Contacts of the helix formed by residues 288 - 302 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B SER* 3.3 10.6 + - - -
106B ASP* 3.6 2.9 - - - -
107B MET* 5.9 0.2 - - - -
283B TYR 3.4 22.3 + - - -
286B CYS* 3.6 4.0 - - - -
287B GLY* 1.3 79.8 - - - +
289B VAL* 1.3 55.8 + - - -
290B THR 3.3 2.7 - - - -
291B GLU* 3.2 1.2 + - - +
292B LEU* 2.8 43.0 + - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 2.9 5.2 + - - +
107B MET* 5.1 13.4 - - + +
110B TYR* 3.7 32.1 - - + -
125B MET* 3.8 40.6 - - + -
283B TYR* 4.9 12.3 - - + -
288B GLY* 1.3 70.4 - - - -
290B THR* 1.3 64.3 + - - +
292B LEU* 3.1 7.1 + - + +
293B LEU* 2.9 31.5 + - + +
319B ALA* 4.8 17.9 - - + +
323B PHE* 4.6 7.0 - - + -
369B LEU* 5.9 0.7 - - + -
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.7 18.5 + - + +
79B ARG* 4.4 13.5 - - + +
82B TYR* 3.9 26.9 - - + -
106B ASP* 2.4 39.0 + - - -
110B TYR* 2.8 24.2 + - - +
289B VAL* 1.3 73.8 - - - +
291B GLU* 1.3 62.8 + - - +
293B LEU* 3.6 7.9 + - + +
294B ARG* 3.5 24.4 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.5 29.6 + - + +
86B TYR* 5.9 0.2 - - - -
263B THR* 3.4 10.6 - - - +
264B ARG* 2.8 65.6 + - - +
265B PHE* 4.8 1.6 - - - -
286B CYS* 3.6 17.3 - - - +
287B GLY 4.0 8.7 + - - -
288B GLY 3.2 7.4 + - - +
289B VAL 3.2 0.4 - - - -
290B THR* 1.3 77.3 - - - +
292B LEU* 1.3 65.8 + - - +
293B LEU 3.2 0.2 - - - -
294B ARG* 3.0 14.1 + - - +
295B ILE* 3.0 26.3 + - + +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 3.5 26.5 - - - +
283B TYR* 3.3 50.9 - - + +
286B CYS* 3.8 14.8 - - - -
288B GLY 2.8 22.7 + - - +
289B VAL* 3.1 7.4 + - - +
291B GLU* 1.3 76.0 - - - +
293B LEU* 1.3 53.6 + - - +
295B ILE* 3.1 7.4 + - + +
296B MET* 2.8 34.3 + - - +
306B LEU* 3.7 19.9 - - + +
308B PRO* 4.2 12.3 - - + -
323B PHE* 3.7 16.2 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.0 18.2 - - - +
124B LEU 5.3 1.1 - - - +
125B MET* 3.9 33.4 - - + +
289B VAL* 2.9 28.0 + - + +
290B THR* 3.7 7.4 - - + +
291B GLU 3.2 0.2 - - - -
292B LEU* 1.3 77.6 - - - +
294B ARG* 1.3 62.0 + - + +
296B MET* 3.5 24.6 + - + +
297B ASP* 3.4 26.7 + - - +
323B PHE* 3.8 21.5 - - + -
326B VAL* 4.3 6.3 - - + -
79D ARG* 3.9 14.2 + - - +
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 3.8 19.4 - - - +
82B TYR* 6.1 2.2 - - - -
83B ASN* 5.6 3.0 + - - -
264B ARG* 3.4 41.3 - - - +
290B THR* 3.5 17.8 + - - +
291B GLU* 3.0 24.7 + - - +
293B LEU* 1.3 79.1 - - + +
295B ILE* 1.3 60.6 + - - +
297B ASP* 3.3 10.3 + - - +
298B ILE* 3.1 29.8 + - - +
297D ASP* 3.2 48.3 + - - +
300D GLU* 2.7 30.1 + - - +
328D HIS* 5.8 1.2 - - - -
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B THR 4.1 3.6 - - - +
264B ARG* 3.6 35.4 - - - +
267B ALA* 3.9 17.9 - - + -
271B LEU* 5.6 0.2 - - + -
279B VAL* 4.1 4.5 - - + -
281B SER* 3.8 24.5 - - - +
286B CYS* 4.3 7.0 - - - -
291B GLU* 3.0 26.4 + - + +
292B LEU* 3.1 9.8 + - + +
294B ARG* 1.3 73.9 - - - +
296B MET* 1.3 53.6 + - - +
298B ILE* 3.2 9.6 + - + +
299B CYS* 2.8 48.7 + - - -
306B LEU* 4.0 16.4 - - + -
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Residues in contact with MET 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLN* 5.5 1.3 - - - +
292B LEU 2.8 16.5 + - - +
293B LEU* 3.5 31.6 - - + +
295B ILE* 1.3 73.6 - - - +
297B ASP* 1.3 71.3 + - - +
299B CYS* 3.1 6.0 + - - +
300B GLU* 2.9 30.3 + - - +
306B LEU* 3.8 14.5 - - + +
323B PHE* 4.4 7.2 - - + -
326B VAL* 4.3 11.0 - - + +
327B CYS* 3.8 34.1 - - - -
328B HIS* 4.9 13.9 - - + +
329B ILE* 3.6 20.0 - - + +
79D ARG* 4.0 21.3 - - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 5.5 0.2 + - - -
293B LEU 3.4 8.0 + - - +
294B ARG* 3.3 10.4 + - - +
296B MET* 1.3 85.1 - - - +
298B ILE* 1.3 62.9 + - + +
300B GLU* 3.5 6.8 + - - +
301B HIS* 3.4 19.2 + - - +
79D ARG* 2.5 46.3 + - - -
294D ARG* 3.3 46.5 + - - +
297D ASP* 4.7 8.0 - - + +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 4.2 32.5 - - + +
267B ALA* 6.1 1.1 - - + -
268B GLN* 3.3 40.6 - - + +
271B LEU* 3.9 19.1 - - + -
294B ARG* 3.1 17.8 + - + +
295B ILE* 3.2 9.2 + - + +
297B ASP* 1.3 76.8 - - + +
299B CYS* 1.3 64.5 + - - +
301B HIS* 3.4 7.1 + - + +
302B HIS* 3.3 31.1 + - + +
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Residues in contact with CYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.1 9.9 - - - -
279B VAL* 3.9 34.8 - - - -
295B ILE* 2.8 33.2 + - - +
296B MET* 3.1 8.5 + - - +
298B ILE* 1.3 73.2 - - - +
300B GLU* 1.3 58.5 + - - +
302B HIS* 3.0 13.0 + - - +
304B ALA* 2.9 42.8 + - - +
305B GLN 4.3 4.0 - - - -
306B LEU* 4.2 11.4 - - + -
329B ILE* 3.6 8.5 - - + -
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASP* 4.2 8.0 - - - +
296B MET* 2.9 15.8 + - - +
297B ASP* 3.6 8.1 - - - +
299B CYS* 1.3 74.4 - - - +
301B HIS* 1.3 65.5 + - - +
303B ASN* 3.2 13.7 + - - +
304B ALA 4.8 1.1 - - - -
328B HIS* 3.6 29.8 + - - -
329B ILE* 3.9 20.7 - - + +
79D ARG* 5.7 0.2 + - - -
83D ASN* 5.8 0.2 + - - -
264D ARG* 3.6 17.4 + - - +
265D PHE* 6.5 0.4 - - + -
294D ARG* 2.7 30.3 + - - +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASP* 4.3 3.5 - - - +
242A ILE* 3.0 52.0 - - + +
273A LYS* 4.5 13.6 + - - -
297B ASP 3.4 9.4 + - - +
298B ILE* 3.7 9.4 - - - +
299B CYS 3.4 0.2 - - - -
300B GLU* 1.3 79.7 - - - +
302B HIS* 1.3 79.5 + + - +
303B ASN 3.3 1.1 + - - -
265D PHE* 6.2 2.2 - - - -
268D GLN* 3.9 35.4 + - - +
272D GLU* 4.5 6.5 + - - -
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Residues in contact with HIS 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.6 18.1 - - + +
246A LYS* 2.8 36.8 + - - +
268B GLN* 5.0 1.1 - - + -
271B LEU* 3.9 43.3 - - + +
272B GLU* 3.1 34.7 + - - +
298B ILE* 3.3 27.9 + - + +
299B CYS 3.0 9.5 + - - +
301B HIS* 1.3 97.3 + + - +
303B ASN* 1.3 66.0 + - - +
304B ALA* 3.4 1.6 + - + +
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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
------------------------------------------------------------
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