Contacts of the helix formed by residues 245 - 253 (chain B) in PDB entry 2WNW
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 LEU 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B TRP* 3.5 28.7 - - + +
241B ASP 4.1 1.0 + - - -
242B LYS* 3.3 24.6 + - + +
244B GLY* 1.3 74.5 - - - +
246B VAL* 1.3 66.6 + - - +
248B TRP* 3.9 1.9 - - - +
249B ALA* 3.1 24.8 + - - +
265B LEU* 4.1 20.5 - - + +
267B PHE* 4.3 22.4 - - + -
277B GLN* 3.3 5.5 + - + +
278B ILE* 4.0 38.6 - - + +
281B LEU* 3.5 19.7 - - + -
290B LEU* 5.5 3.1 - - + -
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Residues in contact with VAL 246 (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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37A LEU* 3.7 23.8 - - + -
40A HIS* 4.1 15.5 - - + +
385A LEU* 4.0 5.2 - - + -
245B LEU* 1.3 71.0 - - - +
247B ASP* 1.3 65.0 + - - +
249B ALA* 3.3 0.9 + - - +
250B GLU* 2.9 25.2 + - + +
277B GLN* 3.0 54.5 + - + +
280B TYR* 4.0 30.5 - - + -
281B LEU* 4.1 12.7 - - + +
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Residues in contact with ASP 247 (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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37A LEU* 3.7 14.8 - - - +
39A ARG* 2.7 36.5 + - - +
243B ASP 4.6 11.1 - - - +
244B GLY* 3.7 10.9 + - - +
245B LEU 3.4 0.4 - - - -
246B VAL* 1.3 77.4 - - - +
248B TRP* 1.3 61.8 + - - +
250B GLU* 3.5 3.0 - - - +
251B LEU* 3.4 29.9 + - + +
277B GLN* 4.6 0.8 + - - -
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Residues in contact with TRP 248 (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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197B PRO* 4.2 6.5 - - + -
198B VAL* 3.4 26.2 - - + -
208B TYR 3.5 17.5 - - - -
209B SER* 3.7 2.7 - - - -
210B VAL* 3.4 46.7 - - + +
213B GLU* 2.7 36.5 + - - -
237B ILE* 4.2 12.5 - - + +
238B TRP* 3.3 46.7 - + + +
244B GLY 3.3 16.6 + - - +
245B LEU 3.9 2.5 - - - +
247B ASP* 1.3 77.8 - - - +
249B ALA* 1.3 60.6 + - - +
251B LEU* 3.2 10.0 + - + +
252B ALA* 2.9 29.1 + - - +
265B LEU* 4.4 2.0 - - + -
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Residues in contact with ALA 249 (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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245B LEU 3.1 17.7 + - - +
246B VAL 3.8 0.7 - - - +
248B TRP* 1.3 76.8 - - - +
250B GLU* 1.3 63.0 + - - +
252B ALA* 4.4 1.6 - - - -
253B PHE* 2.9 38.3 + - + +
265B LEU* 3.8 27.9 - - + +
281B LEU* 3.8 28.0 - - + -
285B LEU* 4.3 2.9 - - + +
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Residues in contact with GLU 250 (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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39A ARG* 2.9 35.3 + - - -
40A HIS* 2.5 38.7 + - + +
246B VAL* 2.9 20.5 + - + +
247B ASP 3.5 5.8 - - - +
248B TRP 3.2 0.2 - - - -
249B ALA* 1.3 78.6 - - - +
251B LEU* 1.3 67.1 + - + +
253B PHE* 4.3 0.7 - - - -
254B ALA* 3.5 21.5 + - - +
281B LEU* 5.5 0.8 - - - +
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Residues in contact with LEU 251 (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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210B VAL* 3.9 28.5 - - + +
211B GLU* 5.0 5.6 - - - +
247B ASP* 3.5 17.0 - - + +
248B TRP* 3.2 10.1 + - + +
250B GLU* 1.3 83.5 - - + +
252B ALA* 1.3 64.3 - - - +
254B ALA* 3.8 12.8 + - + +
255B ASP* 4.7 1.9 + - - +
258B ASN* 5.0 1.6 + - - -
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Residues in contact with ALA 252 (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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210B VAL* 3.7 16.6 - - + +
214B THR* 3.8 7.0 - - + -
237B ILE* 3.5 31.4 - - + -
248B TRP 2.9 17.2 + - - +
249B ALA* 3.3 3.1 + - - +
251B LEU* 1.3 79.1 - - - +
253B PHE* 1.3 62.2 + - + +
254B ALA 3.2 3.4 + - - -
255B ASP 3.7 2.4 + - - -
258B ASN* 2.9 34.4 + - + +
262B ILE* 5.5 0.2 - - + -
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Residues in contact with PHE 253 (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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237B ILE* 4.2 10.8 - - + -
249B ALA* 2.9 27.3 + - + +
250B GLU 4.3 1.1 - - - -
252B ALA* 1.3 74.6 - - + +
254B ALA* 1.3 62.1 + - - +
255B ASP 3.1 9.4 + - - +
258B ASN 4.1 1.3 - - - -
259B TYR* 3.6 41.0 - + + +
262B ILE* 3.8 48.5 - - + -
264B GLY* 4.4 7.6 - - - -
265B LEU* 3.5 33.0 - - + -
285B LEU* 3.8 24.9 - - + -
288B LYS* 4.0 11.9 - - + -
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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