Contacts of the helix formed by residues 245 - 256 (chain D) in PDB entry 1ZWS
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 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D GLU* 2.5 31.3 + - - -
243D HIS 3.8 1.4 + - - -
244D THR* 1.3 90.1 - - - +
246D GLU* 1.3 62.6 - - - +
247D LEU* 3.3 12.5 + - - +
248D ALA 2.7 24.1 + - - -
249D LYS* 3.2 5.1 + - - +
274D TRP* 3.7 0.6 + - - -
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Residues in contact with GLU 246 (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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245D SER* 1.3 70.9 - - - +
247D LEU* 1.3 57.0 + - - +
249D LYS* 3.2 37.3 + - - +
250D ASP* 2.7 36.7 + - - +
253D ARG* 4.5 11.4 + - - -
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Residues in contact with LEU 247 (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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245D SER* 3.4 11.4 - - - +
246D GLU* 1.3 80.3 - - - +
248D ALA* 1.3 65.2 + - - +
250D ASP* 3.4 5.5 - - + +
251D PHE 3.2 12.3 + - - -
272D HIS* 3.3 27.5 - - + +
273D PRO* 3.7 17.7 - - + +
274D TRP* 3.3 32.9 - - + +
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Residues in contact with ALA 248 (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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113D GLU* 3.7 2.5 - - - +
211D LEU* 3.6 18.8 - - + -
244D THR* 3.3 16.8 - - + -
245D SER* 2.7 22.3 + - - +
246D GLU 3.1 0.2 - - - -
247D LEU* 1.3 73.2 - - - +
249D LYS* 1.3 55.5 + - - +
250D ASP 2.6 1.2 + - - -
251D PHE* 2.5 37.5 + - - +
252D ILE* 3.2 6.7 + - - -
274D TRP* 3.4 26.0 - - + +
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Residues in contact with LYS 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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236D PHE* 3.4 29.8 - - + -
238D GLU* 5.0 4.5 + - - -
241D PHE* 3.8 28.9 + - + -
244D THR* 3.1 38.4 + - + +
245D SER 3.2 6.3 + - - +
246D GLU* 3.2 39.9 + - - +
248D ALA* 1.3 78.0 - - - +
250D ASP* 1.3 62.3 + - - +
252D ILE* 3.1 10.4 - - - +
253D ARG* 2.9 48.5 + - - +
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Residues in contact with ASP 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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246D GLU 2.7 21.2 + - - +
247D LEU* 3.4 10.8 - - + +
248D ALA 2.6 4.4 + - - -
249D LYS* 1.3 69.1 - - - +
251D PHE* 1.3 65.1 + - - +
253D ARG* 2.9 27.3 + - - +
254D LYS* 2.7 47.5 + - - +
272D HIS* 2.9 20.0 + - + +
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Residues in contact with PHE 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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120D ILE* 4.0 22.7 - - + -
124D LEU* 4.3 11.4 - - + -
203D ILE* 4.8 1.3 - - + -
207D THR* 4.1 14.4 - - + -
247D LEU 3.2 7.6 + - - +
248D ALA 2.5 15.8 + - - +
250D ASP* 1.3 76.0 + - - +
252D ILE* 1.3 66.1 + - + +
254D LYS* 3.3 4.9 + - - +
255D LEU* 3.3 41.8 + - + +
264D LEU* 4.5 4.3 - - + -
269D ALA* 3.3 42.0 - - + -
272D HIS* 3.6 29.6 + + + -
274D TRP* 3.6 26.5 - + + -
275D ILE* 4.0 11.7 - - + -
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Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D GLY* 3.9 4.7 - - - +
207D THR* 3.5 39.7 - - + -
208D TYR* 3.6 22.4 - - + +
211D LEU* 4.9 5.8 - - + -
234D TYR* 4.4 0.7 - - + -
236D PHE* 3.6 24.5 - - + -
241D PHE* 5.7 1.8 - - + -
248D ALA 3.8 10.5 - - - +
249D LYS* 3.1 17.7 - - - +
251D PHE* 1.3 75.3 - - + +
253D ARG* 1.3 56.5 + - - +
255D LEU* 2.7 30.9 + - - +
256D LEU* 2.9 40.0 + - + +
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Residues in contact with ARG 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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234D TYR* 3.5 16.6 + - - +
236D PHE* 3.4 34.5 - - + -
246D GLU* 4.5 13.9 + - - -
249D LYS* 2.9 42.6 + - - +
250D ASP* 2.9 19.1 + - - +
252D ILE* 1.3 76.6 - - - +
254D LYS* 1.3 60.4 + - + +
256D LEU 3.3 9.0 - - - +
257D VAL* 3.1 21.1 - - - +
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Residues in contact with LYS 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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250D ASP* 2.7 50.1 + - - +
251D PHE 3.8 4.0 - - - +
252D ILE 2.9 0.4 + - - -
253D ARG* 1.3 76.9 - - + +
255D LEU* 1.3 58.2 + - - +
257D VAL* 3.5 15.2 - - - +
262D LYS 4.6 1.2 - - - +
263D ARG* 3.6 1.0 - - - +
264D LEU* 3.3 61.6 + - + -
272D HIS* 4.3 8.7 - - + -
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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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200D MET* 3.7 45.3 - - + +
201D TRP* 3.9 5.9 - - - -
203D ILE* 4.0 8.5 - - + -
204D GLY* 3.5 35.2 - - - +
251D PHE* 3.3 40.4 + - + +
252D ILE 2.7 13.8 + - - +
254D LYS* 1.3 71.7 - - - +
256D LEU* 1.3 60.2 + - - +
257D VAL 2.9 9.0 + - - -
263D ARG* 2.9 24.2 + - - -
264D LEU* 4.0 21.5 - - + +
269D ALA* 4.4 2.2 - - + -
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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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201D TRP* 3.7 35.7 - - + +
204D GLY* 4.0 4.5 - - - -
205D VAL* 3.7 23.6 - - + +
208D TYR* 4.5 1.8 - - + -
216D PRO* 4.4 10.8 - - + -
217D PHE* 4.3 16.4 - - + -
232D VAL* 4.3 6.7 - - - +
234D TYR* 3.5 48.8 + - + +
252D ILE* 2.9 37.9 + - + +
253D ARG 3.3 8.7 - - - +
255D LEU* 1.3 72.0 - - - +
257D VAL* 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