Contacts of the helix formed by residues 264 - 282 (chain M) in PDB entry 6G0L
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 ALA 264 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M THR* 1.3 81.7 - - - +
265M GLU* 1.3 66.9 + - - +
266M ASP 3.3 1.6 - - - -
267M ILE* 3.4 16.1 + - - +
268M GLU* 3.6 17.4 + - - +
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Residues in contact with GLU 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263M THR* 2.7 24.5 + - - +
264M ALA* 1.3 78.4 + - - +
266M ASP* 1.3 69.1 + - - +
268M GLU* 3.1 14.2 + - - +
269M ILE* 2.9 36.6 + - + +
683M ARG* 5.5 4.7 + - - -
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Residues in contact with ASP 266 (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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255M GLN 5.4 0.9 - - - +
261M TYR 4.9 1.0 - - - +
262M VAL* 3.8 23.0 - - + +
263M THR* 3.2 27.5 + - - +
264M ALA 3.3 0.6 - - - -
265M GLU* 1.3 87.8 - - - +
267M ILE* 1.3 58.5 + - - +
269M ILE* 3.8 7.6 - - - +
270M MET* 2.9 40.6 + - + +
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Residues in contact with ILE 267 (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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255M GLN 4.4 1.1 - - - +
256M VAL* 3.3 42.2 - - + +
257M ARG* 5.8 0.9 - - + -
262M VAL* 3.8 14.8 - - + -
263M THR 3.7 18.6 - - - +
264M ALA* 3.4 8.5 + - - +
265M GLU 3.2 0.8 - - - -
266M ASP* 1.3 78.2 - - - +
268M GLU* 1.3 59.2 + - + +
270M MET* 4.9 2.0 - - + -
271M ASP* 2.9 57.3 + - - +
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Residues in contact with GLU 268 (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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264M ALA* 3.6 15.1 + - - +
265M GLU* 3.1 13.7 + - - +
267M ILE* 1.3 80.5 - - + +
269M ILE* 1.3 54.2 + - + +
271M ASP* 4.7 2.0 - - - -
272M MET* 2.6 38.3 + - - +
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Residues in contact with ILE 269 (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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265M GLU* 2.9 26.7 + - + +
266M ASP* 3.8 9.0 - - - +
267M ILE 3.2 0.2 - - - -
268M GLU* 1.3 79.5 - - + +
270M MET* 1.3 68.4 + - - +
272M MET* 3.1 24.3 + - + +
273M GLU* 2.9 29.0 + - + +
737M ASN* 5.2 11.4 - - - +
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Residues in contact with MET 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M GLU* 3.7 44.9 - - + +
255M GLN* 3.8 38.4 - - + +
256M VAL* 5.0 7.9 - - + -
266M ASP* 2.9 24.0 + - + +
267M ILE* 4.4 3.4 - - + +
269M ILE* 1.3 84.2 - - + +
271M ASP* 1.3 65.3 + - - +
273M GLU* 3.4 21.7 + - + +
274M ARG* 3.7 10.9 - - - +
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Residues in contact with ASP 271 (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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256M VAL* 4.9 10.4 - - - +
267M ILE* 2.9 41.0 + - - +
268M GLU* 4.6 2.7 - - - +
270M MET* 1.3 76.8 - - - +
272M MET* 1.3 63.0 + - - +
274M ARG* 3.2 33.5 + - - +
275M GLU* 2.8 26.6 - - - +
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Residues in contact with MET 272 (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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268M GLU 2.6 25.3 + - - +
269M ILE* 3.1 32.0 + - + +
271M ASP* 1.3 75.9 - - - +
273M GLU* 1.3 65.1 + - - +
275M GLU* 3.5 8.1 + - + +
276M ARG* 2.9 42.5 + - - +
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Residues in contact with GLU 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M GLU* 5.9 0.4 - - - +
269M ILE 2.9 12.2 + - - +
270M MET* 3.6 17.5 - - + +
271M ASP 3.2 0.2 - - - -
272M MET* 1.3 84.4 - - - +
274M ARG* 1.3 57.3 + - + +
276M ARG* 3.5 14.8 - - - +
277M ARG* 2.7 72.0 + - + +
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Residues in contact with ARG 274 (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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185M HIS* 3.5 29.8 + - + -
249M PHE* 4.4 10.9 - - - -
252M GLU* 3.0 36.3 + - - +
253M ASP* 4.6 4.0 + - - -
256M VAL* 4.4 12.1 - - - +
270M MET 3.7 9.8 + - - +
271M ASP* 3.4 29.9 + - - +
272M MET 3.2 0.8 - - - -
273M GLU* 1.3 77.8 - - + +
275M GLU* 1.3 66.4 + - - +
277M ARG* 3.2 4.8 + - - +
278M LEU* 2.9 35.8 + - + +
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Residues in contact with GLU 275 (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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271M ASP* 2.8 18.5 - - - +
272M MET* 3.5 7.7 + - + +
274M ARG* 1.3 82.2 - - - +
276M ARG* 1.3 56.6 + - - +
278M LEU* 3.7 20.3 - - + +
279M ASP* 2.9 40.7 + - - +
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Residues in contact with ARG 276 (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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272M MET* 2.9 33.3 + - - +
273M GLU* 3.5 22.2 - - - +
274M ARG 3.1 0.2 - - - -
275M GLU* 1.3 74.1 - - - +
277M ARG* 1.3 60.8 + - - +
279M ASP* 3.2 31.0 + - - +
280M GLU* 2.9 51.4 + - - +
749M GLN* 6.0 3.6 - - - +
752M ILE* 3.4 36.1 - - - +
756M HIS* 4.5 22.6 - - - +
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Residues in contact with ARG 277 (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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183M ILE 5.6 0.4 - - - +
245M TYR* 5.9 7.4 - - + +
273M GLU* 2.7 48.7 + - + +
274M ARG* 3.8 4.9 - - - +
276M ARG* 1.3 76.0 - - - +
278M LEU* 1.3 58.7 + - + +
280M GLU* 3.1 28.8 + - - +
281M PHE* 2.9 61.8 + - + -
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Residues in contact with LEU 278 (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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183M ILE* 5.4 3.1 - - + +
184M ASN* 4.3 29.4 - - + +
274M ARG* 2.9 24.1 + - + +
275M GLU* 3.7 24.7 - - + +
276M ARG 3.2 0.2 - - - -
277M ARG* 1.3 78.6 - - + +
279M ASP* 1.3 60.6 + - - +
281M PHE* 4.4 9.9 - - + +
282M GLU* 2.9 51.9 + - + +
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Residues in contact with ASP 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 GLU* 2.9 27.7 + - - +
276M ARG* 3.2 30.0 + - - +
278M LEU* 1.3 78.4 - - - +
280M GLU* 1.3 60.7 + - - +
281M PHE 3.6 0.2 + - - -
282M GLU* 4.7 10.7 - - - +
283M GLU* 3.4 28.4 + - - +
752M ILE* 5.7 1.7 - - - +
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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 ARG* 2.9 42.1 + - - +
277M ARG* 3.1 37.0 + - - +
279M ASP* 1.3 76.7 - - - +
281M PHE* 1.3 65.3 + - + +
283M GLU* 4.7 4.1 + - - +
284M PHE* 3.3 29.1 - - - -
749M GLN* 3.9 18.1 + - - +
752M ILE* 3.8 26.8 - - + +
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Residues in contact with PHE 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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181M ILE* 4.8 9.4 - - + -
182M VAL 3.5 18.8 - - - -
183M ILE* 3.2 57.8 - - + +
222M HIS* 5.5 0.5 - - - -
245M TYR* 5.7 3.1 - + - -
277M ARG* 2.9 44.3 + - + +
278M LEU* 3.2 9.4 + - + +
280M GLU* 1.3 91.4 - - + +
282M GLU* 1.3 65.4 + - + +
283M GLU 3.2 2.6 + - - -
284M PHE* 3.4 29.2 + + + +
285M HIS* 3.2 18.3 + - - +
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Residues in contact with GLU 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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278M LEU* 2.9 37.1 + - + +
279M ASP* 4.1 10.5 + - - +
281M PHE* 1.3 77.6 - - + +
283M GLU* 1.3 62.6 - - + +
284M PHE 3.2 0.9 + - - -
285M HIS* 3.5 25.8 + - + +
286M VAL* 4.4 9.2 + - - +
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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