Contacts of the helix formed by residues 248 - 259 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D GLU* 2.5 35.9 + - - -
116D ARG* 5.9 0.2 + - - -
246D GLU 3.3 3.9 + - - -
247D THR* 1.3 73.7 - - - +
249D ALA* 1.3 66.6 + - - +
250D PRO* 4.0 11.1 - - - +
251D LEU* 3.4 12.1 + - - +
252D ARG* 2.9 19.2 + - - +
277D PHE* 4.8 2.4 - - - -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 4.6 12.3 - - + -
79B TYR* 3.5 31.1 - - + +
93B GLU* 4.6 12.1 - - - +
247D THR 3.5 2.0 + - - -
248D SER* 1.3 71.4 - - - +
250D PRO* 1.3 65.6 - - + +
252D ARG* 3.2 17.7 + - - +
253D GLN* 2.8 32.0 + - - +
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Residues in contact with PRO 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.4 24.2 - - + -
79B TYR* 4.3 13.0 - - + +
248D SER* 3.5 11.9 - - - +
249D ALA* 1.3 96.7 - - + +
251D LEU* 1.3 57.0 + - - +
253D GLN* 3.3 6.0 + - + +
254D LEU 2.9 24.1 + - - -
275D HIS* 3.4 18.4 - - + -
276D PRO* 5.1 4.9 - - + -
277D PHE* 4.5 20.0 - - + +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLU* 3.5 33.7 - - + +
115D ILE* 4.6 8.1 - - + -
211D VAL* 4.0 22.7 - - + -
215D LEU* 4.4 14.6 - - + -
247D THR* 4.0 12.1 - - + -
248D SER* 3.1 19.5 + - - +
250D PRO* 1.3 76.1 - - - +
252D ARG* 1.3 66.4 + - - +
254D LEU* 3.4 7.1 + - + -
255D LEU* 3.0 29.1 + - + +
277D PHE* 3.8 39.4 - - + -
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Residues in contact with ARG 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS 4.8 1.8 + - - -
73B GLU* 3.6 53.1 + - - +
162B LYS* 5.6 1.7 - - - +
243D ILE* 3.9 26.8 + - + +
244D PRO 3.0 27.1 + - - -
245D ARG* 3.1 23.4 + - - +
247D THR* 3.3 29.1 + - + +
248D SER 2.9 8.8 + - - +
249D ALA* 3.6 18.5 - - - +
251D LEU* 1.3 77.5 - - - +
253D GLN* 1.3 57.5 + - - +
255D LEU* 3.3 8.1 + - - +
256D LEU* 2.9 35.9 + - + +
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Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 2.9 40.3 + - + +
249D ALA 2.8 19.9 + - - +
250D PRO* 3.6 6.3 - - + +
252D ARG* 1.3 71.2 - - - +
254D LEU* 1.3 65.6 + - - +
256D LEU* 3.3 6.2 + - - +
257D ALA* 2.9 28.1 + - - +
267D MET* 4.7 3.4 - - - +
275D HIS* 2.4 36.5 + - - -
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU* 3.5 31.9 - - + -
211D VAL* 5.5 2.5 - - + -
250D PRO 2.9 17.1 + - - +
251D LEU* 3.6 12.1 - - + +
253D GLN* 1.3 77.6 + - - +
255D LEU* 1.3 57.5 + - + +
257D ALA* 3.4 1.2 + - - +
258D LEU* 3.0 54.6 + - + +
267D MET* 3.7 26.0 - - + -
272D PHE* 4.2 8.7 - - + -
275D HIS* 3.6 21.3 - - + +
277D PHE* 3.6 24.2 - - + -
278D LEU* 5.0 2.9 - - + -
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLY* 3.5 28.7 - - - +
211D VAL* 3.8 16.6 - - + -
212D TYR* 3.8 24.0 - - + +
215D LEU* 3.8 28.3 - - + -
243D ILE* 4.2 25.1 - - + -
247D THR* 5.2 0.2 - - + -
251D LEU* 3.0 29.5 + - + +
252D ARG 3.6 4.3 - - - +
254D LEU* 1.3 74.7 - - + +
256D LEU* 1.3 61.7 + - - +
258D LEU* 3.8 4.0 - - + -
259D LEU* 2.8 41.4 + - + +
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.3 27.4 - - - +
149B PRO* 3.9 29.6 - - + -
160B ARG* 4.4 8.7 - - + +
239D LEU 5.2 2.0 - - - +
240D VAL* 4.0 26.9 - - + -
241D PRO* 4.1 11.0 - - + -
243D ILE* 3.8 20.4 - - + -
252D ARG* 2.9 33.4 + - + +
253D GLN* 5.3 0.9 - - - -
255D LEU* 1.3 74.5 - - - +
257D ALA* 1.3 61.7 + - - +
259D LEU* 3.5 8.9 + - - +
260D GLN* 2.9 27.8 + - - +
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 3.7 23.0 - - - +
150B ALA* 5.0 2.0 - - - +
253D GLN* 2.9 19.1 + - - +
254D LEU 3.8 0.2 - - - +
256D LEU* 1.3 76.1 - - - +
258D LEU* 1.3 63.1 + - - +
260D GLN* 3.4 17.1 - - - +
266D ARG* 3.5 1.2 - - - +
267D MET* 3.1 53.7 + - + +
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 3.5 45.1 - - + +
205D TRP* 3.6 11.3 - - - -
207D ILE* 4.7 4.0 - - + -
208D GLY* 3.9 26.5 - - - +
211D VAL* 5.3 5.2 - - + -
254D LEU* 3.0 44.5 + - + +
255D LEU* 3.9 4.7 - - + +
257D ALA* 1.3 76.6 - - - +
259D LEU* 1.3 59.6 + - - +
260D GLN 3.2 1.2 + - - -
266D ARG* 3.3 25.5 + - - -
267D MET* 3.8 22.2 - - + +
272D PHE* 4.4 12.3 - - + -
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D TRP* 3.6 41.9 - - + +
208D GLY* 4.0 18.2 - - - +
209D THR* 3.6 30.5 - - + +
212D TYR* 4.5 2.2 - - + -
220D PRO* 4.4 13.9 - - + -
221D PHE* 4.7 4.9 - - + -
239D LEU* 3.5 18.9 - - - +
241D PRO* 3.8 30.3 - - + -
255D LEU* 2.8 27.9 + - + +
256D LEU* 3.5 9.1 - - - +
258D LEU* 1.3 77.4 - - - +
260D GLN* 1.3 60.6 + - - +
261D ARG 3.7 1.0 + - - -
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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