Contacts of the helix formed by residues 248 - 259 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C GLU* 3.0 34.1 + - - -
246C GLU 3.4 3.6 + - - -
247C THR* 1.3 75.1 - - - +
249C ALA* 1.3 63.8 + - - +
250C PRO* 3.4 11.9 - - - +
251C LEU* 3.2 16.5 + - - +
252C ARG* 3.1 19.9 + - - +
277C PHE* 4.8 1.7 - - - -
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 5.0 4.7 - - + -
79A TYR* 3.0 45.2 - - + +
93A GLU* 4.8 13.0 - - - +
247C THR 3.6 1.4 + - - -
248C SER* 1.3 71.8 - - - +
250C PRO* 1.3 66.3 - - + +
252C ARG* 3.6 12.1 + - - +
253C GLN* 3.1 26.5 + - - +
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Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.4 27.6 - - + -
79A TYR* 4.7 7.6 - - + +
248C SER* 3.4 14.1 - - - +
249C ALA* 1.3 96.8 - - + +
251C LEU* 1.3 56.8 + - - +
253C GLN* 3.2 13.4 - - + +
254C LEU* 2.9 23.7 + - - +
275C HIS* 3.5 12.1 - - + -
276C PRO* 5.1 4.3 - - + -
277C PHE* 4.4 26.5 - - + +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLU* 3.6 27.6 - - + +
115C ILE* 4.8 6.7 - - + -
211C VAL* 3.9 22.4 - - + -
215C LEU* 3.8 24.7 - - + -
247C THR* 3.8 11.2 - - + -
248C SER* 3.2 15.8 + - - +
250C PRO* 1.3 76.1 - - - +
252C ARG* 1.3 60.7 + - - +
254C LEU* 3.2 7.7 + - + +
255C LEU* 2.9 38.8 + - + +
277C PHE* 3.9 36.1 - - + -
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Residues in contact with ARG 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A HIS 5.4 1.0 + - - -
73A GLU* 3.4 56.2 + - - +
162A LYS* 5.4 3.9 - - - +
243C ILE* 3.8 32.0 + - + +
244C PRO 3.2 25.6 + - - -
245C ARG* 3.5 21.2 + - - +
247C THR* 3.3 21.6 + - + +
248C SER 3.1 12.1 + - - +
249C ALA* 4.0 11.0 - - - +
251C LEU* 1.3 75.7 - - - +
253C GLN* 1.3 58.1 + - - +
255C LEU* 3.3 1.5 + - - +
256C LEU* 2.8 50.8 + - + +
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP 5.6 3.2 + - - -
41A LEU* 5.1 9.7 - - - +
79A TYR* 5.6 1.7 + - - -
149A PRO* 6.0 7.1 - - + +
249C ALA* 3.1 16.4 + - - +
250C PRO* 3.2 15.4 - - - +
252C ARG* 1.3 77.2 - - - +
254C LEU* 1.3 57.4 + - - +
256C LEU* 3.8 6.4 - - - +
257C ALA* 3.0 33.4 + - + +
275C HIS* 3.9 19.5 + - - +
276C PRO* 5.0 8.1 - - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.8 19.7 - - + -
211C VAL* 5.6 1.8 - - + -
250C PRO 2.9 14.2 + - - +
251C LEU* 3.2 11.2 + - + +
253C GLN* 1.3 73.8 - - - +
255C LEU* 1.3 59.2 + - + +
257C ALA 4.0 0.3 - - - -
258C LEU* 3.0 40.3 + - + +
267C MET* 3.4 33.9 - - + -
272C PHE* 4.4 5.4 - - + -
275C HIS* 3.6 31.0 - - + +
277C PHE* 3.7 34.1 - - + -
278C LEU* 5.4 1.6 - - + -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLY* 3.6 28.3 - - - +
211C VAL* 3.9 12.3 - - + -
212C TYR* 3.7 26.0 - - + +
215C LEU* 3.9 27.8 - - + -
241C PRO* 5.4 0.2 - - - -
243C ILE* 4.1 24.7 - - + -
251C LEU* 2.9 32.6 + - + +
252C ARG* 3.7 4.0 - - - +
254C LEU* 1.3 77.8 - - + +
256C LEU* 1.3 57.1 + - - +
257C ALA 3.2 0.2 - - - -
258C LEU* 4.6 2.9 - - + -
259C LEU* 2.7 46.6 + - + +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLU* 3.9 17.5 - - - +
160A ARG* 5.9 3.4 - - + -
239C LEU 5.8 0.4 - - - +
240C VAL* 3.9 16.8 - - + -
241C PRO* 3.8 21.8 - - + -
243C ILE* 3.7 19.7 - - + -
252C ARG* 2.8 40.8 + - + +
253C GLN* 3.8 5.6 - - - +
255C LEU* 1.3 76.2 - - - +
257C ALA* 1.3 60.9 + - - +
259C LEU* 3.8 9.8 - - - +
260C GLN* 2.8 30.3 + - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C GLN* 3.0 18.5 + - + +
254C LEU 4.0 0.2 - - - +
256C LEU* 1.3 77.8 - - - +
258C LEU* 1.3 63.4 + - - +
260C GLN* 3.4 17.0 - - - +
265C ASP 5.9 0.2 - - - -
266C ARG* 3.5 1.2 - - - +
267C MET* 3.1 53.0 + - + +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 5.7 0.2 - - + -
204C LEU* 3.5 36.6 - - + +
205C TRP* 3.7 10.6 - - - -
207C ILE* 4.7 3.6 - - + -
208C GLY* 3.9 28.3 - - - +
211C VAL* 5.5 3.8 - - + -
254C LEU* 3.0 47.4 + - + +
255C LEU* 3.9 4.0 - - + +
257C ALA* 1.3 77.6 - - - +
259C LEU* 1.3 60.4 + - - +
260C GLN 3.2 5.0 + - - -
266C ARG* 3.3 21.3 + - - -
267C MET* 3.7 23.1 - - + +
272C PHE* 4.2 20.6 - - + -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C TRP* 3.4 48.0 - - + +
208C GLY* 3.9 13.2 - - - +
209C THR* 3.9 21.3 - - + +
212C TYR* 4.4 7.6 - - + -
220C PRO* 4.0 17.7 - - + -
221C PHE* 4.5 1.3 - - + -
239C LEU* 3.6 18.7 - - - +
241C PRO* 3.6 37.8 - - + +
255C LEU* 2.7 27.1 + - + +
256C LEU 3.8 8.2 - - - +
258C LEU* 1.3 74.1 - - - +
260C GLN* 1.3 58.7 + - - +
261C ARG 3.7 0.5 + - - -
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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