Contacts of the helix formed by residues 262 - 275 (chain M) in PDB entry 3MQT
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 THR 262 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95M ARG* 3.5 12.8 - - - +
96M GLY* 2.9 34.6 + - - +
99M LEU* 4.0 7.4 - - - -
100M PHE* 3.9 18.2 - - + -
260M MET 4.4 4.9 - - - +
261M SER* 1.3 78.6 - - - +
263M THR* 1.3 79.1 + - - +
266M GLU* 3.1 21.0 + - - +
285M ARG* 3.4 25.8 - - + +
286M CYS* 3.8 4.5 - - - +
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Residues in contact with THR 263 (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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86M TYR* 4.2 8.7 - - + -
94M MET 3.1 27.8 - - - +
95M ARG* 3.6 12.1 + - - +
99M LEU* 3.6 18.6 - - + -
261M SER* 4.9 1.9 + - - -
262M THR* 1.3 83.9 + - - +
264M ARG* 1.3 62.4 + - - +
265M PHE* 3.2 27.4 + - + +
266M GLU* 3.4 5.7 + - - +
267M ALA* 3.5 16.1 + - - +
281M SER* 5.1 0.7 + - - -
286M CYS* 2.9 23.3 + - - +
291M GLU* 3.4 10.3 - - - +
295M ILE* 4.1 5.6 - - - +
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Residues in contact with ARG 264 (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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82M TYR* 4.5 10.9 - - - -
83M ASN* 5.2 5.7 + - - -
263M THR* 1.3 69.5 - - - +
265M PHE* 1.3 97.7 + - + +
266M GLU 3.4 0.2 - - - -
267M ALA* 3.8 1.3 - - - +
268M GLN* 3.0 31.8 + - - +
291M GLU* 2.7 43.8 + - - +
294M ARG* 3.4 49.8 - - + +
295M ILE* 3.7 25.4 - - + -
298M ILE* 4.0 15.7 - - + +
300W GLU* 3.3 27.7 + - - +
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Residues in contact with PHE 265 (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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86M TYR* 3.8 12.8 - + - -
95M ARG* 3.6 28.7 - - - +
263M THR* 3.1 19.4 - - + +
264M ARG* 1.3 119.0 - - + +
266M GLU* 1.3 64.3 + - - +
268M GLN* 4.0 6.9 - - - +
269M GLU* 3.2 22.7 + - - +
291M GLU* 4.9 0.7 - - - -
239V ASP* 3.5 44.0 - - + -
269V GLU* 5.3 2.1 - - - +
300W GLU* 5.5 2.0 - - + -
301W HIS* 6.1 2.9 - - - -
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Residues in contact with GLU 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M ARG* 3.9 21.6 + - - +
238M HIS* 5.0 1.9 - - - -
261M SER* 3.0 33.0 - - - -
262M THR* 3.1 28.2 + - - +
263M THR* 3.4 2.0 + - - +
264M ARG 3.4 0.2 - - - -
265M PHE* 1.3 75.5 - - - +
267M ALA* 1.3 66.9 + - - +
269M GLU* 3.2 12.3 + - - +
270M TRP* 3.0 33.9 + - + +
94V MET* 5.8 1.4 - - - +
95V ARG* 3.6 34.9 + - - +
266V GLU* 4.5 1.2 - - - +
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Residues in contact with ALA 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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258M ALA* 4.9 5.4 - - - -
261M SER* 4.6 1.4 + - - -
263M THR 3.5 11.7 + - - +
264M ARG 3.8 7.2 - - - +
265M PHE 3.4 0.4 - - - -
266M GLU* 1.3 79.1 - - - +
268M GLN* 1.3 62.1 + - - +
270M TRP* 3.3 9.7 + - - +
271M LEU* 3.0 27.4 + - + +
279M VAL* 4.3 8.2 - - + +
281M SER* 4.1 10.3 - - - +
295M ILE* 3.9 35.0 - - + -
298M ILE* 5.8 1.1 - - + -
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Residues in contact with GLN 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 ARG* 3.0 19.5 + - - +
265M PHE* 4.0 8.1 - - - +
267M ALA* 1.3 77.7 - - - +
269M GLU* 1.3 57.6 + - - +
271M LEU* 3.3 7.4 + - - +
272M GLU* 2.9 50.0 + - - +
298M ILE* 3.3 40.5 - - + +
302M HIS* 5.4 1.8 - - - -
301W HIS* 3.5 45.5 + - + +
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Residues in contact with GLU 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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241M LEU* 3.6 27.8 - - + +
265M PHE 3.2 15.8 + - - +
266M GLU* 3.2 13.1 + - - +
268M GLN* 1.3 76.2 - - - +
270M TRP* 1.3 65.0 + - + +
272M GLU* 3.2 5.7 + - + +
273M LYS* 2.8 43.7 + - + +
265V PHE 5.6 0.7 - - - +
269V GLU* 3.8 40.1 - - + +
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Residues in contact with TRP 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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238M HIS* 3.1 49.4 + + - -
241M LEU* 3.7 25.0 - - + +
244M HIS* 3.6 47.1 - + + -
257M GLY* 3.7 16.8 - - - -
258M ALA* 3.5 36.9 - - + +
261M SER* 4.2 4.5 - - - -
266M GLU* 3.0 30.6 + - + +
267M ALA 3.4 8.1 - - - +
269M GLU* 1.3 74.3 - - + +
271M LEU* 1.3 63.9 + - - +
274M THR* 2.7 51.3 + - + -
276M ILE* 3.9 14.6 - - + -
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Residues in contact with LEU 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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246J LYS* 5.8 0.5 + - - -
267M ALA* 3.0 17.4 + - + +
268M GLN* 3.3 8.5 - - - +
270M TRP* 1.3 80.6 - - - +
272M GLU* 1.3 63.1 + - - +
275M GLY* 3.3 18.9 + - - +
276M ILE* 3.9 16.8 - - + +
279M VAL* 3.6 24.0 - - + -
298M ILE* 3.6 27.8 - - + -
299M CYS* 4.0 22.2 - - - -
302M HIS* 3.9 33.9 - - + +
304M ALA* 3.8 22.0 - - + -
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Residues in contact with GLU 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 GLN* 2.9 44.4 + - - +
269M GLU* 3.7 6.7 - - + +
271M LEU* 1.3 75.4 - - - +
273M LYS* 1.3 62.5 + - + +
275M GLY 5.0 0.3 + - - -
302M HIS* 3.0 37.2 + - - +
273V LYS* 4.8 10.2 + - - +
301W HIS* 4.6 6.2 + - - -
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Residues in contact with LYS 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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241M LEU* 4.5 29.5 - - + +
242M ILE* 4.2 20.9 - - + +
245M GLN* 3.2 22.1 - - + +
269M GLU* 2.8 33.3 + - + +
272M GLU* 1.3 76.3 - - + +
274M THR* 1.3 63.2 + - + +
301N HIS* 4.0 25.3 + - - -
272V GLU* 4.6 12.6 + - - -
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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
----------------------------------------------------------
241M LEU* 3.5 43.1 - - + +
244M HIS* 4.0 9.6 - - + -
245M GLN* 3.3 32.0 - - - +
248M ALA* 3.7 11.1 - - - +
270M TRP* 2.7 33.4 + - + +
273M LYS* 1.3 80.6 - - - +
275M GLY* 1.3 63.5 + - - +
276M ILE* 3.1 22.7 + - - +
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Residues in contact with GLY 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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214J TRP* 6.2 0.2 - - - -
246J LYS* 4.9 18.5 + - - +
248M ALA* 4.2 9.6 - - - +
271M LEU 3.3 16.7 + - - -
272M GLU 4.9 0.2 - - - -
273M LYS 3.8 0.4 - - - -
274M THR* 1.3 80.0 + - - +
276M ILE* 1.3 69.7 + - - +
277M SER* 3.5 7.1 + - - -
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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
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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