Contacts of the helix formed by residues 288 - 303 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A SER* 3.3 14.2 + - - -
106A ASP* 3.7 3.4 - - - -
107A MET* 5.3 0.9 - - - -
283A TYR 3.4 21.3 + - - -
286A CYS* 3.6 2.8 - - - -
287A GLY* 1.3 78.6 - - - +
289A VAL* 1.3 56.9 + - - -
290A THR 3.3 2.7 - - - -
291A GLU* 3.2 1.6 + - - +
292A LEU* 2.8 40.1 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASP* 2.9 4.6 + - - +
107A MET* 5.0 12.3 - - + +
110A TYR* 3.7 32.3 - - + +
125A MET* 3.8 39.3 - - + -
283A TYR* 5.0 11.9 - - + +
288A GLY* 1.3 68.0 - - - -
290A THR* 1.3 67.9 + - - +
292A LEU* 3.1 8.5 + - + +
293A LEU* 2.9 31.8 + - + +
319A ALA* 4.8 17.0 - - + -
323A PHE* 4.7 9.4 - - + -
369A LEU* 5.9 0.7 - - + -
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.5 19.4 + - + +
79A ARG* 4.3 13.2 - - + +
82A TYR* 3.9 28.0 - - + -
106A ASP* 2.6 38.6 + - - -
110A TYR* 2.9 23.4 + - - +
289A VAL* 1.3 73.7 - - - +
291A GLU* 1.3 60.8 + - - +
293A LEU* 3.5 12.1 + - + +
294A ARG* 3.6 19.1 + - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.5 27.7 + - + +
86A TYR* 6.1 0.2 - - - -
263A THR* 3.4 8.8 - - - -
264A ARG* 2.7 66.2 + - - +
265A PHE* 4.8 0.7 - - - -
286A CYS* 3.6 17.9 - - - +
287A GLY 4.0 13.1 + - - -
288A GLY 3.2 7.8 + - - +
290A THR* 1.3 78.3 - - - +
292A LEU* 1.3 65.5 + - - +
293A LEU 3.1 0.2 - - - -
294A ARG* 3.1 15.6 + - - +
295A ILE* 3.1 25.0 + - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 3.4 29.6 - - - +
283A TYR* 3.3 51.4 - - + -
286A CYS* 3.7 14.6 - - - -
288A GLY 2.8 24.2 + - - +
289A VAL* 3.1 7.4 + - - +
291A GLU* 1.3 74.1 - - - +
293A LEU* 1.3 56.2 + - - +
295A ILE* 3.4 6.2 + - + -
296A MET* 2.9 28.6 + - - +
306A LEU* 3.7 24.8 - - + +
308A PRO* 4.0 7.0 - - + -
323A PHE* 3.9 14.1 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 4.0 18.2 - - - +
124A LEU 5.4 0.7 - - - +
125A MET* 3.9 34.1 - - + +
289A VAL* 2.9 30.3 + - + +
290A THR* 3.7 7.2 - - + +
291A GLU 3.1 0.4 - - - -
292A LEU* 1.3 73.8 - - - +
294A ARG* 1.3 64.4 + - + +
296A MET* 3.3 27.8 - - + +
297A ASP* 3.3 26.8 + - - +
323A PHE* 4.0 16.4 - - + -
326A VAL* 4.2 5.8 - - + -
79C ARG* 4.3 12.9 + - - +
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.1 15.1 - - - +
82A TYR* 5.8 2.5 - - - -
83A ASN* 5.7 1.8 + - - -
264A ARG* 3.2 44.2 - - - +
290A THR* 3.6 17.4 + - + +
291A GLU* 3.1 28.3 + - - +
293A LEU* 1.3 74.8 - - + +
295A ILE* 1.3 64.5 + - - +
297A ASP* 3.2 11.6 + - - +
298A ILE* 3.1 25.9 + - + +
297C ASP* 2.9 51.5 + - - +
300C GLU* 3.0 28.1 + - - -
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A THR 4.1 6.1 - - - +
264A ARG* 3.6 31.9 - - - +
267A ALA* 3.8 20.2 - - + -
271A LEU* 5.6 0.4 - - + -
279A VAL* 4.1 4.3 - - + -
281A SER* 3.7 24.9 - - - +
286A CYS* 4.3 7.6 - - - -
291A GLU* 3.1 20.6 + - + +
292A LEU* 3.7 10.1 - - + +
294A ARG* 1.3 74.6 - - - +
296A MET* 1.3 52.9 + - - +
298A ILE* 3.1 9.6 + - + +
299A CYS* 2.7 49.3 + - - -
306A LEU* 4.0 15.9 - - + -
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Residues in contact with MET 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 5.5 0.7 - - - +
292A LEU 2.9 15.3 + - - +
293A LEU* 3.3 30.5 - - + +
295A ILE* 1.3 77.4 - - - +
297A ASP* 1.3 60.8 + - - +
299A CYS* 3.3 4.6 + - - +
300A GLU* 3.0 26.9 + - + +
306A LEU* 3.7 14.3 - - + +
323A PHE* 4.3 6.5 - - + -
326A VAL* 4.3 13.9 - - + +
327A CYS* 3.9 42.6 - - - -
328A HIS* 4.9 13.0 - - + -
329A ILE* 3.6 14.6 - - + +
79C ARG* 3.8 33.4 - - - +
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Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU 3.6 8.5 - - - +
294A ARG* 3.2 11.6 + - - +
296A MET* 1.3 80.6 - - - +
298A ILE* 1.3 62.7 + - + +
300A GLU* 3.5 7.2 + - - +
301A HIS* 3.3 19.4 + - - +
79C ARG* 2.6 46.2 + - - -
294C ARG* 2.8 39.5 + - - +
297C ASP* 4.6 10.1 - - + +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 4.2 31.0 - - + +
267A ALA* 5.5 0.4 - - + -
268A GLN* 3.9 46.9 - - + +
271A LEU* 3.8 20.6 - - + -
294A ARG* 3.1 16.0 + - + +
295A ILE* 3.5 10.1 - - + +
297A ASP* 1.3 76.2 - - + +
299A CYS* 1.3 65.9 + - - +
301A HIS* 3.2 15.0 + - + +
302A HIS* 3.2 20.5 + - + +
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Residues in contact with CYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.0 11.0 - - - -
279A VAL* 3.6 36.3 - - - -
295A ILE* 2.7 33.7 + - - +
296A MET 3.5 5.4 - - - +
298A ILE* 1.3 70.5 - - - +
300A GLU* 1.3 63.6 + - - +
302A HIS* 3.0 3.7 + - - +
303A ASN 3.0 4.7 + - - -
304A ALA* 3.0 42.0 + - - +
305A GLN 4.3 3.1 - - - -
306A LEU* 4.1 11.2 - - - -
329A ILE* 3.6 9.0 - - + -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A MET* 3.0 12.6 + - + +
297A ASP* 3.5 10.8 - - - +
298A ILE 3.2 0.2 - - - -
299A CYS* 1.3 75.1 - - - +
301A HIS* 1.3 64.0 + - - +
303A ASN* 3.1 13.9 + - - +
304A ALA 4.9 0.9 - - - -
328A HIS* 3.8 26.6 + - - -
329A ILE* 4.1 21.0 - - + +
264C ARG* 3.3 20.6 + - - +
265C PHE* 6.5 0.2 - - + -
294C ARG* 2.7 28.5 + - - +
240F ASP* 4.4 7.1 - - - +
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASP 3.3 8.7 + - - +
298A ILE* 3.2 12.6 + - - +
300A GLU* 1.3 80.0 - - - +
302A HIS* 1.3 84.8 + + - +
303A ASN 3.3 0.7 + - - -
265C PHE* 6.3 0.8 - - - -
268C GLN* 3.4 38.7 + - - +
272C GLU* 4.6 6.7 + - - -
240F ASP* 4.3 3.5 - - - +
242F ILE* 3.6 37.8 + - + +
273F LYS* 5.5 6.1 - - - -
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLN* 4.9 2.5 - - + -
271A LEU* 3.9 47.0 - - + +
272A GLU* 3.6 28.9 + - - +
298A ILE* 3.2 29.7 + - + +
299A CYS 3.0 8.3 + - - +
301A HIS* 1.3 94.3 + + - +
303A ASN* 1.3 69.4 + - - +
304A ALA* 3.2 5.0 + - + +
242F ILE* 3.6 21.4 - - + +
246F LYS* 3.1 30.9 + - - +
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A SER* 5.5 1.9 - - - -
299A CYS 3.0 4.2 + - - -
300A GLU* 3.1 12.6 + - - +
301A HIS 3.3 1.0 + - - -
302A HIS* 1.3 80.3 - - - +
304A ALA* 1.3 58.1 + - - +
305A GLN* 5.9 0.2 - - - +
212F THR 2.7 20.4 + - - +
213F ASP* 4.1 7.5 - - - +
214F TRP* 2.8 64.6 + - + +
236F LEU* 4.6 0.2 - - - +
240F ASP* 3.2 33.0 + - - +
243F GLY* 3.7 8.0 - - - -
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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