Contacts of the helix formed by residues 189 - 204 (chain B) in PDB entry 3QI5
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B THR* 5.1 4.0 - - - -
116B GLU 4.3 4.7 - - - -
117B LEU* 3.4 19.7 - - - +
188B GLU* 1.3 79.5 - - - +
190B LEU* 1.3 58.9 + - - +
191B GLU 3.2 3.8 - - - -
192B THR* 3.2 8.5 + - - -
193B MET* 3.1 24.8 + - - +
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Residues in contact with LEU 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 PRO* 3.8 34.8 - - + +
187B LEU 3.7 9.6 - - - +
188B GLU* 3.6 26.9 - - - +
189B GLY* 1.3 77.4 - - - +
191B GLU* 1.3 60.4 + - + +
193B MET* 3.5 10.3 + - - +
194B ARG* 3.0 38.7 + - - +
211B ASP* 3.8 31.0 - - - +
214B LEU* 4.1 6.9 - - + +
284B TRP* 6.3 0.7 - - + -
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Residues in contact with GLU 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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189B GLY 3.2 0.8 - - - -
190B LEU* 1.3 77.8 - - + +
192B THR* 1.3 63.7 + - - +
194B ARG* 2.8 42.6 + - - +
195B GLN* 3.3 35.0 + - - +
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Residues in contact with THR 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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111B LEU* 3.7 30.5 - - + -
113B ASN* 5.6 3.6 - - - +
115B THR* 3.7 16.4 + - + +
117B LEU* 3.8 8.5 - - + -
189B GLY* 3.2 11.0 + - - -
191B GLU* 1.3 77.1 - - - +
193B MET* 1.3 63.8 + - - +
194B ARG 3.2 0.2 - - - -
195B GLN* 3.2 14.1 + - + +
196B LEU* 2.9 35.1 + - + +
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Residues in contact with MET 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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117B LEU* 4.2 7.0 - - + -
118B ARG 3.4 30.5 - - - +
119B GLY* 5.1 0.2 - - - -
186B PRO* 3.9 26.5 - - + -
188B GLU 3.5 15.7 - - - +
189B GLY 3.1 14.3 + - - +
190B LEU* 3.5 12.8 - - - +
192B THR* 1.3 76.8 - - - +
194B ARG* 1.3 51.6 + - - +
196B LEU* 3.3 2.3 + - - +
197B ARG* 2.8 39.0 + - - +
214B LEU* 4.3 11.0 - - + -
215B CYS* 4.0 14.8 - - - -
224B ALA* 3.5 30.9 + - + +
225B LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 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 LEU* 3.0 28.4 + - - +
191B GLU* 2.8 42.6 + - - +
192B THR 3.2 0.2 - - - -
193B MET* 1.3 76.4 - - - +
195B GLN* 1.3 54.4 + - + +
197B ARG* 3.8 1.6 - - - -
198B SER* 2.7 40.1 + - - +
209B LEU* 2.8 54.5 + - + +
210B LYS* 4.0 4.8 - - - +
211B ASP* 3.0 30.1 + - - -
214B LEU* 3.8 15.6 - - + +
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Residues in contact with GLN 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 GLU* 3.3 21.4 + - - +
192B THR* 3.2 15.4 + - + +
194B ARG* 1.3 77.5 - - + +
196B LEU* 1.3 61.4 + - + +
198B SER* 3.4 7.7 + - - -
199B THR* 3.2 23.9 + - - -
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Residues in contact with LEU 196 (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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111B LEU* 4.6 4.3 - - + -
117B LEU* 4.4 4.5 - - + -
192B THR* 2.9 35.5 + - + +
193B MET 3.7 3.6 - - - +
195B GLN* 1.3 77.9 - - + +
197B ARG* 1.3 60.7 + - - +
198B SER 3.6 0.2 + - - -
199B THR* 3.7 19.3 + - - +
200B LEU 4.8 1.2 + - - -
223B GLN* 3.4 29.4 - - - +
224B ALA 3.5 20.6 - - - +
226B ALA* 4.2 24.0 - - + +
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Residues in contact with ARG 197 (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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193B MET 2.8 20.6 + - - +
194B ARG* 3.9 1.6 - - - +
195B GLN 3.4 0.2 - - - -
196B LEU* 1.3 75.5 - - - +
198B SER* 1.3 62.4 + - - +
199B THR 3.5 0.2 - - - -
200B LEU 4.5 0.4 + - - -
201B ARG* 3.3 35.7 + - - +
209B LEU* 3.7 17.6 - - + +
213B GLU* 2.8 29.4 + - - +
214B LEU* 3.3 19.9 + - + +
220B LYS* 3.3 38.2 - - - +
223B GLN* 2.9 30.4 + - - +
224B ALA* 3.9 9.4 - - + -
9E T 4.6 0.2 + - - -
10E G 2.7 43.2 + - - -
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Residues in contact with SER 198 (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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194B ARG* 2.7 25.6 + - - +
195B GLN* 3.6 8.9 - - - -
196B LEU 3.3 0.6 - - - -
197B ARG* 1.3 78.9 - - - +
199B THR* 1.3 59.5 + - - +
200B LEU 3.5 0.2 - - - -
201B ARG* 3.1 1.1 + - - -
202B LYS* 2.5 57.4 + - - +
209B LEU* 3.6 19.3 - - - +
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Residues in contact with THR 199 (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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195B GLN 3.2 13.6 + - - -
196B LEU* 3.9 14.7 + - - +
197B ARG 3.5 0.8 - - - -
198B SER* 1.3 80.1 - - - +
200B LEU* 1.3 63.0 + - + +
202B LYS* 4.8 0.4 - - - +
203B GLY* 3.4 15.1 + - - -
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Residues in contact with LEU 200 (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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164B MET* 3.7 34.1 - - + +
165B TYR* 3.7 22.2 - - + +
196B LEU 4.8 2.0 + - - -
197B ARG 4.5 1.0 + - - -
198B SER 3.5 0.2 - - - -
199B THR* 1.3 81.7 - - + +
201B ARG* 1.3 53.5 + - - +
203B GLY* 4.3 0.3 - - - -
204B THR* 2.8 36.9 + - + +
223B GLN* 3.3 33.9 - - - +
10E G 6.5 0.9 - - - -
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Residues in contact with ARG 201 (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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197B ARG* 3.3 41.5 + - - +
198B SER* 3.1 2.8 + - - -
200B LEU* 1.3 77.3 - - - +
202B LYS* 1.3 64.8 + - + +
203B GLY 3.2 1.6 - - - -
204B THR* 3.2 25.5 + - - -
208B VAL 6.0 0.9 - - - -
209B LEU* 4.3 29.3 - - + +
213B GLU* 4.1 30.1 + - - +
223B GLN* 5.7 0.2 - - - +
10E G 3.4 64.4 + - - +
11E C 3.9 21.3 + - - +
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Residues in contact with LYS 202 (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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198B SER* 2.5 36.2 + - - +
199B THR 4.8 0.2 - - - +
201B ARG* 1.3 71.3 - - + +
203B GLY* 1.3 65.1 + - - +
204B THR 4.4 1.9 - - - -
207B ARG* 3.8 48.7 + - + +
208B VAL* 3.1 30.3 - - - +
209B LEU* 3.5 26.5 - - + +
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Residues in contact with GLY 203 (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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199B THR 3.4 15.8 + - - -
200B LEU 4.3 0.2 - - - -
201B ARG 3.2 0.8 - - - -
202B LYS* 1.3 82.0 - - - +
204B THR* 1.3 61.9 + - - +
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Residues in contact with THR 204 (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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164B MET* 6.0 5.6 - - + -
200B LEU* 2.8 27.1 + - + +
201B ARG* 3.2 17.7 + - - -
202B LYS 4.4 2.7 - - - -
203B GLY* 1.3 79.1 - - - +
10E G 5.6 6.9 + - - -
11E C 5.1 9.9 + - - +
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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