Contacts of the helix formed by residues 270 - 282 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ALA* 4.1 2.7 - - - -
263B GLU* 3.8 3.1 - - - -
266B TRP 3.9 11.9 - - - -
267B PRO 3.1 12.8 + - - -
268B GLN 2.8 7.2 + - - -
269B PHE* 1.3 78.2 - - - +
271B VAL* 1.3 65.0 + - - +
272B GLY 3.3 3.1 - - - -
273B ALA* 3.0 20.6 + - - +
274B GLU 3.6 2.3 + - - -
138D HIS* 4.0 8.3 - - - -
269D PHE* 4.1 6.6 - - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B CYS* 6.0 0.9 - - - -
133B ALA* 3.8 28.9 - - + -
134B ALA* 4.0 12.8 - - + +
212B HIS* 4.1 13.0 - - + +
238B MET* 4.1 33.0 - - + -
241B ILE* 4.8 5.8 - - + -
244B MET* 4.4 3.8 - - + -
263B GLU* 3.1 20.2 + - + +
270B GLY* 1.3 66.0 - - - -
272B GLY* 1.3 67.5 + - - +
274B GLU* 3.1 12.0 + - - +
275B ILE* 3.4 13.9 + - + +
269D PHE* 3.5 21.5 - - + -
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Residues in contact with GLY 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 3.5 27.6 - - - -
263B GLU* 2.6 25.5 + - - +
271B VAL* 1.3 72.0 - - - +
273B ALA* 1.3 64.8 + - - +
274B GLU 2.8 1.0 + - - -
275B ILE* 2.9 5.6 + - - +
276B CYS* 2.8 23.5 + - - +
294B ARG* 3.9 9.2 - - - -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 4.3 0.2 + - - -
269B PHE 4.3 1.8 - - - -
270B GLY 3.0 21.6 + - - +
272B GLY* 1.3 74.2 - - - +
274B GLU* 1.3 55.6 + - - +
276B CYS* 3.4 2.0 + - - +
277B ALA* 2.9 29.5 + - - +
294B ARG* 3.7 10.0 - - - +
273D ALA* 3.6 24.8 - - + +
274D GLU* 3.7 24.7 - - - +
277D ALA* 3.8 13.7 - - + -
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B MET* 4.6 6.7 - - + -
270B GLY 3.6 1.0 + - - -
271B VAL 3.1 2.7 + - - +
272B GLY 2.8 3.4 + - - -
273B ALA* 1.3 75.5 - - - +
275B ILE* 1.3 67.1 + - - +
278B ARG* 3.0 57.5 + - + +
268D GLN* 3.1 26.9 - - + +
269D PHE* 2.7 58.8 + - + +
273D ALA* 3.7 1.9 - - - +
294D ARG* 3.2 27.1 + - - -
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B VAL* 3.7 26.5 - - + -
238B MET* 3.8 22.9 - - + -
244B MET* 4.0 19.3 - - + -
246B MET* 3.4 21.1 - - + +
249B ILE* 4.3 13.7 - - + -
259B LEU* 4.3 14.1 - - + -
261B THR* 3.8 27.4 - - + -
271B VAL* 3.8 13.7 - - + +
272B GLY 2.9 6.1 + - - +
274B GLU* 1.3 76.4 - - - +
276B CYS* 1.3 58.4 + - - +
278B ARG* 4.4 0.4 - - - -
279B ILE* 2.9 26.7 + - - +
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Residues in contact with CYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU* 5.3 0.9 - - - -
261B THR* 4.8 10.5 - - - -
272B GLY 2.8 18.6 + - - +
273B ALA 3.6 4.3 - - - +
275B ILE* 1.3 82.5 - - - +
277B ALA* 1.3 62.8 + - - +
279B ILE* 3.5 3.4 + - - +
280B MET* 3.4 11.8 + - - +
292B ALA* 4.4 17.9 - - - -
293B VAL 4.9 0.7 - - - -
294B ARG* 4.0 22.9 - - - -
277D ALA* 4.0 16.8 - - + -
280D MET* 3.3 36.6 - - + +
281D GLU* 6.1 1.6 - - - -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA 2.9 17.8 + - - +
274B GLU 3.2 3.3 + - - +
275B ILE 3.2 0.2 - - - -
276B CYS* 1.3 76.4 - - - +
278B ARG* 1.3 65.6 + - - +
280B MET* 3.2 8.8 + - - +
281B GLU* 3.1 25.6 + - - +
273D ALA* 3.9 17.3 - - + +
276D CYS* 4.4 14.5 - - + -
294D ARG* 3.8 30.3 - - - +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ARG* 4.7 6.1 - - - +
244B MET* 4.3 20.0 + - - +
246B MET* 3.6 50.0 - - + +
250B GLU* 4.3 2.0 - - - +
274B GLU* 3.0 39.9 + - + +
275B ILE* 4.9 0.2 - - - -
277B ALA* 1.3 76.2 - - - +
279B ILE* 1.3 55.9 + - - +
281B GLU* 2.7 38.0 + - - +
282B GLY* 2.9 12.8 + - - -
268D GLN* 3.3 27.1 + - - +
294D ARG* 4.7 1.8 - - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B MET* 3.7 11.7 - - + -
249B ILE* 4.7 2.0 - - + +
250B GLU* 4.2 17.9 - - + +
253B VAL* 4.1 18.6 - - + -
259B LEU* 3.7 26.7 - - + -
275B ILE 2.9 18.6 + - - +
276B CYS* 3.8 7.0 - - - +
277B ALA 3.2 0.4 - - - -
278B ARG* 1.3 76.5 - - - +
280B MET* 1.3 62.9 + - - +
282B GLY* 3.6 5.5 + - - +
284B ALA* 3.8 27.6 - - + -
285B PHE* 3.5 21.5 + - - -
288B LEU* 3.8 29.4 - - + -
292B ALA* 5.0 0.2 - - + -
280D MET* 4.6 6.5 - - + -
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B CYS 3.4 8.3 + - - +
277B ALA 3.2 8.2 + - - +
278B ARG 3.2 0.4 - - - -
279B ILE* 1.3 81.8 - - - +
281B GLU* 1.3 60.7 + - + +
282B GLY 3.9 0.3 - - - +
285B PHE* 3.7 34.9 - - + +
276D CYS* 3.1 42.6 - - + +
279D ILE* 5.7 0.7 - - - -
280D MET* 4.5 18.4 - - + +
285D PHE* 4.8 1.6 - - - -
288D LEU* 4.8 11.4 - - - -
291D PRO* 3.2 32.6 - - + +
292D ALA* 3.7 33.4 - - + +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ARG* 2.8 46.2 + - - +
353A GLN* 3.1 37.2 + - + +
277B ALA 3.1 11.9 + - - +
278B ARG* 2.7 18.1 + - - +
280B MET* 1.3 71.2 - - - +
282B GLY* 1.3 65.4 + - - +
276D CYS* 6.4 0.4 - - - -
291D PRO* 5.2 4.1 - - - +
292D ALA 4.2 15.3 - - - +
293D VAL* 4.6 2.0 - - + -
294D ARG* 2.8 43.5 + - + +
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 3.4 11.9 - - - -
278B ARG 2.9 8.3 + - - -
279B ILE 3.6 2.3 + - - +
280B MET 3.2 1.3 - - - +
281B GLU* 1.3 84.1 - - - +
283B PRO* 1.3 77.3 - - - +
284B ALA 3.3 3.2 + - - -
285B PHE* 3.5 14.7 + - - +
286B ASN* 5.7 0.5 + - - -
291D PRO* 6.0 0.3 - - - +
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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