Contacts of the helix formed by residues 286 - 301 (chain A) in PDB entry 1Q20
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 THR 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A HIS 5.0 2.9 - - - +
285A PHE* 1.3 78.2 - - - +
287A VAL* 1.3 65.0 + - - +
288A ALA* 3.5 7.9 + - - +
289A GLN* 3.0 44.3 + - - +
290A SER* 2.9 19.3 + - - -
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Residues in contact with VAL 287 (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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286A THR* 1.3 73.1 - - - +
288A ALA* 1.3 58.4 + - - +
290A SER* 3.1 8.0 + - - -
291A GLU* 2.9 55.8 + - + +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR* 3.2 8.1 + - - +
287A VAL* 1.3 79.8 - - - +
289A GLN* 1.3 61.9 + - + +
291A GLU* 3.3 10.7 + - - +
292A ALA* 3.0 24.8 + - - +
295A ARG* 4.9 1.2 + - - -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 4.3 7.8 - - - +
173A ASP* 3.2 50.5 + - - +
176A LEU* 3.6 25.3 - - + +
284A HIS 3.7 6.1 - - - +
285A PHE* 3.5 15.6 - - + -
286A THR* 3.0 43.1 + - - +
288A ALA* 1.3 76.6 - - + +
290A SER* 1.3 57.2 + - - +
292A ALA* 3.4 5.6 + - - +
293A PHE* 3.0 29.6 + - - +
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Residues in contact with SER 290 (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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150A ARG* 5.5 0.9 + - - +
281A TRP* 3.7 28.0 - - - -
285A PHE* 3.8 12.5 - - - -
286A THR 2.9 14.7 + - - -
287A VAL* 3.4 12.8 - - - -
289A GLN* 1.3 77.5 - - - +
291A GLU* 1.3 56.6 + - - +
293A PHE* 3.3 3.9 + - - +
294A ASP* 3.1 41.7 + - - +
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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
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287A VAL* 2.9 40.0 + - + +
288A ALA* 3.3 8.9 + - - +
290A SER* 1.3 72.7 - - - +
292A ALA* 1.3 65.2 + - - +
294A ASP* 3.4 10.4 + - - +
295A ARG* 3.2 41.5 + - - +
298A ARG* 5.5 0.2 + - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 5.8 2.5 - - + -
180A LEU* 4.6 8.6 - - + +
288A ALA 3.0 17.3 + - - +
289A GLN* 3.8 6.7 - - - +
291A GLU* 1.3 76.3 - - - +
293A PHE* 1.3 65.0 + - - +
295A ARG* 3.4 27.7 + - - +
296A ALA* 3.2 21.1 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 3.8 25.4 - - + -
150A ARG* 3.5 47.8 - - + -
153A VAL* 4.4 9.2 - - + -
176A LEU* 4.1 7.9 - - + -
179A PHE* 4.4 15.0 - + - -
180A LEU* 3.7 30.0 - - + +
190A PHE* 4.6 7.2 - + - -
285A PHE* 3.9 22.4 - + + -
289A GLN 3.0 18.1 + - - +
290A SER 3.6 5.2 - - - +
291A GLU 3.2 0.2 - - - -
292A ALA* 1.3 78.9 - - - +
294A ASP* 1.3 58.3 + - - +
296A ALA* 3.2 7.0 + - - +
297A TYR* 2.8 40.2 + + + -
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Residues in contact with ASP 294 (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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150A ARG* 2.8 31.4 + - - -
290A SER* 3.1 26.5 + - - +
291A GLU* 3.7 8.7 - - - +
292A ALA 3.3 0.2 - - - -
293A PHE* 1.3 75.8 - - - +
295A ARG* 1.3 57.5 + - - +
297A TYR* 3.7 5.2 - - - +
298A ARG* 2.9 60.4 + - - +
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Residues in contact with ARG 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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288A ALA 4.9 1.4 + - - -
291A GLU* 3.2 30.7 + - - +
292A ALA* 3.4 35.9 - - - +
293A PHE 3.2 0.2 - - - -
294A ASP* 1.3 76.8 - - - +
296A ALA* 1.3 63.0 + - - +
298A ARG* 3.8 15.4 - - - +
299A LYS* 3.1 24.8 + - - +
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Residues in contact with ALA 296 (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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180A LEU* 3.7 33.0 - - + +
190A PHE* 4.5 4.0 - - + -
292A ALA 3.2 9.2 + - - +
293A PHE 3.2 8.7 + - - +
295A ARG* 1.3 80.1 - - - +
297A TYR* 1.3 61.4 + - - +
299A LYS* 3.4 4.3 + - - +
300A GLN* 3.0 31.7 + - + +
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Residues in contact with TYR 297 (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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149A PRO* 3.9 19.3 - - + -
150A ARG* 4.4 11.0 - - - +
189A TRP* 4.1 5.6 - + - -
190A PHE* 3.8 21.9 - + - -
293A PHE* 2.8 37.5 + + + +
294A ASP* 3.7 7.2 - - - +
296A ALA* 1.3 76.7 - - - +
298A ARG* 1.3 59.5 + - + +
300A GLN 3.1 0.7 + - - -
301A MET* 2.6 60.9 + - + +
307A PHE* 3.8 9.2 - - - -
309A TRP* 3.1 17.7 + - - -
310A ASP* 3.0 37.7 + - - -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 2.9 61.8 + - - +
295A ARG* 3.8 16.3 - - - +
297A TYR* 1.3 78.5 - - + +
299A LYS* 1.3 60.5 + - - +
301A MET 4.0 1.3 - - - -
302A ARG* 3.4 22.9 + - - +
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Residues in contact with LYS 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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295A ARG 3.1 17.3 + - - +
296A ALA* 3.8 4.7 - - - +
298A ARG* 1.3 77.8 - - - +
300A GLN* 1.3 65.3 + - + +
302A ARG* 3.8 12.8 + - - +
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Residues in contact with GLN 300 (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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180A LEU 5.3 5.9 + - - -
190A PHE* 3.7 45.0 - - + -
191A ASP* 5.1 3.1 - - - +
194A LYS* 3.1 39.5 + - - +
296A ALA* 3.0 22.0 + - + +
299A LYS* 1.3 81.5 - - + +
301A MET* 1.3 58.2 + - - +
302A ARG* 3.3 3.7 + - - +
304A MET* 5.0 0.2 - - - +
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Residues in contact with MET 301 (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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189A TRP* 4.1 15.7 - - + -
190A PHE* 3.8 26.5 - - + -
193A ILE* 4.3 7.9 - - + -
194A LYS* 4.1 15.9 - - - -
297A TYR* 2.6 56.9 + - + +
298A ARG* 4.0 3.1 - - - -
300A GLN* 1.3 70.9 - - - +
302A ARG* 1.3 65.6 + - - +
303A GLY 3.4 2.7 - - - -
304A MET* 3.1 37.8 + - + +
307A PHE* 3.5 33.9 - - + -
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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