Contacts of the helix formed by residues 180 - 195 (chain B) in PDB entry 3U8Z
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 THR 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B GLN* 3.8 24.9 - - + +
179B MET* 1.3 76.8 - - - +
181B PRO* 1.4 69.3 - - + +
182B GLU* 3.4 15.8 - - + +
183B MET* 3.0 32.6 + - - +
184B TRP* 2.9 24.4 + - - +
265D SER* 4.5 2.2 - - - -
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Residues in contact with PRO 181 (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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180B THR* 1.4 82.5 - - + +
182B GLU* 1.3 70.9 + - - +
184B TRP* 3.4 11.2 - - + +
185B GLU* 3.2 30.7 + - - +
263D ASN* 3.8 33.9 - - + +
264D ILE 4.3 4.5 - - - +
265D SER* 4.0 14.6 - - - -
274D LYS* 4.2 15.3 - - - +
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Residues in contact with GLU 182 (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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180B THR* 3.4 19.5 - - - +
181B PRO* 1.3 89.8 - - - +
183B MET* 1.4 57.5 + - + +
185B GLU* 3.3 9.2 + - - +
186B GLU* 3.1 42.3 + - - +
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Residues in contact with MET 183 (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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178B GLN* 3.5 35.9 - - + +
179B MET* 3.9 9.9 - - + -
180B THR* 3.0 42.8 + - - +
182B GLU* 1.4 74.1 - - + +
184B TRP* 1.4 59.9 + - - +
186B GLU* 3.5 17.4 + - - +
187B ARG* 3.0 43.0 + - - +
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Residues in contact with TRP 184 (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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179B MET* 3.8 22.5 - - - +
180B THR 2.9 9.1 + - - +
181B PRO 3.4 7.2 - - - +
182B GLU 3.3 0.2 - - - -
183B MET* 1.4 75.1 - - - +
185B GLU* 1.3 84.0 + - - +
187B ARG* 3.4 3.1 + - - +
188B ILE* 3.0 62.9 + - + +
261D ILE* 4.2 9.6 - - + -
262D ARG 3.1 28.9 - - - -
263D ASN* 3.5 17.3 - - + -
264D ILE* 3.4 54.6 - - + +
297D LEU* 6.1 0.2 - - + -
300D CYS* 5.5 4.1 - - + +
301D ILE* 4.7 16.8 - - + +
304D HIS* 3.9 27.9 - + - +
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Residues in contact with GLU 185 (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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181B PRO 3.2 13.6 + - - +
182B GLU* 3.3 12.3 + - - +
184B TRP* 1.3 99.6 - - - +
186B GLU* 1.3 57.1 + - + +
188B ILE* 3.4 24.8 - - - +
189B THR* 2.8 33.3 + - - +
262D ARG 4.4 3.2 - - - +
263D ASN* 4.9 1.6 - - - +
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Residues in contact with GLU 186 (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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182B GLU* 3.1 34.4 + - - +
183B MET* 3.7 16.1 - - - +
185B GLU* 1.3 74.8 - - + +
187B ARG* 1.4 58.5 + - + +
189B THR* 3.5 6.2 + - - -
190B ALA* 3.1 30.0 + - - +
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Residues in contact with ARG 187 (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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178B GLN 4.5 12.1 + - - -
179B MET* 3.2 25.4 - - - +
183B MET* 3.0 32.0 + - - +
184B TRP* 3.9 4.5 - - - +
186B GLU* 1.4 74.2 - - + +
188B ILE* 1.4 64.1 + - - +
190B ALA* 4.1 5.8 - - + +
191B TRP* 3.3 24.3 + - - +
76D LYS* 5.9 2.4 - - - +
294D LYS 5.4 0.8 + - - -
297D LEU* 4.5 11.3 - - - +
298D GLN* 5.0 10.5 - - - +
301D ILE* 3.2 40.4 - - + +
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Residues in contact with ILE 188 (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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184B TRP* 3.0 55.5 + - + +
185B GLU* 3.4 30.7 - - - +
187B ARG* 1.4 74.8 - - - +
189B THR* 1.4 65.7 + - - +
191B TRP 3.2 6.1 + - - -
192B TYR* 3.3 20.2 - - + +
301D ILE* 4.4 6.0 - - + +
304D HIS* 3.6 26.0 - - + +
305D ASP* 2.6 37.9 - - - +
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Residues in contact with THR 189 (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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185B GLU* 2.8 18.5 + - - +
186B GLU* 3.9 6.3 - - - -
188B ILE* 1.4 79.3 - - - +
190B ALA* 1.4 61.1 + - - +
191B TRP 3.5 0.5 + - - -
192B TYR* 3.6 23.3 + - + +
193B ALA* 4.1 5.9 + - - +
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Residues in contact with ALA 190 (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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186B GLU 3.1 18.5 + - - +
187B ARG* 4.1 7.9 - - + +
188B ILE 3.3 0.2 - - - -
189B THR* 1.4 73.9 - - - +
191B TRP* 1.4 63.2 + - - +
192B TYR 3.5 0.2 + - - -
193B ALA* 3.6 6.8 + - - +
194B GLU* 3.1 43.9 + - - +
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Residues in contact with TRP 191 (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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187B ARG 3.3 13.2 + - - +
188B ILE 3.2 2.0 + - - -
190B ALA* 1.4 76.6 - - - +
192B TYR* 1.4 66.2 + - - +
194B GLU* 3.3 5.0 + - - -
195B HIS* 3.0 77.4 + + + -
60D TRP* 4.4 7.6 - - + -
100D PHE* 4.1 20.2 - + - -
298D GLN 5.2 1.7 + - - -
301D ILE* 3.7 19.1 - - + -
302D GLY* 3.6 21.1 - - - +
305D ASP* 3.1 41.5 - - + +
306D LEU* 3.6 37.9 - - + -
309D ARG* 4.0 12.1 - - - -
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Residues in contact with TYR 192 (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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188B ILE* 3.3 38.6 + - + +
189B THR* 3.6 15.4 + - + +
190B ALA 3.4 0.4 - - - -
191B TRP* 1.4 78.1 - - - +
193B ALA* 1.3 60.9 + - - +
195B HIS 3.5 2.1 + - - -
196B ARG* 3.3 27.6 - - - +
304D HIS* 4.6 0.3 - - - -
305D ASP* 3.4 38.3 + - + -
308D MET* 3.2 30.7 - - + +
309D ARG* 2.6 50.0 + - + +
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Residues in contact with ALA 193 (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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189B THR 4.1 5.3 + - - +
190B ALA* 3.6 7.2 + - - +
191B TRP 3.4 0.2 - - - -
192B TYR* 1.3 78.8 - - - +
194B GLU* 1.3 61.5 + - + +
195B HIS 3.5 0.9 + - - -
196B ARG* 4.0 22.5 + - - +
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Residues in contact with GLU 194 (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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190B ALA* 3.1 38.8 + - - +
191B TRP* 3.3 3.8 + - - -
193B ALA* 1.3 79.7 - - + +
195B HIS* 1.4 81.2 + - + +
196B ARG 4.0 1.2 + - - -
44D LYS* 5.2 20.4 - - - +
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Residues in contact with HIS 195 (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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191B TRP* 3.0 78.1 + + + +
192B TYR 3.7 2.9 - - - -
193B ALA 3.3 0.4 - - - -
194B GLU* 1.4 97.4 + - + +
196B ARG* 1.4 52.9 + - - +
197B GLY 3.7 2.0 - - - +
60D TRP* 4.2 21.6 + - + +
77D MET* 5.6 10.5 - - + -
100D PHE* 6.1 2.2 - + - -
309D ARG* 2.8 33.4 + - - -
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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