Contacts of the helix formed by residues 262 - 279 (chain M) in PDB entry 6QY3
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 LEU 262 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248M ILE* 4.5 16.6 - - + +
249M PHE* 5.3 6.7 + - - -
251M GLU 4.5 6.7 + - - +
253M TYR* 5.2 7.3 - - + +
260M MET 4.0 0.2 + - - -
261M TYR* 1.3 73.8 - - - +
263M SER* 1.3 58.5 + - - +
265M ILE* 3.3 6.5 + - - +
266M VAL* 2.9 30.9 + - - +
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Residues in contact with SER 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M ASP* 6.1 5.2 - - - -
261M TYR* 3.3 5.0 - - - +
262M LEU* 1.3 79.2 - - - +
264M ASN* 1.3 56.1 + - - +
266M VAL* 3.4 6.2 + - - +
267M SER* 2.9 30.0 + - - -
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Residues in contact with ASN 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M MET* 4.5 13.7 - - + -
261M TYR* 3.4 15.6 + - + +
262M LEU 3.3 0.4 - - - -
263M SER* 1.3 75.8 - - - +
265M ILE* 1.3 61.2 + - - +
267M SER* 3.9 5.2 - - - -
268M ASP* 2.9 32.4 + - - +
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Residues in contact with ILE 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253M TYR* 6.1 5.2 - - + +
255M TYR* 5.3 11.9 - - + -
260M MET* 4.9 8.2 - - + +
261M TYR 3.0 18.1 + - - +
262M LEU* 3.7 7.4 - - - +
264M ASN* 1.3 76.3 - - - +
266M VAL* 1.3 58.4 + - - +
268M ASP* 4.4 2.9 - - - +
269M TYR* 2.9 33.1 + - - +
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Residues in contact with VAL 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M MET* 5.8 8.3 - - + +
188M PHE* 5.8 8.1 - - + -
191M GLU* 4.7 8.0 - - + +
262M LEU 2.9 16.6 + - - +
263M SER* 3.8 6.1 - - - +
265M ILE* 1.3 75.9 - - - +
267M SER* 1.3 59.1 + - - +
269M TYR* 3.9 3.9 - - - +
270M THR* 2.9 31.5 + - - -
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Residues in contact with SER 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M GLU* 5.0 8.3 - - - -
263M SER 2.9 17.9 + - - -
264M ASN* 3.9 6.5 - - - -
265M ILE 3.4 0.2 - - - -
266M VAL* 1.3 78.4 - - - +
268M ASP* 1.3 58.8 + - - +
270M THR* 3.4 3.9 + - - -
271M LYS* 2.9 29.2 + - - +
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Residues in contact with ASP 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M ASN 2.9 17.5 + - - +
265M ILE* 4.4 3.4 - - - +
267M SER* 1.3 76.2 - - - +
269M TYR* 1.3 58.2 + - - +
271M LYS* 3.3 8.0 + - - +
272M LYS* 2.9 29.8 + - - +
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Residues in contact with TYR 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ILE 2.9 22.2 + - - +
266M VAL* 3.9 5.2 - - - +
267M SER 3.3 0.2 - - - -
268M ASP* 1.3 78.9 - - - +
270M THR* 1.3 56.5 + - - +
272M LYS* 3.4 5.7 + - - +
273M VAL* 2.9 29.3 + - - +
285M PRO* 4.7 14.3 - - + +
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Residues in contact with THR 270 (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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188M PHE 5.9 0.2 - - - -
191M GLU* 4.2 25.1 - - - -
192M VAL* 5.4 1.6 - - - -
218M ILE* 5.9 8.7 - - - -
266M VAL 2.9 19.0 + - - -
267M SER 3.8 3.1 - - - -
269M TYR* 1.3 76.1 - - - +
271M LYS* 1.3 58.8 + - - +
273M VAL* 3.3 6.4 + - - +
274M ILE* 2.9 30.7 + - - +
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Residues in contact with LYS 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M SER 2.9 17.2 + - - +
268M ASP* 3.6 8.1 - - - +
269M TYR 3.2 0.2 - - - -
270M THR* 1.3 77.0 - - - +
272M LYS* 1.3 57.6 + - - +
274M ILE* 3.4 5.0 + - - +
275M LYS* 2.9 31.2 + - - +
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Residues in contact with LYS 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 ASP 2.9 16.9 + - - +
269M TYR 3.4 4.2 + - - +
271M LYS* 1.3 75.5 - - - +
273M VAL* 1.3 58.5 + - - +
275M LYS* 4.0 5.1 - - - +
276M ALA* 2.9 30.1 + - - +
283M GLU 4.3 4.7 - - - +
285M PRO* 4.0 24.2 - - + -
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Residues in contact with VAL 273 (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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218M ILE* 6.0 6.1 - - + -
269M TYR 2.9 17.7 + - - +
270M THR* 3.6 7.9 - - - +
271M LYS 3.2 0.2 - - - -
272M LYS* 1.3 76.0 - - - +
274M ILE* 1.3 60.0 + - - +
276M ALA* 3.3 5.6 + - - +
277M LEU* 2.9 29.1 + - - +
285M PRO* 5.5 1.8 - - + +
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Residues in contact with ILE 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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195M CYS* 4.7 19.5 - - + -
270M THR 2.9 17.1 + - - +
271M LYS* 4.0 4.7 - - - +
273M VAL* 1.3 75.9 - - - +
275M LYS* 1.3 57.0 + - - +
277M LEU* 3.2 6.8 + - - +
278M ASN* 2.9 30.7 + - - +
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Residues in contact with LYS 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 LYS 2.9 18.1 + - - +
272M LYS* 4.0 6.1 - - - +
274M ILE* 1.3 75.7 - - - +
276M ALA* 1.3 57.6 + - - +
278M ASN* 3.9 4.6 - - - +
279M GLN* 2.9 33.3 + - - +
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Residues in contact with ALA 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 LYS 2.9 20.5 + - - +
273M VAL* 3.7 6.7 - - - +
275M LYS* 1.3 77.6 - - - +
277M LEU* 1.3 58.4 + - - +
279M GLN* 4.8 0.4 - - - -
280M LEU 3.0 7.3 + - - -
281M GLY* 2.6 39.1 + - - +
282M GLU* 4.4 7.0 - - - +
283M GLU 3.3 24.7 - - - +
284M ILE* 5.3 1.8 - - - -
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Residues in contact with LEU 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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97M TRP* 5.7 5.0 - - - +
101M VAL* 5.1 10.8 - - + +
273M VAL 2.9 17.4 + - - +
274M ILE* 3.2 8.0 + - - +
276M ALA* 1.3 77.5 - - - +
278M ASN* 1.3 60.9 + - - +
280M LEU* 3.5 9.8 + - - +
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Residues in contact with ASN 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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93M ARG* 5.3 14.1 - - + -
274M ILE 2.9 16.9 + - - +
275M LYS* 4.1 5.4 - - - +
277M LEU* 1.3 76.8 - - - +
279M GLN* 1.3 59.4 + - - +
280M LEU* 3.3 1.9 + - - +
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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 LYS 2.9 18.4 + - - +
276M ALA 4.5 0.7 - - - +
278M ASN* 1.3 75.2 - - + +
280M LEU* 1.3 71.3 + - - +
281M GLY 3.6 0.2 - - - -
282M GLU* 4.2 22.8 + - + +
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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