Contacts of the helix formed by residues 262 - 273 (chain M) in PDB entry 6D6Q
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 ARG 262 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190M PRO* 3.8 23.0 - - - +
191M ILE* 5.4 1.4 - - - +
228M THR* 5.5 0.4 - - - -
229M THR* 5.5 5.1 - - - +
230M GLU* 3.6 21.0 + - - +
256M TYR* 3.5 28.3 + - - -
259M ASP* 3.4 17.5 + - - +
261M GLU* 1.3 88.6 - - + +
263M GLY* 1.3 57.3 + - - +
264M VAL* 2.9 12.7 + - - +
265M VAL* 3.1 15.2 + - + +
266M TRP* 3.0 32.2 - - + -
20O C 2.5 36.2 + - - -
21O A 2.9 57.3 + - + +
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Residues in contact with GLY 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M MET* 3.3 46.1 - - - +
259M ASP* 2.8 14.7 + - - -
260M SER 4.4 2.6 + - - -
261M GLU 3.9 0.4 - - - -
262M ARG* 1.3 76.7 - - - +
264M VAL* 1.3 60.8 + - - +
265M VAL 3.4 0.4 + - - -
266M TRP 4.7 0.4 - - - -
267M GLU* 3.6 18.4 - - - +
561M SER* 4.3 2.1 + - - -
562M ALA* 4.9 4.0 - - - -
563M PHE 4.8 4.5 - - - -
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Residues in contact with VAL 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233M ARG* 5.4 3.1 - - - +
262M ARG* 2.9 2.4 - - - -
263M GLY* 1.3 79.9 - - - +
265M VAL* 1.3 62.5 + - + +
267M GLU* 3.5 7.4 + - - +
268M GLU* 2.9 47.8 + - + +
563M PHE* 3.9 18.8 - - + +
564M HIS* 3.4 62.6 - - + +
565M LEU* 6.1 0.4 - - - -
566M THR* 5.4 7.9 - - + +
569M MET* 5.9 3.1 - - + -
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Residues in contact with VAL 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229M THR* 3.5 31.6 - - + -
230M GLU* 3.9 38.8 - - + +
233M ARG* 4.3 20.6 - - - +
262M ARG* 3.1 23.0 + - + +
264M VAL* 1.3 80.7 - - + +
266M TRP* 1.3 61.0 + - + +
268M GLU* 3.9 1.0 - - - +
269M THR* 2.6 41.4 + - - +
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Residues in contact with TRP 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M THR* 5.2 0.4 + - - -
190M PRO* 3.6 31.9 - - + +
229M THR* 3.7 20.5 + - + -
251M PHE* 3.7 31.8 - + - -
252M ASP 4.5 6.1 + - - -
253M GLU 4.2 13.5 + - - -
254M ILE* 4.8 12.8 - - + -
256M TYR* 3.4 34.3 - + - -
257M MET* 3.5 33.4 - - + -
262M ARG* 3.0 47.6 - - + -
263M GLY 4.5 0.2 + - - -
265M VAL* 1.3 83.9 - - + +
267M GLU* 1.3 63.9 + - - +
269M THR* 3.4 5.5 + - - -
270M ILE* 2.9 36.8 + - + +
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Residues in contact with GLU 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M MET* 3.7 15.4 - - + +
263M GLY 3.6 13.1 - - - +
264M VAL* 3.5 7.2 + - - +
265M VAL 3.3 0.6 - - - -
266M TRP* 1.3 76.6 - - - +
268M GLU* 1.3 60.6 + - - +
270M ILE* 2.9 5.5 + - - +
271M ILE* 2.7 41.1 + - + +
295M TRP* 4.3 16.2 - - + -
561M SER* 2.0 39.1 + - - -
563M PHE* 3.2 21.6 - - + +
588M SER* 2.7 24.8 + - - -
589M PHE* 3.2 11.1 - - + +
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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
----------------------------------------------------------
233M ARG* 2.7 30.1 + - + +
237M TYR* 1.8 37.5 + - - +
264M VAL* 2.9 35.3 + - + +
265M VAL 3.9 2.2 - - - +
267M GLU* 1.3 72.6 - - - +
269M THR* 1.3 63.3 + - - +
271M ILE* 3.2 10.0 + - - +
272M LEU* 3.0 36.1 + - + +
563M PHE* 6.2 2.2 - - + -
569M MET* 3.2 19.4 - - - +
573M LEU* 4.2 1.2 - - - +
584M MET* 3.8 22.7 - - + -
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Residues in contact with THR 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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229M THR* 3.9 12.6 - - + +
232M LEU* 3.6 38.4 - - + -
233M ARG* 4.1 13.6 - - - +
236M LEU* 4.2 8.9 - - + +
251M PHE* 4.6 12.3 - - + -
265M VAL* 2.6 28.2 + - - +
266M TRP* 3.6 6.3 - - - -
268M GLU* 1.3 75.5 - - - +
270M ILE* 1.3 63.9 + - - +
272M LEU* 3.1 18.2 + - - +
273M LEU* 3.2 21.7 + - + +
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Residues in contact with ILE 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251M PHE* 4.2 19.3 - - + -
257M MET* 5.6 2.7 - - - -
266M TRP* 2.9 31.1 + - + +
267M GLU* 3.4 5.8 - - - +
269M THR* 1.3 76.6 - - - +
271M ILE* 1.3 64.2 + - - +
272M LEU 3.0 0.9 + - - -
273M LEU* 3.0 17.4 + - - +
279M TYR* 3.4 23.1 - - + +
281M PHE* 4.1 22.7 - - + -
292M PHE* 5.0 3.8 - - + -
295M TRP* 4.0 26.9 - - + -
296M ILE* 4.1 10.3 - - + -
299M LEU* 4.0 15.5 - - + -
300M HIS* 3.6 13.5 + - - -
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Residues in contact with ILE 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M GLU* 2.7 43.1 + - + +
268M GLU 3.6 4.9 - - - +
270M ILE* 1.3 76.0 - - - +
272M LEU* 1.3 62.1 + - + +
273M LEU 3.6 4.7 + - - +
295M TRP* 4.0 18.4 - - + -
299M LEU* 4.2 16.1 - - + +
563M PHE* 6.1 0.2 - - + -
579M ILE* 5.2 1.0 - - + +
583M TYR* 4.1 30.1 + - + -
584M MET* 3.5 36.1 - - + -
587M LYS* 3.8 29.2 - - + +
588M SER* 4.3 7.9 - - - -
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Residues in contact with LEU 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233M ARG* 4.6 4.0 - - + +
236M LEU* 3.4 47.9 - - + +
237M TYR* 3.6 34.3 - - + +
268M GLU* 3.0 29.2 + - + +
269M THR* 3.6 2.0 - - - +
270M ILE 3.0 0.6 - - - -
271M ILE* 1.3 78.5 - - + +
273M LEU* 1.3 65.2 + - - +
274M PRO* 3.7 2.4 - - - +
573M LEU* 5.4 2.7 - - + -
579M ILE* 4.7 18.6 - - + -
584M MET* 4.3 17.5 - - + -
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Residues in contact with LEU 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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232M LEU* 5.1 4.3 - - + -
236M LEU* 3.9 23.6 - - + -
243M MET* 5.7 2.7 - - + -
249M VAL* 4.4 22.7 - - + -
251M PHE* 4.8 8.3 - - + -
269M THR* 3.2 21.2 + - + +
270M ILE* 3.0 13.1 + - - +
271M ILE 3.9 5.0 - - - +
272M LEU* 1.3 80.3 - - - +
274M PRO* 1.3 74.6 - - + +
275M ASP 4.0 0.5 + - - -
277M VAL* 4.2 8.7 - - + -
279M TYR* 3.9 39.3 - - + +
300M HIS* 3.7 17.1 + - - +
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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