Contacts of the helix formed by residues 269 - 286 (chain Y) 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 269 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268Y PRO* 1.3 73.2 - - - +
270Y VAL* 1.3 51.1 + - - +
271Y ALA* 2.8 6.2 + - - -
272Y TYR* 2.7 37.0 + - - +
273Y ARG* 3.7 2.4 + - - +
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Residues in contact with VAL 270 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267Y ASP 4.6 1.3 - - - +
268Y PRO* 2.9 44.3 - - + +
269Y GLY* 1.3 73.9 - - - +
271Y ALA* 1.3 56.0 + - + +
272Y TYR 3.3 0.4 - - - -
273Y ARG* 4.1 17.1 - - + +
274Y THR* 2.9 21.2 + - + +
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Residues in contact with ALA 271 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267Y ASP 4.2 10.1 - - - +
268Y PRO 3.4 18.1 + - - +
269Y GLY* 4.8 0.4 - - - -
270Y VAL* 1.3 76.6 - - - +
272Y TYR* 1.3 61.5 - - - +
274Y THR* 3.1 16.9 + - - -
275Y ARG* 3.3 29.0 + - - +
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Residues in contact with TYR 272 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269Y GLY* 2.7 18.7 + - - +
271Y ALA* 1.3 79.9 - - - +
273Y ARG* 1.3 68.9 + - + +
275Y ARG* 3.5 24.8 + - - +
276Y GLU* 3.4 28.5 + - + +
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Residues in contact with ARG 273 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269Y GLY 3.7 2.6 + - - +
270Y VAL* 4.5 17.1 - - + +
272Y TYR* 1.3 82.3 - - - +
274Y THR* 1.3 73.3 - - + +
275Y ARG 3.0 0.5 + - - -
276Y GLU* 3.1 5.7 + - - +
277Y GLU* 2.8 46.4 + - + +
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Residues in contact with THR 274 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270Y VAL* 2.9 23.9 + - + +
271Y ALA* 3.1 16.0 + - - -
273Y ARG* 1.3 82.9 - - + +
275Y ARG* 1.3 54.4 + - - -
277Y GLU* 3.2 18.2 + - - +
278Y ILE* 2.9 43.5 + - + +
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Residues in contact with ARG 275 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271Y ALA* 3.3 19.7 + - - +
272Y TYR* 3.8 31.6 + - - +
273Y ARG 3.0 1.6 + - - -
274Y THR* 1.3 76.2 - - - +
276Y GLU* 1.3 61.0 + - + +
278Y ILE* 3.6 6.4 + - - +
279Y GLN* 2.9 28.9 + - + +
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Residues in contact with GLU 276 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272Y TYR* 3.4 22.6 + - + +
273Y ARG* 3.1 5.0 + - - +
275Y ARG* 1.3 79.8 - - + +
277Y GLU* 1.3 60.9 + - - +
279Y GLN* 3.2 19.8 - - - +
280Y GLU* 2.8 47.5 + - - +
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Residues in contact with GLU 277 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258Y TYR* 4.1 18.3 + - + +
273Y ARG* 2.8 42.8 + - + +
274Y THR* 3.4 16.6 - - - +
276Y GLU* 1.3 82.0 - - - +
278Y ILE* 1.4 59.1 + - - +
280Y GLU* 3.7 5.0 - - - +
281Y VAL* 3.2 28.0 + - + +
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Residues in contact with ILE 278 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258Y TYR* 3.4 30.1 - - + +
259Y ARG 5.0 1.1 - - - +
260Y TYR* 4.2 31.6 - - + +
274Y THR* 2.9 39.6 + - + +
275Y ARG* 3.6 9.0 - - - +
277Y GLU* 1.4 71.1 - - + +
279Y GLN* 1.3 70.0 + - - +
280Y GLU 2.7 2.9 + - - -
281Y VAL* 2.8 16.2 + - - +
282Y ARG* 2.8 38.9 + - - +
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Residues in contact with GLN 279 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y ARG* 2.9 24.7 + - + +
276Y GLU* 3.2 23.3 - - - +
278Y ILE* 1.3 77.3 - - - +
280Y GLU* 1.3 58.1 - - - +
282Y ARG* 3.1 23.9 + - - +
283Y SER* 2.8 41.2 + - - -
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Residues in contact with GLU 280 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276Y GLU* 2.8 36.8 + - - +
277Y GLU* 3.7 7.4 - - - +
278Y ILE 2.7 3.8 + - - -
279Y GLN* 1.3 72.1 - - - +
281Y VAL* 1.3 65.0 + - + +
283Y SER* 3.7 11.2 + - - -
284Y LYS* 3.4 43.3 + - - +
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Residues in contact with VAL 281 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228Y MET* 4.5 9.4 - - + -
258Y TYR* 3.7 51.4 - - + -
260Y TYR* 4.2 11.9 - - + -
277Y GLU* 3.2 15.7 + - + +
278Y ILE* 2.8 10.2 + - - +
280Y GLU* 1.3 78.2 - - + +
282Y ARG* 1.3 57.3 + - - +
284Y LYS* 3.2 3.2 + - - -
285Y SER* 2.9 34.6 + - - +
286Y ASP 4.0 0.5 + - - -
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Residues in contact with ARG 282 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Y ARG* 4.5 9.7 - - - +
260Y TYR* 3.4 61.9 - - + +
278Y ILE* 2.8 29.9 + - - +
279Y GLN* 3.5 30.3 - - - +
281Y VAL* 1.3 70.9 - - - +
283Y SER* 1.3 68.3 + - - +
284Y LYS 3.1 0.7 + - - -
286Y ASP* 3.2 30.3 + - + +
289Y MET* 4.2 2.3 - - - +
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Residues in contact with SER 283 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279Y GLN* 2.8 26.2 + - - -
280Y GLU* 3.7 18.0 + - - -
282Y ARG* 1.3 76.6 - - - +
284Y LYS* 1.3 60.7 + - - +
289Y MET* 3.4 20.3 - - - +
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Residues in contact with LYS 284 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Y GLU* 3.4 35.8 + - - +
281Y VAL* 3.2 3.8 + - - +
282Y ARG 3.1 0.8 - - - -
283Y SER* 1.3 82.2 + - - +
285Y SER* 1.3 66.3 + - - +
289Y MET* 3.6 11.9 - - - +
290Y LEU* 3.9 4.0 - - - +
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Residues in contact with SER 285 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228Y MET* 3.3 37.9 - - - +
281Y VAL* 2.9 17.2 + - - +
284Y LYS* 1.3 84.5 - - - +
286Y ASP* 1.3 69.4 + - - +
287Y PRO 3.2 2.6 - - - -
289Y MET* 4.1 0.2 - - - -
290Y LEU* 3.7 23.5 - - - +
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Residues in contact with ASP 286 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Y ARG* 3.0 37.1 + - - -
260Y TYR* 3.1 19.6 + - - +
281Y VAL 4.0 1.2 + - - -
282Y ARG* 3.2 27.5 + - + +
285Y SER* 1.3 74.8 - - - +
287Y PRO* 1.3 71.1 - - - +
288Y ILE* 3.0 13.0 + - - +
289Y MET* 2.9 36.7 + - + +
290Y LEU* 3.0 21.7 + - - +
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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