Contacts of the helix formed by residues 270 - 281 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138N HIS* 4.0 2.7 - - - -
269N PHE* 3.5 13.1 - - - +
134P ALA* 3.8 9.6 - - - -
263P GLU* 3.9 3.8 - - - -
266P TRP 3.8 13.2 - - - -
267P PRO 3.1 11.6 + - - -
268P GLN 3.1 4.4 - - - -
269P PHE* 1.3 84.1 - - - +
271P VAL* 1.3 62.6 + - - -
272P GLY 3.5 2.2 - - - -
273P ALA* 3.5 14.9 - - - +
274P GLU 3.7 0.9 + - - -
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Residues in contact with VAL 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269N PHE* 3.6 24.2 - - + -
133P ALA* 4.2 17.3 - - + -
134P ALA* 4.5 6.7 - - + +
212P HIS* 4.1 17.5 - - + +
238P MET* 3.7 31.2 - - + -
241P ILE* 4.8 7.2 - - + -
244P MET* 4.4 4.3 - - + -
263P GLU* 3.3 21.3 + - + +
270P GLY* 1.3 67.4 - - - -
272P GLY* 1.3 66.8 + - - +
273P ALA 3.2 2.0 - - - -
274P GLU* 2.9 13.3 + - - +
275P ILE* 3.0 18.6 + - + +
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Residues in contact with GLY 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P THR* 3.3 28.9 + - - -
263P GLU* 3.0 17.9 + - - +
271P VAL* 1.3 76.0 - - - +
273P ALA* 1.3 56.8 + - - +
275P ILE* 3.3 4.3 + - - +
276P CYS* 2.8 34.5 + - - -
294P ARG* 3.4 11.9 - - - -
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Residues in contact with ALA 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273N ALA* 3.7 20.3 - - + +
274N GLU* 4.0 9.9 - - - +
277N ALA* 3.7 20.2 - - + -
263P GLU* 4.7 0.2 + - - -
269P PHE* 4.5 1.6 - - - +
270P GLY 3.5 16.7 + - - +
271P VAL 3.2 0.6 - - - -
272P GLY* 1.3 76.2 - - - +
274P GLU* 1.3 61.8 + - - +
276P CYS* 3.7 0.9 - - - +
277P ALA* 2.9 25.5 + - - +
294P ARG* 3.4 23.4 - - - +
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Residues in contact with GLU 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267N PRO 5.2 0.2 - - - -
268N GLN* 3.2 16.5 - - + +
269N PHE* 2.7 57.8 + - + +
273N ALA* 3.4 2.9 - - - +
294N ARG* 3.0 41.6 + - - -
244P MET* 3.8 17.0 - - + -
270P GLY 3.7 1.4 + - - -
271P VAL 2.9 5.1 + - - +
273P ALA* 1.3 78.8 - - - +
275P ILE* 1.3 63.3 + - - +
277P ALA* 3.5 0.2 - - - +
278P ARG* 2.9 51.4 + - - +
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Residues in contact with ILE 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P VAL* 4.0 14.1 - - + +
238P MET* 3.9 33.0 - - + -
244P MET* 4.0 20.0 - - + -
246P MET* 4.5 7.2 - - + -
249P ILE* 4.0 22.0 - - + -
259P LEU* 4.5 12.6 - - + -
261P THR* 3.8 29.6 - - + -
271P VAL* 3.0 16.3 + - + +
272P GLY* 3.8 5.4 - - - +
274P GLU* 1.3 74.7 - - - +
276P CYS* 1.3 57.0 + - - +
278P ARG* 3.2 7.4 + - - +
279P ILE* 2.8 28.6 + - + +
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Residues in contact with CYS 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N CYS* 5.5 0.4 - - - -
277N ALA* 4.0 17.7 - - + -
280N MET* 3.6 25.7 - - + +
281N GLU* 5.8 0.7 - - - -
259P LEU* 5.8 0.4 - - - -
261P THR* 4.9 7.0 - - - -
272P GLY 2.8 27.1 + - - +
273P ALA 3.7 3.6 - - - +
275P ILE* 1.3 71.1 - - - +
277P ALA* 1.3 64.6 + - - +
279P ILE* 3.5 5.5 + - - +
280P MET* 3.2 19.1 + - - +
292P ALA* 4.0 27.1 - - - -
293P VAL 5.1 0.2 - - - -
294P ARG* 3.7 24.9 - - - -
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Residues in contact with ALA 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273N ALA* 4.1 10.3 - - - +
276N CYS* 4.3 15.6 - - + +
294N ARG* 3.4 37.5 - - - +
273P ALA 2.9 17.5 + - - +
274P GLU 3.5 3.1 - - - +
276P CYS* 1.3 76.0 - - - +
278P ARG* 1.3 65.1 + - - +
280P MET* 3.1 5.5 + - - +
281P GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N GLN* 3.2 28.6 + - - +
294N ARG* 4.2 7.9 - - - +
349O ARG* 4.7 6.1 - - - +
244P MET* 4.1 20.6 + - - +
246P MET* 3.6 43.2 - - + +
250P GLU* 3.7 5.7 - - - +
274P GLU* 2.9 32.9 + - - +
275P ILE* 3.5 4.0 - - - +
277P ALA* 1.3 81.6 - - - +
279P ILE* 1.3 61.4 + - - +
281P GLU* 3.6 10.5 + - - +
282P GLY* 3.1 20.8 + - - -
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Residues in contact with ILE 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280N MET* 5.2 4.0 - - - -
246P MET* 3.7 18.2 - - + -
249P ILE* 4.3 4.3 - - + -
250P GLU* 4.5 3.6 - - + -
253P VAL* 4.0 16.8 - - + -
259P LEU* 3.3 33.0 - - + -
275P ILE* 2.8 19.3 + - + +
276P CYS* 3.6 7.2 - - - +
278P ARG* 1.3 75.8 - - - +
280P MET* 1.3 66.7 + - + +
282P GLY* 3.0 12.5 + - - -
284P ALA* 4.3 16.9 + - + -
285P PHE* 3.6 17.6 + - - +
288P LEU* 3.4 32.3 - - + -
292P ALA* 5.2 1.1 - - + -
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Residues in contact with MET 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N CYS* 3.5 50.9 - - + +
279N ILE* 4.6 3.4 - - + -
280N MET* 4.4 15.0 - - + +
285N PHE* 4.6 6.3 - - - -
288N LEU* 4.0 17.0 - - - -
291N PRO* 3.1 34.8 - - + +
292N ALA* 3.8 23.8 - - + +
276P CYS 3.2 6.8 + - - +
277P ALA 3.1 7.9 + - - +
279P ILE* 1.3 79.5 - - - +
281P GLU* 1.3 60.9 + - + +
282P GLY 3.9 0.5 - - - +
285P PHE* 3.3 41.7 - - + +
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Residues in contact with GLU 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N CYS* 6.2 1.8 - - - -
291N PRO* 5.1 1.8 - - - -
292N ALA 4.1 14.4 - - - +
293N VAL* 4.0 1.3 - - - -
294N ARG* 3.1 55.7 + - - +
349O ARG* 2.9 33.5 + - - -
353O GLN* 3.2 35.4 + - + +
277P ALA* 2.9 18.2 + - - +
278P ARG* 4.0 9.4 - - - +
280P MET* 1.3 77.5 - - + +
282P GLY* 1.3 62.2 + - - +
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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