3.9 18.4 - - + -
249R ILE* 4.1 11.9 - - + -
259R LEU* 4.2 16.4 - - + -
261R THR* 4.0 24.2 - - + -
271R VAL* 3.1 11.8 + - + +
272R GLY* 3.0 7.9 + - - +
274R GLU* 1.3 76.2 - - - +
276R CYS* 1.3 57.6 + - - +
278R ARG* 3.3 3.1 + - - +
279R ILE* 2.9 26.9 + - - +
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Residues in contact with CYS 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259R LEU* 5.7 0.4 - - - -
261R THR* 4.2 14.1 - - - -
272R GLY 3.0 16.1 + - - -
273R ALA 3.7 5.8 - - - +
275R ILE* 1.3 73.0 - - - +
277R ALA* 1.3 68.8 + - - +
279R ILE* 3.2 6.3 + - - +
280R MET* 3.0 24.6 + - - +
292R ALA* 4.4 14.4 - - - -
294R ARG* 3.8 22.7 - - - -
277T ALA* 3.8 13.5 - - + -
280T MET* 3.3 32.0 - - + +
281T GLU* 6.1 0.2 - - - -
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Residues in contact with ALA 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273R ALA 3.0 13.3 + - - +
274R GLU 3.8 6.1 - - - +
276R CYS* 1.3 77.3 - - - +
278R ARG* 1.3 62.6 + - - +
280R MET* 3.2 3.7 + - - +
281R GLU* 2.9 28.5 + - + +
273T ALA* 3.9 19.0 + - + +
276T CYS* 4.1 17.9 - - + +
294T ARG* 3.7 30.3 - - - +
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Residues in contact with ARG 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349Q ARG* 4.7 5.8 - - - +
244R MET* 4.2 20.0 + - - +
246R MET* 3.5 48.5 - - + +
250R GLU* 4.2 3.1 - - - +
274R GLU* 2.9 44.2 + - + +
275R ILE* 3.6 4.3 - - - +
277R ALA* 1.3 76.6 - - - +
279R ILE* 1.3 57.1 + - - +
281R GLU* 3.2 16.6 + - - +
282R GLY* 2.9 30.3 + - - -
268T GLN* 3.6 21.0 + - - +
294T ARG* 4.4 2.5 - - - +
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Residues in contact with ILE 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246R MET* 4.1 16.2 - - + -
249R ILE* 4.4 2.7 - - + -
250R GLU* 4.3 11.2 - - + -
253R VAL* 4.0 18.4 - - + -
259R LEU* 3.4 24.7 - - + -
275R ILE 2.9 17.8 + - - +
276R CYS* 3.2 6.3 + - - +
278R ARG* 1.3 77.9 - - - +
280R MET* 1.3 64.9 + - - +
282R GLY 3.5 6.6 + - - +
284R ALA* 4.0 22.2 + - + -
285R PHE* 3.5 20.8 + - - +
288R LEU* 3.9 33.9 - - + -
292R ALA* 5.3 2.9 - - + -
280T MET* 5.3 2.7 - - + -
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Residues in contact with MET 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276R CYS 3.0 11.4 + - - +
277R ALA* 3.4 7.6 - - - +
279R ILE* 1.3 80.7 - - - +
281R GLU* 1.3 61.5 + - - +
285R PHE* 3.5 40.1 - - + +
276T CYS* 3.5 44.2 - - + +
279T ILE* 5.1 1.6 - - + -
280T MET* 4.3 19.7 - - + +
285T PHE* 4.6 9.4 - - - -
288T LEU* 4.7 5.2 - - - -
291T PRO* 3.4 15.6 - - + +
292T ALA* 3.8 42.2 - - + +
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Residues in contact with GLU 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349Q ARG* 3.0 34.6 + - - -
353Q GLN* 3.1 37.0 + - + +
277R ALA* 2.9 21.5 + - - +
278R ARG* 3.9 11.3 - - - +
280R MET* 1.3 74.8 - - - +
282R GLY* 1.3 62.1 + - - +
276T CYS* 6.3 0.2 - - - -
291T PRO* 5.2 4.9 - - - +
292T ALA 4.1 16.6 - - - +
293T VAL* 4.6 2.2 - - - -
294T ARG* 2.8 49.2 + - + +
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Residues in contact with GLY 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250R GLU* 3.7 4.9 - - - -
278R ARG 2.9 16.3 + - - -
279R ILE 3.5 2.5 + - - +
280R MET 3.3 3.5 - - - +
281R GLU* 1.3 82.8 - - - +
283R PRO* 1.3 76.3 - - - +
284R ALA 3.3 3.4 + - - -
285R PHE* 3.6 11.6 + - - +
286R ASN* 5.6 0.5 + - - -
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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