Contacts of the helix formed by residues 269 - 286 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268M PRO* 1.3 74.0 - - - +
270M VAL* 1.3 72.3 + - - +
271M ALA* 3.2 0.9 - - - -
272M TYR* 2.6 28.3 + - - +
273M ARG* 3.1 4.3 + - - +
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Residues in contact with VAL 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M ASP* 4.3 2.2 - - + +
268M PRO* 2.7 43.7 - - + +
269M GLY* 1.3 71.8 - - - +
271M ALA* 1.3 55.1 + - - +
272M TYR 2.3 0.5 + - - -
273M ARG* 2.3 50.5 + - + +
274M THR* 3.2 12.5 + - + -
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Residues in contact with ALA 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M ASP 3.4 24.0 - - - +
268M PRO 3.8 6.7 - - - +
269M GLY* 4.6 0.4 - - - -
270M VAL* 1.3 74.1 - - - +
272M TYR* 1.3 55.5 + - - +
274M THR* 2.9 23.5 + - - +
275M ARG* 3.2 28.6 + - - +
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Residues in contact with TYR 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269M GLY* 2.6 21.6 + - - +
270M VAL 2.3 13.1 + - - -
271M ALA* 1.3 71.6 - - + +
273M ARG* 1.3 66.4 + - - -
275M ARG* 3.9 28.6 - - - +
276M GLU* 3.2 45.0 + - + +
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Residues in contact with ARG 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269M GLY 3.1 5.0 + - - +
270M VAL* 2.3 35.9 + - + +
272M TYR* 1.3 70.0 - - - +
274M THR* 1.3 61.6 + - + +
276M GLU* 3.0 4.8 + - - +
277M GLU* 2.6 61.3 + - - +
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Residues in contact with THR 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M VAL* 4.3 17.0 - - + +
271M ALA* 2.9 22.7 + - - +
273M ARG* 1.3 82.2 - - + +
275M ARG* 1.3 60.7 + - - -
277M GLU* 2.4 48.7 + - - +
278M ILE* 2.7 19.5 + - - -
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Residues in contact with ARG 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M ALA* 3.2 29.2 + - - +
272M TYR* 3.9 30.9 - - - +
273M ARG 3.3 0.4 - - - -
274M THR* 1.3 85.1 + - - +
276M GLU* 1.3 82.1 + - + +
278M ILE* 3.8 12.8 + - - +
279M GLN* 3.1 21.3 + - - +
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Residues in contact with GLU 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M TYR* 3.2 43.9 + - + +
273M ARG* 3.0 5.1 + - - +
274M THR 2.8 0.6 + - - -
275M ARG* 1.3 102.0 + - + +
277M GLU* 1.3 60.7 + - - +
278M ILE 3.4 0.4 - - - -
279M GLN* 3.4 19.9 - - + +
280M GLU* 3.0 25.8 + - - +
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Residues in contact with GLU 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258M TYR* 4.2 15.2 + - + +
273M ARG* 2.6 41.4 + - - +
274M THR* 2.4 43.9 + - - +
276M GLU* 1.3 68.3 - - - +
278M ILE* 1.3 55.2 + - - +
280M GLU* 3.0 23.2 - - - +
281M VAL* 3.0 12.2 + - + +
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Residues in contact with ILE 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258M TYR* 3.5 25.8 - - + +
259M ARG 4.7 1.3 - - - +
260M TYR* 3.3 40.6 - - + +
274M THR* 2.7 20.3 + - - +
275M ARG* 3.8 14.4 - - - +
277M GLU* 1.3 68.9 - - - +
279M GLN* 1.3 72.3 + - - +
280M GLU 2.8 2.5 + - - -
281M VAL* 2.9 7.7 + - - +
282M ARG* 2.9 44.0 + - - +
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Residues in contact with GLN 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275M ARG 3.1 13.8 + - - +
276M GLU* 3.4 28.3 - - + +
278M ILE* 1.3 82.8 - - - +
280M GLU* 1.3 65.3 + - - +
282M ARG* 3.3 19.3 + - - +
283M SER* 3.0 24.1 + - - -
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Residues in contact with GLU 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276M GLU 3.0 11.3 + - - +
277M GLU* 3.0 13.5 - - - +
278M ILE 2.8 0.4 - - - -
279M GLN* 1.3 85.1 - - - +
281M VAL* 1.3 73.4 + - - +
283M SER* 3.2 15.9 + - - -
284M LYS* 3.2 42.1 + - - +
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Residues in contact with VAL 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M MET* 4.3 18.6 - - + -
258M TYR* 3.9 35.0 - - + -
260M TYR* 4.1 16.6 - - + -
277M GLU* 3.0 13.2 + - + +
278M ILE* 2.9 9.7 + - - +
280M GLU* 1.3 86.4 + - - +
282M ARG* 1.3 64.1 + - - +
284M LYS* 2.9 18.8 + - - +
285M SER* 2.9 18.2 + - - +
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Residues in contact with ARG 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M ARG* 4.4 10.5 - - - +
260M TYR* 3.5 62.7 - - + +
278M ILE* 2.9 28.1 + - - +
279M GLN* 3.7 21.2 + - - +
281M VAL* 1.3 78.1 - - - +
283M SER* 1.3 67.7 + - - +
284M LYS 3.2 0.3 + - - -
286M ASP* 3.2 29.9 + - + +
289M MET* 4.4 2.8 - - - +
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Residues in contact with SER 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279M GLN* 3.0 18.7 + - - -
280M GLU* 3.4 13.9 + - - -
282M ARG* 1.3 84.4 - - - +
284M LYS* 1.3 64.1 + - - +
289M MET* 3.8 15.8 - - - +
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Residues in contact with LYS 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280M GLU* 3.2 33.8 + - - +
281M VAL* 2.9 9.0 + - - +
283M SER* 1.3 83.0 + - - +
285M SER* 1.3 65.2 + - - +
289M MET* 4.3 4.6 - - - +
290M LEU* 4.0 9.9 - - - +
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Residues in contact with SER 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228M MET* 3.4 39.0 - - - +
281M VAL* 2.9 15.4 + - - +
283M SER 3.6 0.6 - - - -
284M LYS* 1.3 82.6 - - - +
286M ASP* 1.3 67.2 + - - +
287M PRO 3.4 1.0 - - - -
290M LEU* 3.8 21.3 - - - -
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Residues in contact with ASP 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M ARG* 3.0 25.9 + - - -
260M TYR* 2.8 25.9 + - - +
282M ARG* 3.2 27.2 + - + +
285M SER* 1.3 77.0 - - - +
287M PRO* 1.3 68.9 - - - +
288M ILE* 2.7 30.8 + - - +
289M MET* 2.8 23.8 + - + +
290M LEU* 3.0 22.2 + - - +
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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
------------------------------------------------------------
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