Contacts of the helix formed by residues 183 - 198 (chain A) in PDB entry 5L0U
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 ARG 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A PHE 3.8 2.9 - - - -
167A TRP* 2.9 67.7 + - - +
182A GLY* 1.3 74.7 - - - +
184A TRP* 1.3 65.6 + - - +
185A ASP* 2.9 35.7 + - - +
186A LEU* 3.1 40.7 + - + +
187A PHE* 2.9 18.4 + - - +
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Residues in contact with TRP 184 (chain A).
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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165A THR 5.0 0.7 - - - +
166A PHE* 3.0 49.2 + + + +
182A GLY 3.3 4.1 + - - -
183A ARG* 1.3 73.2 - - - +
185A ASP* 1.3 57.2 + - - +
187A PHE* 4.2 4.3 - - + -
188A ARG* 2.8 53.7 + - + +
191A LEU* 4.7 1.3 - - + -
281A LYS* 3.7 45.5 - - + -
282A HIS* 3.6 33.9 - + - -
285A LEU* 3.6 23.1 - - + -
346A ILE* 3.7 20.0 - - + -
350A LEU* 2.7 33.0 + - + +
352A MET* 4.6 16.4 - - - -
355A ILE* 4.7 1.8 - - + -
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TRP* 4.6 2.3 - - - -
183A ARG* 2.9 50.3 + - - -
184A TRP* 1.3 76.6 - - - +
186A LEU* 1.3 69.1 + - + +
188A ARG* 3.7 12.3 - - - +
189A GLU* 3.4 25.2 + - - +
352A MET* 3.7 32.9 - - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG* 3.1 53.5 + - + +
185A ASP* 1.3 82.9 + - - +
187A PHE* 1.3 66.5 + - - +
189A GLU* 3.2 22.9 + - - +
190A ASP* 3.1 28.7 + - - +
193A ARG* 4.8 0.2 + - - -
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TYR* 3.9 17.0 - + - -
181A LEU* 3.4 29.6 - - + -
182A GLY 3.9 11.2 - - - -
183A ARG 2.9 13.8 + - - +
184A TRP* 3.3 9.8 + - + +
186A LEU* 1.3 74.5 - - - +
188A ARG* 1.3 65.4 + - - +
190A ASP* 3.1 10.3 + - + +
191A LEU* 2.9 33.9 + - + +
258A HIS* 3.3 32.3 - + - -
259A LEU* 3.8 23.3 - - + -
260A VAL* 4.2 5.4 - - + -
282A HIS* 3.5 27.8 - + + +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 2.8 65.3 + - + +
185A ASP* 3.7 10.5 + - - +
187A PHE* 1.3 77.1 - - - +
189A GLU* 1.3 59.1 + - + +
191A LEU* 3.2 2.1 + - - +
192A VAL* 2.9 35.7 + - + +
285A LEU* 3.7 16.8 - - + +
346A ILE* 2.9 29.7 + - - +
347A ARG* 2.8 28.8 + - - +
350A LEU 3.0 15.0 + - - -
351A GLN* 3.6 20.7 - - - +
352A MET 4.9 1.8 - - - +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASP* 3.4 18.4 - - - +
186A LEU* 3.2 22.8 + - - +
188A ARG* 1.3 76.6 - - + +
190A ASP* 1.3 63.5 + - - +
192A VAL* 3.4 7.0 + - - +
193A ARG* 3.1 49.9 + - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 3.1 17.6 + - - +
187A PHE* 3.1 14.2 + - + +
189A GLU* 1.3 75.8 - - - +
191A LEU* 1.3 58.6 + - - +
193A ARG* 2.7 35.3 + - - +
194A SER* 3.0 26.9 + - - -
258A HIS* 5.6 2.8 - - - -
260A VAL* 3.9 21.7 - - + +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 4.7 0.2 - - + -
187A PHE* 2.9 40.6 + - + +
188A ARG 3.7 3.4 - - - +
190A ASP* 1.3 75.0 - - - +
192A VAL* 1.3 58.6 + - - +
194A SER* 3.2 3.9 + - - -
195A ALA* 2.8 31.7 + - - +
259A LEU* 3.9 17.3 - - + +
260A VAL* 4.0 9.6 - - + +
263A CYS* 3.9 24.1 - - - -
282A HIS* 3.6 36.6 - - + +
285A LEU* 3.5 26.8 - - + +
286A CYS* 3.9 9.4 - - - -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 2.9 25.9 + - + +
189A GLU* 3.8 7.2 - - - +
190A ASP 3.4 0.2 - - - -
191A LEU* 1.3 75.2 - - - +
193A ARG* 1.3 65.3 + - + +
195A ALA* 3.4 3.3 + - - +
196A ALA* 3.1 22.9 + - + +
285A LEU* 4.4 18.4 - - + +
347A ARG* 3.5 43.5 + - + +
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU 4.8 0.4 + - - -
189A GLU* 3.1 37.0 + - - +
190A ASP* 2.7 43.4 + - - +
191A LEU 3.2 0.2 - - - -
192A VAL* 1.3 79.8 - - + +
194A SER* 1.3 61.3 + - - +
196A ALA* 3.3 8.0 + - - +
197A GLN* 3.2 25.6 + - - +
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Residues in contact with SER 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP 3.0 16.5 + - - -
191A LEU 3.7 4.5 - - - -
193A ARG* 1.3 74.8 - - - +
195A ALA* 1.3 64.5 + - - +
197A GLN* 3.0 25.8 + - - +
198A TRP* 3.2 19.9 + - - -
260A VAL* 2.7 36.6 + - - -
263A CYS* 3.3 14.9 - - - +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU 2.8 12.6 + - - +
192A VAL* 3.8 6.3 - - - +
193A ARG 3.3 0.2 - - - -
194A SER* 1.3 72.3 - - - +
196A ALA* 1.3 57.6 + - - +
198A TRP 3.0 28.0 + - - +
199A PRO* 3.6 3.1 - - - +
263A CYS* 4.5 3.9 - - - -
285A LEU 3.4 20.4 - - - +
286A CYS 3.3 28.5 - - - +
287A GLY* 4.2 3.4 - - - +
347A ARG* 5.4 5.6 - - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 3.1 13.7 + - + +
193A ARG* 3.6 11.2 - - - +
194A SER 3.2 0.4 - - - -
195A ALA* 1.3 78.4 - - - +
197A GLN* 1.3 61.4 + - + +
198A TRP 3.4 0.3 + - - -
199A PRO* 3.6 11.5 - - - +
202A LYS* 5.4 1.0 + - - -
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Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG 3.2 12.4 + - - +
194A SER* 3.0 20.5 + - - +
196A ALA* 1.3 77.4 - - + +
198A TRP* 1.3 79.8 + - + +
199A PRO* 3.4 7.2 - - - +
202A LYS* 4.4 10.0 + - - +
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Residues in contact with TRP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A SER* 3.2 29.0 + - - +
195A ALA 3.0 10.4 + - - +
197A GLN* 1.3 97.2 + - + +
199A PRO* 1.3 64.5 - - - +
202A LYS* 3.7 34.1 - - + -
203A LYS* 2.8 25.7 + - + +
204A ASN 6.0 0.2 - - - -
260A VAL 5.6 0.4 - - - -
263A CYS 3.7 14.8 - - - +
264A LYS* 3.6 55.9 - - + +
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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