Contacts of the helix formed by residues 288 - 303 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103W SER* 3.3 12.6 + - - -
106W ASP* 3.7 4.5 - - - -
107W MET* 5.3 0.9 - - - -
283W TYR 3.4 22.2 + - - -
286W CYS* 3.7 2.6 - - - -
287W GLY* 1.3 79.5 - - - +
289W VAL* 1.3 54.3 + - - -
290W THR 3.3 2.2 - - - -
291W GLU 3.2 1.7 + - - -
292W LEU* 2.8 41.2 + - - +
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Residues in contact with VAL 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W ASP* 2.9 5.0 + - - +
107W MET* 4.9 13.4 - - + +
110W TYR* 3.6 29.4 - - + +
125W MET* 3.8 43.5 - - + -
283W TYR* 4.7 10.3 + - + +
288W GLY* 1.3 71.6 - - - -
290W THR* 1.3 64.5 + - - +
292W LEU* 3.2 8.3 + - + +
293W LEU* 2.8 31.5 + - + +
319W ALA* 4.9 15.3 - - + -
323W PHE* 4.5 9.2 - - + -
369W LEU* 6.1 0.4 - - + -
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Residues in contact with THR 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78W PHE* 3.5 15.5 + - + +
79W ARG* 3.7 30.9 + - + +
82W TYR* 4.0 23.1 - - + -
106W ASP* 2.6 30.0 + - - -
110W TYR* 2.7 25.8 + - - +
289W VAL* 1.3 76.7 - - - +
291W GLU* 1.3 60.9 + - - +
293W LEU* 3.6 13.1 + - + +
294W ARG* 3.6 17.1 + - - +
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Residues in contact with GLU 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82W TYR* 3.4 37.6 + - + +
263W THR* 3.4 8.2 - - - -
264W ARG* 2.7 68.9 + - - +
265W PHE* 5.0 0.7 - - - -
286W CYS* 3.9 12.3 - - - +
287W GLY* 3.9 6.7 - - - +
288W GLY 3.2 7.8 + - - +
289W VAL 3.1 0.2 - - - -
290W THR* 1.3 78.2 - - - +
292W LEU* 1.3 64.0 + - - +
294W ARG* 3.1 13.9 + - - +
295W ILE* 3.0 30.5 + - + +
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Residues in contact with LEU 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281W SER* 3.5 31.0 - - - +
283W TYR* 3.4 49.4 - - + -
286W CYS* 3.6 15.7 - - - -
288W GLY 2.8 26.0 + - - +
289W VAL* 3.7 6.7 - - - +
291W GLU* 1.3 74.1 - - - +
293W LEU* 1.3 55.6 + - - +
295W ILE* 3.3 5.7 + - + +
296W MET* 2.8 28.9 + - - +
306W LEU* 3.5 15.5 - - + +
308W PRO* 4.1 12.8 - - + -
323W PHE* 4.0 16.6 - - + -
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Residues in contact with LEU 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 4.0 14.7 + - - +
79W ARG* 6.3 0.2 - - - +
110W TYR* 4.0 18.4 - - - +
124W LEU 5.4 0.7 - - - +
125W MET* 3.8 34.8 - - + +
289W VAL* 2.8 31.1 + - + +
290W THR* 3.7 7.9 - - + +
291W GLU 3.2 0.2 - - - -
292W LEU* 1.3 74.3 - - - +
294W ARG* 1.3 61.9 + - + +
296W MET* 3.4 26.8 - - + +
297W ASP* 3.3 26.8 + - - +
323W PHE* 4.0 16.2 - - + -
326W VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 294 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 6.3 0.2 - - - +
297M ASP* 3.4 38.8 + - - +
300M GLU* 2.7 32.3 + - - +
328M HIS* 5.5 1.4 - - - -
79W ARG* 3.4 44.5 - - - +
82W TYR* 6.5 0.2 - - - -
83W ASN* 4.8 11.7 + - - +
264W ARG* 3.4 54.8 - - + +
290W THR* 3.6 11.8 + - - +
291W GLU* 3.1 14.1 + - - +
293W LEU* 1.3 74.1 - - + +
295W ILE* 1.3 65.2 + - - +
297W ASP* 3.2 19.6 + - - +
298W ILE* 3.2 19.8 + - + +
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Residues in contact with ILE 295 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263W THR 4.1 4.0 - - - +
264W ARG* 3.7 31.6 - - + +
267W ALA* 3.9 24.2 - - + -
271W LEU* 5.7 0.4 - - + -
279W VAL* 4.1 3.8 - - + -
281W SER* 3.8 23.3 - - - +
286W CYS* 4.4 7.0 - - + -
291W GLU* 3.0 24.7 + - + +
292W LEU* 3.6 9.2 - - - +
294W ARG* 1.3 77.1 - - - +
296W MET* 1.3 52.7 + - - +
298W ILE* 3.1 9.7 + - + +
299W CYS* 2.8 48.1 + - - -
306W LEU* 4.1 17.3 - - + -
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Residues in contact with MET 296 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 3.8 36.6 - - - +
129W GLN* 5.8 0.4 - - - +
292W LEU 2.8 16.7 + - - +
293W LEU* 3.4 25.1 - - + +
294W ARG 3.1 0.2 - - - -
295W ILE* 1.3 76.4 - - - +
297W ASP* 1.3 64.3 + - - +
299W CYS* 3.3 4.0 + - - +
300W GLU* 2.9 26.8 + - + +
306W LEU* 3.6 14.3 - - + +
323W PHE* 4.6 3.4 - - + -
326W VAL* 4.4 9.0 - - + +
327W CYS* 3.9 33.4 - - - -
328W HIS* 5.0 11.0 - - + -
329W ILE* 3.5 26.5 - - + +
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Residues in contact with ASP 297 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 2.8 40.5 + - - -
294M ARG* 3.2 43.2 + - - +
297M ASP* 4.6 10.8 - - + +
79W ARG* 5.5 0.2 + - - -
293W LEU 3.3 10.9 + - - +
294W ARG* 3.2 12.1 + - - +
296W MET* 1.3 81.1 - - - +
298W ILE* 1.3 63.0 + - + +
300W GLU* 3.5 6.5 + - - +
301W HIS* 3.3 20.1 + - - +
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Residues in contact with ILE 298 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264W ARG* 4.1 31.0 - - + +
267W ALA* 6.1 0.7 - - + -
268W GLN* 3.3 45.1 - - + +
271W LEU* 3.6 20.6 - - + -
294W ARG* 3.2 15.4 + - + +
295W ILE* 3.1 10.9 + - + +
297W ASP* 1.3 76.3 - - + +
299W CYS* 1.3 65.5 + - - +
301W HIS* 3.2 7.5 + - + +
302W HIS* 3.2 30.6 + - + +
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Residues in contact with CYS 299 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271W LEU* 4.1 9.9 - - - -
279W VAL* 3.7 35.4 - - - -
295W ILE* 2.8 25.3 + - - -
296W MET 3.4 9.0 - - - +
298W ILE* 1.3 74.4 - - - +
300W GLU* 1.3 60.9 + - - +
302W HIS 3.0 2.9 + - - -
303W ASN 2.9 4.3 + - - -
304W ALA* 2.9 42.6 + - - +
305W GLN 4.1 4.0 - - - -
306W LEU* 3.9 16.4 - - + -
329W ILE* 3.7 8.1 - - + -
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Residues in contact with GLU 300 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M ARG* 3.3 22.4 + - - -
265M PHE* 5.5 1.8 - - + -
294M ARG* 3.0 20.9 + - - +
240V ASP* 4.3 7.1 - - - +
296W MET* 2.9 17.6 + - + +
297W ASP* 3.7 7.8 - - - +
298W ILE 3.2 0.6 - - - -
299W CYS* 1.3 74.0 - - - +
301W HIS* 1.3 64.8 + - - +
303W ASN* 3.0 14.3 + - - +
304W ALA 4.8 1.1 - - - -
328W HIS* 4.0 26.9 + - - -
329W ILE* 4.0 19.0 - - + +
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Residues in contact with HIS 301 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M PHE* 6.1 3.0 - - - -
268M GLN* 3.5 38.5 + - - +
272M GLU* 4.6 6.1 + - - -
240V ASP* 4.2 3.8 - - - +
242V ILE* 3.5 39.6 - - + +
273V LYS* 4.3 16.0 + - - -
297W ASP 3.3 9.7 + - - +
298W ILE* 3.2 11.0 + - + +
300W GLU* 1.3 79.3 - - - +
302W HIS* 1.3 83.1 + + - +
303W ASN 3.4 0.7 + - - -
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Residues in contact with HIS 302 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242V ILE* 3.5 24.5 - - + +
246V LYS* 3.1 28.8 + - - +
268W GLN* 5.2 1.1 - - + -
271W LEU* 3.9 40.1 - - + +
272W GLU* 3.4 37.5 + - - +
298W ILE* 3.2 27.3 + - + +
299W CYS 3.0 7.6 + - - +
301W HIS* 1.3 92.6 - + - +
303W ASN* 1.3 68.7 + - - +
304W ALA* 3.2 3.5 + - + +
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Residues in contact with ASN 303 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212V THR 2.7 21.5 + - - +
213V ASP* 4.3 6.4 - - - +
214V TRP* 3.0 64.4 + - + +
236V LEU* 4.6 0.4 - - - +
240V ASP* 3.0 27.7 + - - +
243V GLY* 3.4 12.9 - - - +
246V LYS* 5.1 0.7 + - - -
277W SER* 4.9 1.9 + - - +
299W CYS 2.9 5.0 + - - -
300W GLU* 3.0 13.4 + - - +
301W HIS 3.2 1.0 + - - -
302W HIS* 1.3 79.6 - - - +
304W ALA* 1.3 59.4 + - - +
305W GLN* 5.9 0.2 - - - +
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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
------------------------------------------------------------
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