Contacts of the helix formed by residues 181 - 196 (chain K) in PDB entry 1QDU
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 GLY 181 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179K ARG 3.0 0.6 + - - -
180K ASN* 1.3 73.7 - - - +
182K THR* 1.3 64.8 + - - +
183K HIS* 3.2 10.9 - - - -
184K LEU* 3.2 31.5 + - - +
185K ASP* 3.6 2.8 + - - -
341L ARG* 5.0 4.0 - - - -
342L ASN 4.5 3.4 - - - -
343L PRO* 4.0 17.5 + - - -
346L GLY* 3.7 11.7 - - - -
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Residues in contact with THR 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K ASN* 3.2 25.0 + - - +
170K ASN 4.0 1.6 - - - +
171K HIS* 3.8 13.7 + - - +
179K ARG* 2.5 72.2 + - - +
180K ASN 3.7 0.2 - - - -
181K GLY* 1.3 71.1 - - - +
183K HIS* 1.3 59.3 + - - +
185K ASP* 2.6 32.4 + - - +
186K ALA 2.8 10.9 + - - -
235K LEU* 3.7 13.0 - - + -
341L ARG* 5.0 2.5 - - - +
347L THR* 6.0 0.2 - - - -
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Residues in contact with HIS 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ASN* 4.3 6.5 + - - +
171K HIS* 2.7 49.7 + + + -
181K GLY* 4.6 4.5 - - - -
182K THR* 1.3 80.1 - - - +
184K LEU* 1.3 60.0 + - + +
186K ALA* 3.2 9.6 + - - +
187K GLY* 2.7 32.9 + - - -
204K HIS* 5.1 16.4 + + - -
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Residues in contact with LEU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K GLY* 3.5 24.9 - - - +
182K THR 3.0 0.4 - - - -
183K HIS* 1.3 82.2 - - + +
185K ASP* 1.3 66.7 + - - +
187K GLY* 3.8 1.7 - - - +
188K ALA* 3.0 23.6 + - - +
343L PRO 5.2 2.2 - - - +
344L ALA* 4.0 6.7 - - - +
345L GLU* 3.4 42.6 - - - +
351L GLN* 3.7 3.7 + - - +
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Residues in contact with ASP 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K GLY 3.6 0.6 + - - -
182K THR* 2.6 22.3 + - - +
184K LEU* 1.3 72.9 - - - +
186K ALA* 1.3 65.1 + - - +
188K ALA* 2.9 5.4 + - - +
189K LEU* 2.8 27.7 + - - +
235K LEU* 3.7 16.5 - - + +
283K GLN* 4.3 2.8 - - - +
346L GLY* 4.2 2.2 - - - -
347L THR* 2.8 52.6 + - - +
350L ILE* 3.3 18.1 - - + +
351L GLN* 2.9 23.2 + - - +
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Residues in contact with ALA 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ILE* 4.0 13.0 - - + +
169K ASN* 3.5 26.2 - - + +
182K THR 2.8 3.6 + - - -
183K HIS* 3.3 11.2 - - - +
185K ASP* 1.3 78.5 - - - +
187K GLY* 1.3 52.3 + - - +
189K LEU* 3.2 10.8 + - - +
190K THR* 2.7 41.3 + - - +
204K HIS* 5.7 6.3 - - + -
235K LEU* 4.0 2.6 - - - +
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Residues in contact with GLY 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K HIS 2.7 18.7 + - - -
184K LEU* 3.8 2.2 - - - -
185K ASP 3.2 0.2 - - - -
186K ALA* 1.3 72.9 - - - +
188K ALA* 1.3 53.4 + - - +
190K THR* 2.9 10.3 + - - +
191K THR* 2.7 39.7 + - - -
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Residues in contact with ALA 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LEU 3.0 12.2 + - - +
185K ASP 2.9 8.2 + - - +
187K GLY* 1.3 74.7 - - - +
189K LEU* 1.3 64.1 + - - +
191K THR* 3.7 5.1 - - - +
192K THR* 3.0 31.3 + - + +
350L ILE* 5.1 0.4 - - + -
351L GLN* 4.1 18.2 - - - +
354L CYS* 3.6 22.0 - - + -
358L ARG* 5.5 2.0 - - - +
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Residues in contact with LEU 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ILE* 3.8 14.8 - - + -
185K ASP 2.8 27.3 + - - +
186K ALA* 3.5 6.7 - - - +
188K ALA* 1.3 72.7 - - - +
190K THR* 1.3 64.4 + - - +
192K THR* 4.1 1.6 - - - -
193K PHE* 3.0 48.4 + - + +
233K CYS* 3.4 34.5 - - + -
235K LEU* 4.0 21.8 - - + -
281K PHE* 5.0 3.4 - - + -
350L ILE* 3.5 36.6 - - + -
353L LEU* 5.1 3.6 - - + -
354L CYS* 3.9 8.7 - - - -
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Residues in contact with THR 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 3.7 15.2 - - - +
186K ALA* 2.7 20.0 + - - +
187K GLY* 2.9 12.9 + - - +
189K LEU* 1.3 72.6 - - - +
191K THR* 1.3 71.4 + - - +
194K GLU* 3.0 43.7 + - - +
200K ILE* 3.9 18.5 - - + +
202K PRO* 4.8 5.0 - - - +
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Residues in contact with THR 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K GLY 2.7 21.1 + - - -
188K ALA* 3.7 5.1 - - - -
190K THR* 1.3 81.6 - - - +
192K THR* 1.3 56.4 + - - +
194K GLU* 2.9 13.1 + - - +
195K GLU* 2.8 47.2 + - - +
358L ARG* 3.3 16.2 - - - +
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Residues in contact with THR 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K ALA* 3.0 20.7 + - - +
189K LEU 3.6 3.1 + - - -
191K THR* 1.3 72.1 - - - +
193K PHE* 1.3 74.6 + - - +
195K GLU* 3.5 13.6 - - - +
196K LEU* 3.1 30.5 + - - +
354L CYS* 3.7 25.9 - - + +
357L LEU* 4.6 7.2 - - - +
358L ARG* 3.2 45.3 - - + +
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Residues in contact with PHE 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K CYS* 4.0 20.6 - - - -
189K LEU* 3.0 48.7 + - + +
192K THR* 1.3 85.0 + - - +
194K GLU* 1.3 64.7 + - - +
196K LEU* 3.2 19.2 + - + +
198K PHE* 3.1 35.4 + + + +
200K ILE* 4.1 6.3 - - + -
231K ILE* 3.0 34.8 - - + -
281K PHE* 3.8 24.7 - + - -
353L LEU* 5.4 0.9 - - + -
354L CYS* 5.7 0.7 - - - -
357L LEU* 3.4 31.9 - - + -
400L PHE* 4.1 15.0 - + - -
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Residues in contact with GLU 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K THR* 3.0 32.1 + - - +
191K THR* 2.9 9.0 + - - +
193K PHE* 1.3 76.0 - - - +
195K GLU* 1.3 54.9 + - + +
197K HIS* 2.7 30.3 + - - -
198K PHE 3.7 12.0 + - - +
200K ILE* 3.8 21.8 - - + +
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Residues in contact with GLU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K THR* 2.8 37.2 + - + +
192K THR* 3.5 10.5 - - - +
194K GLU* 1.3 74.3 - - + +
196K LEU* 1.3 58.2 + - + +
197K HIS* 3.0 21.5 + - - -
358L ARG* 2.9 31.7 + - - -
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Residues in contact with LEU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162K ARG* 3.4 17.8 + - - +
192K THR* 3.1 23.3 - - - +
193K PHE* 3.2 30.9 + - + +
194K GLU 3.0 1.2 + - - -
195K GLU* 1.3 78.6 - - + +
197K HIS* 1.3 72.5 - - - +
198K PHE* 3.3 12.6 + - + -
357L LEU* 4.7 13.0 - - + +
358L ARG* 6.2 1.8 - - - -
361L CYS* 4.0 26.5 - - + -
400L PHE* 4.0 32.8 - - + +
401L PRO* 4.8 8.2 - - - +
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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