Contacts of the helix formed by residues 288 - 302 (chain N) 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 GLY 288 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N SER* 3.4 13.1 + - - -
106N ASP* 3.8 3.6 - - - -
107N MET* 6.0 0.4 - - - -
283N TYR 3.5 21.3 + - - -
286N CYS* 3.7 5.4 - - - -
287N GLY* 1.3 77.8 - - - +
289N VAL* 1.3 61.2 + - - -
290N THR 3.2 3.1 - - - -
291N GLU 3.3 0.5 + - - -
292N LEU* 2.8 37.0 + - - +
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Residues in contact with VAL 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N ASP* 3.0 4.6 + - - +
107N MET* 5.0 13.6 - - + +
110N TYR* 3.7 24.0 - - + -
125N MET* 3.7 48.9 - - + -
283N TYR* 5.0 10.3 - - + +
288N GLY* 1.3 71.2 - - - -
290N THR* 1.3 54.6 + - - +
292N LEU* 3.1 7.0 + - + +
293N LEU* 2.7 42.7 + - + +
319N ALA* 4.7 17.0 - - + -
323N PHE* 4.3 9.6 - - + -
369N LEU* 6.0 0.7 - - + -
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Residues in contact with THR 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N PHE* 3.6 16.9 - - + +
79N ARG* 4.3 13.2 - - + +
82N TYR* 3.8 28.7 - - + -
106N ASP* 2.5 34.0 + - - -
110N TYR* 2.9 22.8 + - - +
289N VAL* 1.3 79.1 - - - +
291N GLU* 1.3 60.5 + - - +
293N LEU* 3.5 11.8 + - + +
294N ARG* 3.5 19.9 + - - +
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Residues in contact with GLU 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N TYR* 3.5 22.2 + - + +
263N THR* 3.4 8.7 - - - -
264N ARG* 2.6 67.5 + - - +
265N PHE* 4.8 1.2 - - - -
286N CYS* 3.7 17.5 - - - +
287N GLY* 3.9 22.2 + - - -
288N GLY 3.3 2.7 + - - +
290N THR* 1.3 76.5 - - - +
292N LEU* 1.3 61.8 + - - +
293N LEU 3.2 0.2 - - - -
294N ARG* 3.1 12.3 + - - +
295N ILE* 2.9 37.1 + - + +
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Residues in contact with LEU 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281N SER* 3.6 29.2 - - - +
283N TYR* 3.3 50.0 - - + -
286N CYS* 3.7 16.8 - - - -
288N GLY 2.8 22.6 + - - +
289N VAL* 3.5 6.5 - - - +
291N GLU* 1.3 77.3 - - - +
293N LEU* 1.3 56.2 + - - +
295N ILE* 3.2 5.4 + - + -
296N MET* 2.9 29.5 + - - +
306N LEU* 3.6 15.5 - - + +
308N PRO* 4.1 13.0 - - + -
323N PHE* 3.7 15.9 - - + -
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Residues in contact with LEU 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N TYR* 3.8 22.9 - - - +
124N LEU 5.2 0.9 - - - +
125N MET* 3.9 37.0 - - + +
289N VAL* 2.7 26.3 + - + +
290N THR* 3.6 7.4 - - + +
292N LEU* 1.3 73.2 - - - +
294N ARG* 1.3 60.1 + - + +
296N MET* 3.4 33.9 - - + +
297N ASP* 3.5 16.3 + - - +
323N PHE* 3.8 22.7 - - + -
326N VAL* 4.5 5.2 - - + -
79V ARG* 4.4 18.3 + - - +
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Residues in contact with ARG 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N ARG* 4.0 15.0 - - - +
82N TYR* 6.1 1.8 - - - -
83N ASN* 5.8 1.8 + - - -
264N ARG* 3.3 42.4 - - - +
290N THR* 3.5 16.0 + - - +
291N GLU* 3.1 25.3 + - - +
293N LEU* 1.3 75.3 - - + +
295N ILE* 1.3 64.6 + - - +
297N ASP* 3.3 10.7 + - - +
298N ILE* 3.2 30.4 + - - +
79V ARG* 6.2 0.4 - - - +
297V ASP* 3.3 52.8 + - - +
300V GLU* 3.0 27.9 + - - -
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Residues in contact with ILE 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263N THR 4.1 2.9 - - - +
264N ARG* 3.7 31.2 - - + +
267N ALA* 3.9 24.2 - - + -
271N LEU* 5.6 0.9 - - + -
279N VAL* 4.0 11.2 - - + -
281N SER* 3.7 24.9 - - - +
286N CYS* 4.4 5.6 - - - -
291N GLU* 2.9 27.1 + - + +
292N LEU* 3.2 9.6 + - + +
294N ARG* 1.3 72.7 - - - +
296N MET* 1.3 58.4 + - - +
298N ILE* 3.3 8.9 + - + +
299N CYS* 2.9 41.8 + - - -
306N LEU* 4.1 9.6 - - + -
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Residues in contact with MET 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N GLN* 5.8 1.1 - - - +
292N LEU 2.9 12.8 + - - +
293N LEU* 3.4 33.4 - - + +
294N ARG 3.1 0.4 - - - -
295N ILE* 1.3 78.2 - - - +
297N ASP* 1.3 71.5 + - - +
299N CYS* 3.3 3.7 + - - +
300N GLU* 2.9 28.6 + - - +
306N LEU* 3.8 13.0 - - + +
323N PHE* 4.5 6.7 - - + -
326N VAL* 4.3 8.7 - - + +
327N CYS* 3.7 37.5 - - - -
328N HIS* 4.8 14.6 - - + -
329N ILE* 3.5 23.2 - - + +
79V ARG* 4.3 20.0 - - - +
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Residues in contact with ASP 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293N LEU 3.5 11.6 + - - +
294N ARG* 3.3 11.5 + - - +
296N MET* 1.3 83.4 - - - +
298N ILE* 1.3 63.7 + - + +
300N GLU* 3.3 6.2 + - - +
301N HIS* 3.2 19.9 + - - +
79V ARG* 3.3 36.9 + - - -
294V ARG* 3.3 47.7 + - - +
297V ASP* 4.5 10.0 - - + +
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Residues in contact with ILE 298 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264N ARG* 4.0 34.3 - - + +
267N ALA* 6.1 0.7 - - + -
268N GLN* 3.7 42.0 - - + +
271N LEU* 3.7 20.2 - - + -
294N ARG* 3.2 21.0 + - + +
295N ILE* 3.7 8.5 - - + +
296N MET 3.3 0.2 - - - -
297N ASP* 1.3 75.4 - - + +
299N CYS* 1.3 65.1 + - - +
301N HIS* 3.3 7.4 + - - +
302N HIS* 3.2 34.3 + - + +
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Residues in contact with CYS 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271N LEU* 4.2 8.1 - - - -
279N VAL* 3.8 31.6 - - - -
295N ILE* 2.9 35.6 + - - -
296N MET 3.4 8.3 - - - +
298N ILE* 1.3 70.5 - - - +
300N GLU* 1.3 66.6 + - - +
302N HIS* 2.8 13.1 + - - +
303N ASN 3.0 10.0 + - - -
304N ALA* 3.0 31.6 + - - +
305N GLN 4.2 3.4 - - - -
306N LEU* 4.1 12.8 - - - -
329N ILE* 3.6 7.6 - - + -
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Residues in contact with GLU 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M ASP* 4.4 6.8 - - - +
296N MET* 2.9 17.0 + - - +
297N ASP* 3.3 11.4 + - - +
299N CYS* 1.3 72.7 - - - +
301N HIS* 1.3 64.0 + - - +
303N ASN* 3.2 13.1 + - - +
304N ALA 4.8 1.1 - - - -
328N HIS* 3.9 29.9 + - - -
329N ILE* 3.9 19.6 - - + +
83V ASN* 5.9 0.5 + - - -
264V ARG* 3.2 17.5 + - - +
265V PHE* 5.6 1.1 - - + -
294V ARG* 2.7 30.6 + - - +
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Residues in contact with HIS 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240M ASP* 4.4 3.5 - - - +
242M ILE* 3.2 42.0 + - + +
273M LYS* 4.0 16.0 + - - -
297N ASP 3.2 9.8 + - - +
298N ILE* 3.4 10.5 - - + +
299N CYS 3.2 0.6 - - - -
300N GLU* 1.3 80.9 - - - +
302N HIS* 1.3 82.0 + + - +
303N ASN 3.3 0.7 + - - -
265V PHE* 6.1 3.0 - - - -
268V GLN* 3.3 38.9 + - - +
272V GLU* 4.5 5.7 + - - -
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Residues in contact with HIS 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M ILE* 3.9 19.3 - - + +
246M LYS* 3.2 30.5 + - - +
268N GLN* 5.2 2.5 - - + -
271N LEU* 4.0 43.4 - - + +
272N GLU* 2.9 29.8 + - - -
298N ILE* 3.2 30.1 + - + +
299N CYS 2.8 12.5 + - - +
301N HIS* 1.3 90.7 + + - +
303N ASN* 1.3 69.3 + - - +
304N ALA* 3.1 5.8 + - + +
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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