Contacts of the helix formed by residues 283 - 294 (chain B) in PDB entry 1WSQ
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 SER 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLU* 2.6 33.7 + - - -
282B TYR* 1.3 76.3 - - - +
284B GLN* 1.3 64.9 + - - +
285B ASP* 3.7 6.2 + - - -
286B MET* 3.1 22.2 + - - +
287B HIS* 3.2 13.0 + - - -
314B LEU* 3.9 7.6 - - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B TYR 4.0 0.2 + - - -
283B SER* 1.3 75.0 - - - +
285B ASP* 1.3 64.4 + - - +
287B HIS* 3.2 14.0 + - - +
288B CYS* 2.9 34.8 + - - -
335B GLU* 3.2 33.1 + - - +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B SER* 3.1 4.2 - - - +
284B GLN* 1.3 87.2 + - - +
286B MET* 1.3 56.2 + - - +
288B CYS* 3.8 7.5 - - - +
289B LEU* 2.9 28.6 + - - +
314B LEU* 3.7 29.0 - - + +
333B LEU* 5.2 2.3 - - - +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU* 4.0 26.9 - - + +
151B VAL* 3.9 23.8 - - + -
152B LEU* 4.0 17.7 - - + -
252B LEU* 3.7 30.3 - - - -
256B CYS* 3.8 15.7 - - - -
282B TYR* 3.7 23.1 - - + -
283B SER* 3.1 20.8 + - - +
285B ASP* 1.3 76.7 - - - +
287B HIS* 1.3 66.1 + - + +
289B LEU* 3.2 5.4 + - - +
290B ILE* 3.1 26.6 + - + +
314B LEU* 3.8 9.3 - - + +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.4 16.8 + - - -
276B ILE* 3.7 23.3 - - + +
280B SER* 2.7 30.3 + - - -
282B TYR* 3.5 25.6 + - + -
283B SER 3.2 9.1 + - - -
284B GLN* 3.2 14.6 + - + +
286B MET* 1.3 78.0 - - + +
288B CYS* 1.3 62.8 + - - +
290B ILE* 3.4 6.1 + - + +
291B ARG 3.1 17.8 + - - -
335B GLU* 4.4 7.1 + - - +
336B PRO* 3.5 30.1 - - + +
338B LYS* 4.3 15.2 + - - +
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Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B GLN* 2.9 29.3 + - - +
285B ASP* 3.8 9.9 - - - +
287B HIS* 1.3 74.0 - - - +
289B LEU* 1.3 61.6 + - - +
291B ARG* 3.7 0.9 - - - +
292B TYR* 2.8 30.8 + - - +
333B LEU* 3.7 26.4 - - + +
334B PRO 3.5 24.9 - - - +
335B GLU* 3.9 27.4 - - - -
336B PRO* 4.2 0.7 - - - -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 4.9 4.5 - - + -
155B PHE* 4.6 0.9 - - + -
252B LEU* 3.8 21.3 - - + -
285B ASP 2.9 18.2 + - - +
286B MET* 3.2 7.6 + - - +
288B CYS* 1.3 73.5 - - - +
290B ILE* 1.3 67.0 + - - +
292B TYR* 3.3 18.5 + - + +
293B MET* 3.3 28.6 + - + +
307B VAL* 4.2 13.2 - - + +
310B PHE* 4.0 25.6 - - + +
311B SER* 3.5 33.0 - - - +
314B LEU* 4.6 12.3 - - + -
333B LEU* 4.2 4.2 - - + +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLY* 4.1 8.1 - - - +
252B LEU* 3.7 20.6 - - + -
253B TYR* 4.0 26.7 - - + +
256B CYS* 4.3 12.8 - - - -
257B TYR* 4.1 20.9 - - + +
274B PHE* 3.9 15.5 - - + -
276B ILE* 4.3 8.3 - - + -
286B MET* 3.1 18.4 + - + +
287B HIS* 3.6 7.2 - - - +
289B LEU* 1.3 76.4 - - - +
291B ARG* 1.3 64.0 + - - +
293B MET* 3.2 10.2 + - - +
294B LEU* 3.1 41.9 + - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLY 6.0 0.2 - - - -
274B PHE* 3.9 25.8 - - - -
287B HIS 3.1 14.0 + - - +
288B CYS 3.8 3.8 - - - +
290B ILE* 1.3 79.9 - - - +
292B TYR* 1.3 63.3 + - - +
294B LEU 3.1 25.1 + - - +
295B GLU* 3.8 23.8 + - - +
296B PRO* 5.6 3.2 - - - +
334B PRO* 3.6 41.8 - - + +
335B GLU 4.7 4.4 + - - -
336B PRO* 3.8 25.0 - - + +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B CYS 2.8 18.3 + - - +
289B LEU* 3.4 17.0 - - + +
291B ARG* 1.3 79.8 + - - +
293B MET* 1.3 60.6 + - - +
295B GLU* 4.0 7.8 - - - +
300B LYS 5.7 1.6 - - - -
302B PRO* 3.2 52.9 - - + +
306B GLN* 3.6 28.7 + - - +
307B VAL* 5.0 2.9 - - + -
310B PHE* 3.8 21.5 - + - -
330B PRO* 3.5 25.4 - - + +
333B LEU* 3.6 33.2 - - + -
334B PRO* 4.1 17.7 - - + +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 3.5 34.3 - - + -
245B ILE* 3.7 10.3 - - + +
246B TRP* 4.0 6.1 - - - -
248B LEU* 3.8 8.7 - - - +
249B GLY* 3.6 35.0 - - - -
252B LEU* 3.8 17.3 - - + -
289B LEU* 3.3 25.7 + - + +
290B ILE* 3.2 3.8 + - - +
291B ARG 3.2 0.4 - - - -
292B TYR* 1.3 75.9 - - + +
294B LEU* 1.3 59.0 + - - +
295B GLU 2.9 12.6 + - - -
301B ARG* 3.4 21.0 + - - -
302B PRO* 4.3 4.7 - - - -
307B VAL* 3.6 33.2 - - + -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TRP* 3.5 56.5 - - + +
249B GLY* 4.0 7.0 - - - +
250B CYS* 3.9 12.1 - - - +
261B PRO* 4.3 13.5 - - + -
262B PHE* 4.1 9.6 - - + -
272B GLY* 5.0 4.0 - - - +
274B PHE* 3.8 30.9 - - + -
290B ILE* 3.1 35.0 + - + +
291B ARG* 3.1 21.6 + - - +
293B MET* 1.3 75.8 - - - +
295B GLU* 1.3 57.2 + - - +
296B PRO* 3.5 9.5 - - - +
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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