Contacts of the helix formed by residues 192 - 212 (chain A) in PDB entry 1Q99
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 ASP 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ARG* 3.0 13.0 + - + -
191A GLY* 1.3 75.4 - - - +
193A LYS* 1.3 58.6 + - - +
194A VAL* 2.6 39.9 + - - +
195A TYR* 3.1 33.8 + - + -
196A THR* 2.7 40.0 + - - -
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Residues in contact with LYS 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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192A ASP* 1.3 77.1 + - - +
194A VAL* 1.3 70.3 + - + +
196A THR* 3.3 6.4 + - - +
197A GLU* 3.1 52.6 + - + +
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Residues in contact with VAL 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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192A ASP* 2.6 16.2 + - - +
193A LYS* 1.3 80.8 - - + +
195A TYR* 1.3 64.9 + - + +
197A GLU* 3.4 14.9 + - - +
198A ALA* 3.2 21.2 + - + +
2001A MOH 5.2 12.6 - - - -
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Residues in contact with TYR 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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168A HIS 4.7 1.8 + - - -
169A PHE* 3.1 43.5 - + + -
189A VAL* 4.0 7.3 - - + +
190A ARG* 3.3 62.5 + - + +
192A ASP* 3.1 32.6 + - + +
194A VAL* 1.3 79.6 - - + +
196A THR* 1.3 59.9 + - - +
198A ALA* 3.2 10.1 + - + +
199A ALA* 2.9 28.6 + - - +
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Residues in contact with THR 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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189A VAL* 5.1 0.4 - - - -
190A ARG 4.4 3.9 + - - -
192A ASP 2.7 29.1 + - - -
193A LYS* 3.5 7.0 - - - +
195A TYR* 1.3 74.5 - - - +
197A GLU* 1.3 62.8 + - + +
199A ALA* 3.2 3.6 + - - +
200A GLU* 3.0 30.6 + - + +
233A ASN* 5.6 1.1 - - - +
240A VAL* 4.2 11.3 + - - +
242A VAL* 3.8 28.1 + - + +
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Residues in contact with GLU 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 LYS* 3.1 43.5 + - + +
194A VAL* 3.6 19.0 - - - +
195A TYR 3.2 0.2 - - - -
196A THR* 1.3 75.7 - - + +
198A ALA* 1.3 66.3 + - - +
200A GLU* 3.2 9.8 + - - +
201A ASP* 3.1 26.5 + - - +
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Residues in contact with ALA 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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169A PHE* 5.7 9.0 - - + -
194A VAL* 3.2 10.0 + - + +
195A TYR* 3.2 13.9 + - + +
197A GLU* 1.3 78.5 - - - +
199A ALA* 1.3 63.2 + - - +
201A ASP* 3.0 11.7 + - - +
202A GLU* 3.0 17.8 + - - +
1440A EDO 3.2 34.3 + - - +
2001A MOH 4.2 9.3 + - - +
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Residues in contact with ALA 199 (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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169A PHE* 5.5 3.5 - - + -
189A VAL* 3.9 22.7 - - + -
195A TYR 2.9 13.6 + - - +
196A THR 3.5 8.7 - - - +
198A ALA* 1.3 77.0 - - - +
200A GLU* 1.3 56.2 + - - +
202A GLU* 3.2 11.0 + - - +
203A ILE* 2.9 33.7 + - - +
242A VAL* 3.9 26.2 - - + -
244A MET* 4.4 4.1 - - + +
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Residues in contact with GLU 200 (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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196A THR* 3.0 25.8 + - + +
197A GLU* 3.6 10.5 - - - +
199A ALA* 1.3 76.5 - - - +
201A ASP* 1.3 63.7 + - - +
203A ILE* 3.3 24.2 + - - +
204A LYS* 3.1 30.0 + - - +
231A HIS* 5.5 3.6 + - - -
233A ASN* 4.5 6.8 + - - +
242A VAL* 3.7 22.5 - - - +
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Residues in contact with ASP 201 (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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197A GLU* 3.1 18.1 + - - +
198A ALA* 3.0 11.3 + - - +
200A GLU* 1.3 75.6 - - - +
202A GLU* 1.3 66.5 + - - +
204A LYS* 3.0 25.0 + - - +
205A LEU* 3.0 16.5 + - - +
556A TRP* 5.0 0.5 - - - -
561A TYR* 3.7 28.6 + - + +
1440A EDO 3.2 25.2 + - - -
2001A MOH 4.3 5.5 + - - -
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Residues in contact with GLU 202 (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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169A PHE* 3.4 21.0 - - - -
187A LYS* 3.4 22.0 + - - -
198A ALA 3.0 11.3 + - - +
199A ALA* 3.5 9.1 - - - +
201A ASP* 1.3 75.3 - - - +
203A ILE* 1.3 58.0 + - - +
205A LEU* 3.0 12.5 + - - +
206A LEU* 2.8 48.0 + - + +
244A MET* 3.7 22.9 - - - +
246A PHE* 4.6 0.3 - - - -
551A LEU* 3.4 22.2 + - + +
552A GLY* 3.4 25.1 + - - -
1440A EDO 4.4 5.3 - - - +
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Residues in contact with ILE 203 (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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199A ALA 2.9 14.7 + - - +
200A GLU* 3.4 25.8 - - - +
201A ASP 3.1 0.2 - - - -
202A GLU* 1.3 77.0 - - - +
204A LYS* 1.3 56.8 + - + +
206A LEU* 3.5 2.7 + - - +
207A GLN* 2.8 55.9 + - + +
228A LEU* 4.3 11.8 - - + +
231A HIS* 3.6 39.5 - - + +
242A VAL* 3.7 29.4 - - + -
244A MET* 3.9 19.1 - - + -
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Residues in contact with LYS 204 (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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200A GLU* 3.1 17.6 + - - +
201A ASP* 3.0 17.4 + - - +
203A ILE* 1.3 74.5 - - + +
205A LEU* 1.3 67.3 + - - +
207A GLN* 3.2 17.5 + - - +
208A ARG* 2.9 23.2 + - - +
556A TRP* 3.9 16.3 - - + -
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Residues in contact with LEU 205 (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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201A ASP 3.0 10.6 + - - +
202A GLU* 3.0 25.1 + - + +
204A LYS* 1.3 77.0 - - - +
206A LEU* 1.3 61.8 + - + +
208A ARG* 3.0 15.2 + - - +
209A VAL* 3.1 11.3 + - - +
290A ILE* 3.4 42.9 - - + +
551A LEU* 4.2 12.6 - - + +
554A ALA* 3.3 33.4 - - + +
555A CYS 3.9 9.2 - - - +
556A TRP* 3.6 31.2 - - + +
561A TYR* 4.4 8.3 - - + -
1440A EDO 5.5 1.8 - - - -
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Residues in contact with LEU 206 (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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202A GLU* 2.8 38.9 + - + +
203A ILE 3.8 3.8 - - - +
205A LEU* 1.3 73.9 - - - +
207A GLN* 1.3 61.5 + - - +
209A VAL* 3.3 11.4 + - + +
210A ASN* 3.3 25.4 + - - -
226A LEU 4.0 21.1 - - - +
227A LYS* 5.2 0.6 - - - -
228A LEU* 3.7 25.5 + - + +
244A MET* 4.0 11.2 - - - -
246A PHE* 3.7 32.3 - - + -
551A LEU* 3.6 29.8 - - + +
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Residues in contact with GLN 207 (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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203A ILE* 2.8 39.7 + - + +
204A LYS* 3.5 18.9 - - - +
205A LEU 3.2 0.4 - - - -
206A LEU* 1.3 74.5 - - - +
208A ARG* 1.3 59.5 - - - +
210A ASN* 3.3 10.8 + - - +
211A ASP* 2.8 44.6 + - - +
228A LEU* 4.5 8.1 - - + -
231A HIS* 3.9 22.6 + - - -
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Residues in contact with ARG 208 (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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204A LYS 2.9 11.7 + - - +
205A LEU 3.0 9.6 + - - +
207A GLN* 1.3 75.3 - - - +
209A VAL* 1.3 66.4 + - - +
211A ASP* 3.1 7.4 + - - -
212A ALA* 2.8 34.6 + - - +
287A ARG 4.5 7.5 + - - -
288A CYS* 3.6 42.5 + - + +
290A ILE* 3.8 4.3 - - + -
556A TRP* 3.6 27.0 - - + -
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Residues in contact with VAL 209 (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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205A LEU 3.1 11.1 + - - +
206A LEU* 3.4 11.0 - - + +
208A ARG* 1.3 80.1 - - - +
210A ASN* 1.3 56.5 + - - +
213A ASP* 4.0 4.3 + - - +
222A ALA 5.3 0.2 - - - +
225A ILE* 3.8 29.4 - - + -
226A LEU 5.5 0.4 - - - +
227A LYS* 4.1 24.5 - - + -
283A TYR* 2.6 33.6 + - + -
284A MET* 5.1 4.3 - - + -
288A CYS* 3.8 20.2 - - + -
290A ILE* 4.2 6.3 - - + -
551A LEU* 4.1 21.8 - - + -
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Residues in contact with ASN 210 (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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206A LEU 3.3 13.8 + - - +
207A GLN* 3.3 12.2 + - - +
208A ARG 3.0 0.4 - - - -
209A VAL* 1.3 77.3 - - - +
211A ASP* 1.3 67.8 + - - +
212A ALA 3.3 0.6 + - - -
213A ASP* 3.5 18.9 + - - +
227A LYS* 3.2 38.9 + - - +
228A LEU* 3.2 31.5 + - - +
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Residues in contact with ASP 211 (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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207A GLN* 2.8 40.2 + - - +
208A ARG* 3.9 7.7 - - - +
210A ASN* 1.3 76.8 - - - +
212A ALA* 1.3 58.5 + - - +
213A ASP 3.3 0.2 - - - -
214A ASN* 3.4 20.6 + - - +
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Residues in contact with ALA 212 (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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208A ARG* 2.8 25.0 + - - +
211A ASP* 1.3 75.8 - - - +
213A ASP* 1.3 58.4 + - - +
214A ASN* 2.9 19.7 + - - +
218A ASP* 3.2 16.6 - - - +
283A TYR* 3.1 13.0 - - + +
287A ARG* 4.2 18.5 - - + +
288A CYS* 4.0 14.1 - - - -
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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
------------------------------------------------------------
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