Contacts of the helix formed by residues 248 - 259 (chain B) in PDB entry 4WNP
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.7 33.4 + - - -
116B ARG* 5.3 1.2 + - - -
246B GLU 3.4 4.5 + - - -
247B THR* 1.3 74.8 - - - +
249B ALA* 1.3 65.7 + - - +
250B PRO* 3.5 20.8 - - - +
251B LEU* 3.2 8.5 + - - +
252B ARG* 3.0 20.3 + - - +
277B PHE* 4.8 1.7 - - - -
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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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247B THR 3.7 1.2 + - - -
248B SER* 1.3 71.2 - - - +
250B PRO* 1.3 72.0 - - + +
252B ARG* 3.2 14.6 + - - +
253B GLN* 2.9 29.4 + - - +
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Residues in contact with PRO 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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116B ARG* 5.7 2.5 - - - +
248B SER* 3.5 17.5 - - - +
249B ALA* 1.3 96.5 - - + +
251B LEU* 1.3 54.2 + - - +
253B GLN* 4.1 3.8 - - + +
254B LEU* 3.1 12.3 + - - +
275B HIS* 3.0 28.5 - - + -
276B PRO* 4.7 9.2 - - + +
277B PHE* 4.0 31.6 - - + +
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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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112B GLU* 3.5 33.0 - - + +
115B ILE* 4.5 9.2 - - + -
211B VAL* 3.9 24.7 - - + -
215B LEU* 3.9 19.1 - - + -
247B THR* 3.7 9.6 - - + -
248B SER* 3.2 15.6 + - - +
250B PRO* 1.3 77.4 - - - +
252B ARG* 1.3 66.4 + - - +
254B LEU* 3.5 6.9 + - + -
255B LEU* 3.0 31.2 + - + +
277B PHE* 4.0 33.4 - - + -
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Residues in contact with ARG 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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243B ILE* 3.3 41.1 + - + +
244B PRO 3.0 26.2 + - - -
245B ARG* 3.6 19.0 + - - +
247B THR* 3.5 19.0 + - + +
248B SER 3.0 11.5 + - - +
249B ALA* 3.8 14.6 - - - +
251B LEU* 1.3 75.9 - - - +
253B GLN* 1.3 62.6 + - - +
255B LEU 3.2 1.9 + - - -
256B LEU* 3.0 43.6 + - + +
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Residues in contact with GLN 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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249B ALA* 2.9 17.6 + - - +
250B PRO* 4.1 4.9 - - + +
252B ARG* 1.3 77.9 - - - +
254B LEU* 1.3 64.0 + - - +
256B LEU* 3.4 10.8 + - - +
257B ALA* 3.1 25.7 + - + +
275B HIS* 4.1 14.8 + - + +
276B PRO* 5.7 6.2 - - - +
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Residues in contact with LEU 254 (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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119B LEU* 3.8 20.2 - - + -
211B VAL* 5.6 1.1 - - + -
250B PRO 3.1 19.2 + - - +
251B LEU* 3.7 10.8 - - + +
252B ARG 3.3 0.2 - - - -
253B GLN* 1.3 77.9 - - - +
255B LEU* 1.3 63.8 + - + +
257B ALA* 3.4 2.5 + - - +
258B LEU* 3.1 33.4 + - + +
267B MET* 3.3 34.8 - - + -
272B PHE* 4.5 4.3 - - + -
275B HIS* 3.5 30.7 + - + +
277B PHE* 3.6 33.4 - - + -
278B LEU* 5.2 2.2 - - + -
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Residues in contact with LEU 255 (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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208B GLY* 3.6 28.3 - - - +
211B VAL* 3.8 22.0 - - + -
212B TYR* 3.9 17.0 - - + +
215B LEU* 3.7 30.1 - - + -
243B ILE* 3.7 22.2 - - + -
247B THR* 5.0 0.4 - - + -
251B LEU* 3.0 31.6 + - + +
252B ARG* 3.2 4.2 + - - +
254B LEU* 1.3 76.6 - - + +
256B LEU* 1.3 59.3 + - - +
258B LEU* 3.3 4.9 + - + -
259B LEU* 2.9 43.0 + - + +
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Residues in contact with LEU 256 (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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240B VAL* 4.4 10.1 - - + -
241B PRO* 3.7 30.5 - - + +
243B ILE* 3.6 19.3 - - + -
252B ARG* 3.0 42.8 + - + +
253B GLN* 3.8 7.9 - - - +
254B LEU 3.3 0.2 - - - -
255B LEU* 1.3 77.4 - - - +
257B ALA* 1.3 61.4 + - - +
258B LEU 3.4 0.2 + - - -
259B LEU 3.5 8.5 + - - +
260B GLN* 2.9 27.9 + - - +
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Residues in contact with ALA 257 (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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253B GLN* 3.1 19.7 + - + +
254B LEU* 3.9 4.7 - - - +
255B LEU 3.3 0.2 - - - -
256B LEU* 1.3 77.8 - - - +
258B LEU* 1.3 59.4 + - - +
260B GLN* 3.3 17.2 - - - +
265B ASP 6.0 0.2 - - - +
266B ARG* 3.5 1.6 - - - +
267B MET* 3.1 48.3 + - + +
275B HIS* 6.0 1.1 - - + -
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Residues in contact with LEU 258 (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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204B LEU* 3.5 40.8 - - + +
205B TRP* 3.7 10.0 - - - -
207B ILE* 4.7 9.6 - - + +
208B GLY* 3.8 24.9 - - - +
211B VAL* 5.1 4.9 - - + -
254B LEU* 3.1 38.2 + - + +
255B LEU* 3.9 5.2 - - + +
256B LEU 3.3 0.2 - - - -
257B ALA* 1.3 74.3 - - - +
259B LEU* 1.3 60.0 + - - +
260B GLN 3.2 9.4 + - - -
266B ARG* 3.2 23.4 + - + -
267B MET* 3.1 33.2 - - + -
272B PHE* 4.4 5.8 - - + -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TRP* 3.5 28.9 - - + +
208B GLY* 3.8 14.1 - - - +
209B THR* 3.6 38.6 - - + +
212B TYR* 4.1 18.6 - - + -
220B PRO* 4.2 11.2 - - + -
221B PHE* 4.7 2.7 - - + -
239B LEU 3.3 21.0 - - - +
241B PRO* 3.7 35.0 - - + +
255B LEU* 2.9 23.6 + - + +
256B LEU 3.7 6.8 - - - +
257B ALA 3.5 0.2 - - - -
258B LEU* 1.3 75.4 - - - +
260B GLN* 1.3 58.9 + - - +
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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