Contacts of the helix formed by residues 288 - 302 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q SER* 3.2 12.8 + - - -
106Q ASP* 3.4 4.3 - - - -
107Q MET* 5.5 1.3 - - - -
283Q TYR 3.4 21.6 + - - -
286Q CYS* 3.7 3.6 - - - -
287Q GLY* 1.3 78.3 - - - +
289Q VAL* 1.3 62.4 + - - -
290Q THR 3.3 2.5 - - - -
291Q GLU 3.1 1.7 + - - -
292Q LEU* 2.8 36.0 + - - +
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Residues in contact with VAL 289 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q ASP* 2.9 4.6 + - - +
107Q MET* 5.0 13.9 - - + +
110Q TYR* 3.6 24.9 - - + +
125Q MET* 3.6 48.7 - - + -
283Q TYR* 4.8 9.6 + - + +
288Q GLY* 1.3 71.0 - - - -
290Q THR* 1.3 59.2 + - - +
292Q LEU* 3.2 8.2 + - - +
293Q LEU* 2.8 38.2 + - + +
319Q ALA* 4.7 16.6 - - + -
323Q PHE* 4.4 9.9 - - + -
369Q LEU* 6.1 0.4 - - + -
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Residues in contact with THR 290 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q PHE* 3.8 19.0 - - + +
79Q ARG* 4.4 13.5 - - + -
82Q TYR* 4.0 25.8 - - + -
106Q ASP* 2.5 31.6 + - - -
110Q TYR* 2.8 22.6 + - - +
289Q VAL* 1.3 78.0 - - - +
291Q GLU* 1.3 61.4 + - - +
293Q LEU* 3.6 11.4 + - + +
294Q ARG* 3.6 20.6 + - - +
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Residues in contact with GLU 291 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q TYR* 3.3 32.6 + - + +
86Q TYR* 6.1 0.2 - - - -
263Q THR* 3.2 10.7 - - - -
264Q ARG* 2.5 67.4 + - - +
265Q PHE* 4.9 0.3 - - - -
286Q CYS* 3.8 16.4 - - - +
287Q GLY* 3.9 7.9 + - - -
288Q GLY 3.1 8.4 + - - +
290Q THR* 1.3 76.8 - - - +
292Q LEU* 1.3 60.1 + - - +
293Q LEU 3.2 0.2 - - - -
294Q ARG* 3.0 14.1 + - - +
295Q ILE* 2.9 31.6 + - + +
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Residues in contact with LEU 292 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281Q SER* 3.5 30.3 - - - +
283Q TYR* 3.5 50.7 - - + +
286Q CYS* 3.5 14.8 - - - -
288Q GLY 2.8 23.3 + - - +
289Q VAL* 3.6 7.2 - - - +
291Q GLU* 1.3 77.0 - - - +
293Q LEU* 1.3 52.3 + - - +
295Q ILE* 3.2 5.1 + - + +
296Q MET* 2.7 34.1 + - - +
306Q LEU* 3.5 16.9 - - + +
308Q PRO* 4.0 12.8 - - + -
323Q PHE* 3.9 14.1 - - + -
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Residues in contact with LEU 293 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O ARG* 4.3 10.9 + - - +
110Q TYR* 3.9 18.8 - - - +
124Q LEU 5.1 1.6 - - - +
125Q MET* 3.8 36.8 - - + +
289Q VAL* 2.8 29.7 + - + +
290Q THR* 3.7 6.7 - - + +
291Q GLU 3.2 0.4 - - - -
292Q LEU* 1.3 73.3 - - - +
294Q ARG* 1.3 62.1 + - + +
296Q MET* 3.4 38.5 + - + +
297Q ASP* 3.4 17.5 + - - +
323Q PHE* 3.9 19.5 - - + -
326Q VAL* 4.4 5.2 - - + -
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Residues in contact with ARG 294 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297O ASP* 2.7 50.1 + - - +
300O GLU* 2.9 28.3 + - - +
79Q ARG* 3.9 19.7 - - - +
82Q TYR* 6.2 1.8 - - - -
83Q ASN* 5.8 2.2 + - - -
264Q ARG* 3.1 47.7 - - - +
290Q THR* 3.6 18.5 + - - +
291Q GLU* 3.0 21.8 + - - +
293Q LEU* 1.3 74.5 - - + +
295Q ILE* 1.3 66.8 + - - +
296Q MET 3.1 0.2 - - - -
297Q ASP* 3.2 10.0 + - - +
298Q ILE* 3.2 27.9 + - + +
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Residues in contact with ILE 295 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263Q THR 4.2 2.7 - - - +
264Q ARG* 3.8 24.2 - - - +
267Q ALA* 3.8 22.7 - - + -
271Q LEU* 5.6 0.9 - - + -
279Q VAL* 4.0 9.0 - - + -
281Q SER* 3.6 26.2 - - - +
286Q CYS* 4.3 5.2 - - + -
291Q GLU* 2.9 30.8 + - + +
292Q LEU* 3.6 14.6 - - + +
294Q ARG* 1.3 74.8 - - - +
296Q MET* 1.3 63.8 + - - +
298Q ILE* 3.1 9.6 + - + +
299Q CYS* 2.9 26.4 + - - -
306Q LEU* 4.0 21.8 - - + -
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Residues in contact with MET 296 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O ARG* 4.2 17.7 - - - +
129Q GLN* 6.0 0.9 - - - +
292Q LEU 2.7 17.6 + - - +
293Q LEU* 3.4 36.1 - - + +
294Q ARG 3.1 0.2 - - - -
295Q ILE* 1.3 72.9 - - - +
297Q ASP* 1.3 71.9 + - - +
299Q CYS* 3.2 4.9 + - - +
300Q GLU* 3.0 25.9 + - + +
306Q LEU* 3.6 13.9 - - + -
323Q PHE* 4.6 2.5 - - - -
326Q VAL* 4.3 9.4 - - + +
327Q CYS* 3.8 43.1 - - - -
328Q HIS* 4.9 10.5 - - + +
329Q ILE* 3.5 17.6 - - + +
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Residues in contact with ASP 297 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O ARG* 2.7 33.3 + - - -
294O ARG* 3.2 43.8 + - - +
297O ASP* 4.8 7.6 - - - +
293Q LEU 3.5 9.7 - - - +
294Q ARG* 3.2 10.9 + - - +
296Q MET* 1.3 86.8 - - - +
298Q ILE* 1.3 66.7 + - + +
300Q GLU* 3.6 7.1 + - - +
301Q HIS* 3.5 17.5 + - - +
328Q HIS* 6.1 0.3 - - - -
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Residues in contact with ILE 298 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264Q ARG* 4.1 29.8 - - + +
267Q ALA* 6.0 0.4 - - + -
268Q GLN* 3.4 47.8 - - + +
271Q LEU* 4.0 17.9 - - + -
294Q ARG* 3.2 16.5 + - + +
295Q ILE* 3.1 9.0 + - + +
297Q ASP* 1.3 77.0 - - + +
299Q CYS* 1.3 64.9 + - - +
301Q HIS* 3.3 13.1 + - + +
302Q HIS* 3.2 30.0 + - + -
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Residues in contact with CYS 299 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271Q LEU* 4.0 10.3 - - - -
279Q VAL* 3.7 36.3 - - - -
295Q ILE* 2.9 26.5 + - - -
296Q MET 3.4 7.9 - - - +
298Q ILE* 1.3 77.4 - - - +
300Q GLU* 1.3 60.7 + - - +
302Q HIS* 3.1 3.6 + - - -
303Q ASN 3.0 4.2 + - - -
304Q ALA* 2.8 44.2 + - - +
305Q GLN 4.1 7.2 - - - -
306Q LEU* 4.1 7.6 - - - -
329Q ILE* 3.6 7.6 - - + -
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Residues in contact with GLU 300 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264O ARG* 3.4 21.9 + - - -
294O ARG* 3.0 24.7 + - - +
296Q MET* 3.0 16.3 + - - +
297Q ASP* 3.8 8.1 - - - +
298Q ILE 3.3 0.2 - - - -
299Q CYS* 1.3 75.2 - - - +
301Q HIS* 1.3 64.7 + - - +
303Q ASN* 3.0 14.8 + - - +
304Q ALA 4.7 1.3 - - - -
328Q HIS* 3.8 28.3 + - - -
329Q ILE* 3.9 21.2 - - + +
240S ASP* 4.3 6.1 - - - +
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Residues in contact with HIS 301 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O PHE* 6.0 4.4 - - - -
268O GLN* 3.4 37.8 + - - +
272O GLU* 4.6 6.6 + - - -
297Q ASP 3.5 9.1 + - - +
298Q ILE* 3.3 11.1 + - + +
300Q GLU* 1.3 81.0 - - - +
302Q HIS* 1.3 80.9 + + - +
303Q ASN 3.5 0.3 + - - -
240S ASP* 4.2 4.3 - - - +
242S ILE* 3.4 41.3 + - + +
273S LYS* 5.1 8.9 + - - -
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Residues in contact with HIS 302 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268Q GLN* 5.3 2.0 - - + -
271Q LEU* 3.8 42.2 - - + +
272Q GLU* 3.8 28.5 - - + +
298Q ILE* 3.2 30.9 + - + -
299Q CYS 3.1 8.0 + - - +
301Q HIS* 1.3 91.8 + + - +
303Q ASN* 1.3 71.1 + - - +
304Q ALA* 3.2 5.6 + - + +
242S ILE* 3.6 22.5 - - + +
246S LYS* 3.3 29.4 + - - +
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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