Contacts of the helix formed by residues 261 - 277 (chain M) in PDB entry 3Q84
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 ASN 261 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97M LEU* 3.4 22.2 - - + +
100M GLU* 4.6 6.2 - - - +
257M ASN 4.2 1.5 + - - +
258M LEU* 2.7 27.0 + - + +
259M ALA 3.7 5.9 - - - +
260M GLU* 1.3 79.5 + - - +
262M SER* 1.3 74.2 + - - +
263M SER* 3.1 22.1 + - - +
264M TYR* 3.2 12.7 + - + +
265M ILE* 4.0 3.6 - - - +
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Residues in contact with SER 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M ALA 5.1 0.9 - - - -
260M GLU 3.8 3.6 + - - -
261M ASN* 1.3 77.3 + - - +
263M SER* 1.3 61.6 + - - +
264M TYR 3.0 1.6 + - - -
265M ILE* 3.1 13.1 + - - +
266M HIS* 2.7 45.2 + - - -
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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
----------------------------------------------------------
97M LEU* 4.2 12.9 - - - +
261M ASN* 3.5 22.9 - - - -
262M SER* 1.3 81.4 + - - +
264M TYR* 1.3 56.4 + - - +
266M HIS* 3.2 12.1 + - - +
267M VAL* 3.0 26.6 + - - +
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Residues in contact with TYR 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M VAL* 4.0 16.7 - - + +
97M LEU* 3.7 23.3 - - + +
98M HIS* 5.7 0.7 - - - -
258M LEU* 3.7 38.4 - - + +
259M ALA* 4.7 1.6 - - - -
261M ASN* 3.2 13.5 + - + +
262M SER 3.0 0.6 + - - -
263M SER* 1.3 72.8 - - - +
265M ILE* 1.3 66.1 + - + +
266M HIS 3.0 0.2 - - - -
267M VAL* 2.3 32.2 - - + +
268M TYR* 3.2 34.9 + + - -
98N HIS* 6.0 0.2 - - - -
256N LEU 4.7 0.9 + - - -
258N LEU* 3.4 26.7 + - + +
259N ALA* 3.7 34.8 - - + -
264N TYR* 4.5 12.2 + + - -
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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
----------------------------------------------------------
259M ALA* 4.8 13.9 - - + +
261M ASN 4.0 10.3 - - - +
262M SER* 3.4 15.7 - - - +
264M TYR* 1.3 78.4 - - + +
266M HIS* 1.3 67.1 + - + +
268M TYR* 3.2 5.9 + - + +
269M ARG* 3.0 48.4 + - - +
259N ALA* 3.5 31.4 - - + -
260N GLU* 5.5 2.0 - - + +
265N ILE* 6.1 1.8 - - + -
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Residues in contact with HIS 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M SER* 2.7 44.6 + - - -
263M SER* 3.3 11.4 - - - +
264M TYR 3.0 0.6 - - - -
265M ILE* 1.3 84.8 - - + +
267M VAL* 1.3 63.0 + - - +
269M ARG* 3.7 19.5 + - - +
270M GLU* 2.9 26.0 + - - +
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Residues in contact with VAL 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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90M GLU* 4.1 27.5 - - + +
93M LYS* 4.1 31.0 - - + -
94M VAL* 4.5 5.4 - - + -
97M LEU* 4.5 7.2 - - + -
263M SER 3.0 7.8 + - - +
264M TYR* 2.3 57.4 - - + +
266M HIS* 1.3 72.0 - - - +
268M TYR* 1.3 71.6 + - + +
270M GLU* 3.3 12.0 + - - +
271M LEU* 3.0 20.3 + - - +
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Residues in contact with TYR 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M GLU* 2.4 34.1 + - + -
94M VAL* 3.6 14.2 - - + +
264M TYR* 3.2 43.9 + + - +
265M ILE* 3.2 7.5 + - - +
267M VAL* 1.3 82.5 - - + +
269M ARG* 1.3 61.9 + - - +
271M LEU* 3.2 21.6 + - + +
272M GLU* 3.0 22.0 + - - +
49N ARG* 4.3 2.9 + - - -
253N LYS* 4.0 10.6 - - + -
256N LEU* 3.3 32.2 + - + +
257N ASN* 3.4 43.5 - - + +
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Residues in contact with ARG 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ILE* 3.0 46.2 + - - +
266M HIS* 3.7 18.9 + - - +
268M TYR* 1.3 73.2 - - - +
270M GLU* 1.3 65.6 + - - +
272M GLU* 3.2 7.3 + - + +
273M GLN* 3.0 29.4 + - - +
253N LYS* 5.7 0.2 - - - +
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Residues in contact with GLU 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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89M THR* 4.4 10.9 - - - +
93M LYS* 2.5 40.4 + - - +
266M HIS 2.9 16.3 + - - +
267M VAL* 3.4 5.4 - - - +
269M ARG* 1.3 78.8 - - - +
271M LEU* 1.3 62.3 + - - +
273M GLN* 3.2 20.3 + - - +
274M ALA* 3.1 22.7 + - + +
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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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86M ALA* 3.7 25.6 - - + +
87M ILE* 3.7 32.5 - - + +
90M GLU* 4.1 20.9 - - + -
267M VAL 3.0 12.9 + - - +
268M TYR* 3.2 23.1 + - + +
270M GLU* 1.3 75.3 - - - +
272M GLU* 1.3 67.5 + - - +
273M GLN 3.1 0.2 + - - -
274M ALA* 3.2 3.8 + - - +
275M ILE* 3.1 27.3 + - + +
253N LYS* 3.6 31.6 - - + -
256N LEU* 5.0 2.5 - - + -
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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 TYR 3.0 8.7 + - - +
269M ARG* 3.2 8.9 + - + +
271M LEU* 1.3 77.0 - - - +
273M GLN* 1.3 64.0 + - - +
275M ILE* 3.4 5.0 + - - +
276M ARG* 3.0 62.7 + - + +
250N LEU* 4.5 7.9 - - + -
253N LYS* 3.1 44.1 + - + +
254N ARG* 4.8 7.9 + - - -
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Residues in contact with GLN 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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269M ARG* 3.0 23.9 + - + +
270M GLU* 3.4 17.6 - - - +
271M LEU 3.1 0.2 - - - -
272M GLU* 1.3 80.3 - - - +
274M ALA* 1.3 61.0 + - - +
276M ARG* 3.6 6.5 + - - +
277M GLY* 3.3 18.0 + - - -
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Residues in contact with ALA 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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82M ARG* 5.1 2.0 - - - +
83M ALA* 3.9 12.8 + - - +
86M ALA* 3.6 26.5 - - + -
270M GLU* 3.1 16.2 + - + +
271M LEU* 3.2 2.4 + - - +
273M GLN* 1.3 75.1 - - - +
275M ILE* 1.3 66.2 + - - +
277M GLY* 3.5 10.3 + - - -
278M ALA 4.1 1.4 + - - -
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Residues in contact with ILE 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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83M ALA* 3.9 23.8 - - + +
86M ALA* 5.1 0.2 - - + -
87M ILE* 4.3 7.9 - - + -
271M LEU* 3.1 33.3 + - + +
272M GLU 3.8 2.9 - - - +
274M ALA* 1.3 77.0 - - - +
276M ARG* 1.3 56.8 + - - +
278M ALA* 3.0 29.6 + - - +
246N LYS* 4.2 8.0 - - + +
249N LEU* 3.8 39.3 - - + +
250N LEU* 3.1 38.4 - - + +
253N LYS* 4.1 14.4 - - + -
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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 GLU* 3.0 49.7 + - + +
273M GLN* 3.9 6.7 - - - +
274M ALA 3.4 0.2 - - - -
275M ILE* 1.3 71.3 - - - +
277M GLY* 1.3 56.6 + - - +
278M ALA 2.9 10.6 + - - +
246N LYS* 3.5 26.6 + - - +
250N LEU* 3.9 30.7 - - + +
254N ARG* 4.5 13.5 - - - +
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Residues in contact with GLY 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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79M SER* 4.3 7.2 + - - -
82M ARG* 5.5 1.6 + - - -
273M GLN 3.3 13.5 + - - -
274M ALA* 3.5 6.4 + - - -
275M ILE 3.2 1.8 - - - -
276M ARG* 1.3 74.9 - - - +
278M ALA* 1.3 61.2 + - - +
279M ASP* 3.6 6.6 + - - +
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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
------------------------------------------------------------
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