Contacts of the helix formed by residues 284 - 298 (chain A) in PDB entry 2WQN
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 ASP 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LYS* 3.1 25.7 + - - +
219A ILE* 4.0 3.4 - - - -
283A PRO* 1.3 79.9 - - - +
285A VAL* 1.3 66.9 + - + +
286A THR* 3.2 9.4 + - - +
287A TYR* 3.5 8.0 + - + +
288A VAL* 3.3 18.5 + - - +
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Residues in contact with VAL 285 (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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146A CYS* 4.2 7.4 - - - +
149A LEU* 3.9 23.1 - - + -
150A GLU* 3.6 43.5 - - + +
153A HIS* 3.7 31.2 + - + +
219A ILE* 3.6 14.5 - - + +
222A LEU* 4.6 8.5 - - + -
284A ASP* 1.3 76.2 - - + +
286A THR* 1.3 62.3 + - - +
288A VAL* 3.3 3.5 + - + +
289A TYR* 2.9 28.5 + - - +
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Residues in contact with THR 286 (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 GLU* 3.3 29.1 + - - +
284A ASP* 3.2 6.7 - - - +
285A VAL* 1.3 82.2 - - - +
287A TYR* 1.3 63.4 + - - +
289A TYR* 3.6 3.8 + - + +
290A ASP* 3.0 38.1 + - - +
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.4 2.0 - - + -
273A MET* 3.3 36.0 - - + +
283A PRO* 3.6 23.3 - - + -
284A ASP* 3.5 13.8 + - + +
285A VAL 3.3 0.4 - - - -
286A THR* 1.3 77.6 - - - +
288A VAL* 1.3 68.0 + - - +
290A ASP* 3.2 11.2 + - + +
291A VAL* 3.1 44.6 + - + +
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Residues in contact with VAL 288 (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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142A PHE* 4.0 12.8 - - + -
146A CYS* 3.8 20.2 - - - -
219A ILE* 4.7 7.0 - - + -
222A LEU* 3.9 14.6 - - + -
270A LEU* 4.1 16.8 - - + +
274A CYS* 3.9 15.0 - - - -
283A PRO* 3.6 23.3 - - + -
284A ASP 3.3 17.7 - - - +
285A VAL* 3.3 10.0 + - - +
287A TYR* 1.3 78.4 - - - +
289A TYR* 1.3 62.9 + - - +
291A VAL* 3.2 5.2 + - - +
292A ALA* 3.0 21.0 + - - +
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 3.4 23.3 - - + +
146A CYS* 3.3 31.6 - - + +
147A SER* 2.9 29.8 + - - -
150A GLU* 3.9 32.8 - - + -
285A VAL 2.9 17.3 + - - +
286A THR* 3.8 5.6 - - + +
288A VAL* 1.3 76.6 - - - +
290A ASP* 1.3 63.5 + - - +
292A ALA* 3.2 1.0 + - - +
293A LYS* 3.0 65.5 + - + +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR* 3.0 36.8 + - - +
287A TYR* 3.2 9.4 + - + +
289A TYR* 1.3 77.2 - - - +
291A VAL* 1.3 63.6 + - + +
293A LYS* 3.6 26.0 + - - +
294A ARG* 3.1 27.1 + - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TRP* 4.4 2.2 - - + -
266A GLU* 5.0 7.0 - - + +
270A LEU* 4.1 26.9 - - + -
287A TYR* 3.1 44.7 + - + +
288A VAL 3.6 5.8 - - - +
290A ASP* 1.3 73.7 - - + +
292A ALA* 1.3 62.9 + - - +
294A ARG* 3.1 28.0 + - - +
295A MET* 2.8 44.9 + - + +
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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
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139A TRP* 3.8 16.2 - - + -
142A PHE* 4.1 11.4 - - + -
143A VAL* 3.8 29.0 - - + +
146A CYS* 4.0 13.7 - - - -
288A VAL 3.0 14.2 + - - +
289A TYR* 3.2 8.5 + - - +
291A VAL* 1.3 75.5 - - - +
293A LYS* 1.3 53.9 + - - +
295A MET* 3.4 0.9 + - - +
296A HIS* 2.7 36.6 + - - +
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Residues in contact with LYS 293 (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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143A VAL* 3.7 20.2 - - + -
289A TYR* 3.0 54.1 + - + +
290A ASP* 3.6 27.5 + - - +
292A ALA* 1.3 73.7 - - - +
294A ARG* 1.3 65.7 + - - +
296A HIS* 3.9 3.0 - - - +
297A ALA* 2.9 25.8 + - - +
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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
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266A GLU* 4.4 8.7 - - - +
290A ASP* 3.1 14.1 + - - +
291A VAL* 3.5 34.8 - - - +
293A LYS* 1.3 78.6 - - - +
295A MET* 1.3 94.8 + - + +
297A ALA* 3.2 6.1 + - - +
298A CYS* 3.1 24.8 + - - +
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Residues in contact with MET 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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135A GLU* 5.1 0.9 - - - +
139A TRP* 3.3 47.8 - - + +
264A SER* 4.9 2.9 - - - -
266A GLU* 3.6 35.7 - - + +
291A VAL* 2.8 26.6 + - + +
292A ALA 4.0 0.2 - - - +
294A ARG* 1.3 112.7 - - + +
296A HIS* 1.3 62.3 + - - +
298A CYS* 4.3 17.0 - - - -
299A THR* 2.8 36.9 + - + +
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Residues in contact with HIS 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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136A ARG 4.9 2.0 + - - -
139A TRP* 4.0 8.2 - - + +
140A LYS* 3.6 43.1 + - + +
143A VAL* 4.0 25.4 - - + +
292A ALA 2.7 22.9 + - - +
293A LYS* 3.9 4.7 - - - +
295A MET* 1.3 72.2 - - - +
297A ALA* 1.3 65.4 + - - +
299A THR* 3.5 5.1 + - - -
300A ALA* 3.3 39.4 + - + +
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Residues in contact with ALA 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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293A LYS 2.9 18.8 + - - +
294A ARG* 3.4 7.9 - - - +
296A HIS* 1.3 81.1 - - - +
298A CYS* 1.3 58.8 + - + +
300A ALA* 3.1 23.5 - - - +
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Residues in contact with CYS 298 (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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294A ARG 3.1 18.5 + - - +
295A MET* 3.4 25.5 + - - -
296A HIS 3.4 0.2 - - - -
297A ALA* 1.3 75.6 - - + +
299A THR* 1.3 63.6 + - - +
300A ALA 3.6 0.7 - - - -
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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