Contacts of the helix formed by residues 192 - 204 (chain D) in PDB entry 3C6Q
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 TYR 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D SER* 3.0 24.9 + - - -
11D VAL 3.2 16.3 + - - -
12D HIS* 3.2 30.5 - + + -
39D GLN 5.4 1.9 + - - -
162D ASP* 4.7 6.3 - - - +
164D GLU* 3.3 52.1 + - + -
165D ASP 4.9 0.7 - - - +
166D GLY* 3.7 33.4 - - - -
169D ALA* 5.0 3.4 - - + -
190D TYR* 3.3 8.5 - + + -
191D ALA* 1.3 77.6 - - + +
193D ASN* 1.3 65.1 + - - +
195D PRO* 2.9 18.7 - - - +
196D ALA* 3.3 15.2 + - - +
501D XYP 5.4 2.2 - - - -
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Residues in contact with ASN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLY* 2.7 45.9 - - - +
130D THR* 3.1 10.7 - - - +
131D GLY* 3.8 0.3 + - - -
162D ASP* 3.1 21.9 + - - +
169D ALA* 4.7 3.6 - - - +
188D GLY* 3.6 14.6 - - - -
190D TYR* 3.2 28.5 + - - +
192D TYR* 1.3 76.6 - - - +
194D GLY* 1.3 69.4 - - - +
196D ALA* 3.9 4.9 - - - +
197D GLN* 3.1 32.6 + - - +
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Residues in contact with GLY 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D TYR 3.7 7.1 + - - -
191D ALA 4.0 0.4 + - - -
192D TYR 3.3 0.2 - - - -
193D ASN* 1.3 82.4 - - - +
195D PRO* 1.3 67.5 - - - +
197D GLN* 3.6 4.4 - - - +
198D ALA* 3.1 17.8 + - - +
212D ILE* 4.4 1.6 - - - +
214D CYS* 3.6 35.4 - - - +
221D ILE* 4.6 2.2 - - - -
230D ILE* 3.9 9.1 - - - +
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Residues in contact with PRO 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D HIS* 5.9 0.9 - - - +
191D ALA 3.1 15.5 - - - +
192D TYR* 2.9 19.1 - - - +
194D GLY* 1.3 80.6 - - - +
196D ALA* 1.3 64.2 + - - +
198D ALA* 3.1 10.5 + - + +
199D LEU* 2.9 23.8 + - - +
218D THR* 4.9 0.4 - - - +
220D ASP* 3.1 28.9 - - - +
221D ILE* 3.3 22.2 - - + +
224D TYR* 3.8 21.1 - - + -
230D ILE* 4.6 1.3 - - + -
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLY* 4.8 1.1 - - - +
169D ALA* 3.9 26.5 - - + -
170D VAL* 4.2 22.0 - - + +
173D ALA* 5.2 1.1 - - + -
192D TYR* 3.3 16.5 + - + +
193D ASN* 3.9 4.7 - - - +
194D GLY 3.3 0.2 - - - -
195D PRO* 1.3 76.2 - - - +
197D GLN* 1.3 65.7 + - + +
199D LEU* 2.8 20.3 + - - +
200D VAL* 3.1 16.6 + - - +
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Residues in contact with GLN 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLY* 3.6 20.2 - - - +
173D ALA* 4.6 13.4 - - + +
186D PHE* 3.3 43.6 - - + +
187D PHE 3.5 21.2 + - - -
188D GLY* 3.5 17.2 + - - -
193D ASN* 3.1 22.6 + - - +
194D GLY* 3.6 2.1 - - - +
196D ALA* 1.3 79.4 - - + +
198D ALA* 1.3 63.1 + - - +
200D VAL* 3.3 1.7 + - - +
201D VAL* 2.9 28.6 + - - +
212D ILE* 3.5 23.0 - - + +
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLY 3.1 10.0 + - - +
195D PRO 3.1 9.8 + - - +
196D ALA 3.1 0.4 - - - -
197D GLN* 1.3 78.1 - - - +
199D LEU* 1.3 57.2 + - - +
201D VAL* 3.5 0.3 + - - +
202D LYS* 2.9 28.6 + - - +
212D ILE* 3.4 11.4 - - - +
224D TYR* 3.4 35.4 - - + -
229D VAL* 3.6 11.5 - - + +
230D ILE* 3.8 15.3 - - + -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 4.1 24.2 - - + -
195D PRO 2.9 10.5 + - - +
196D ALA* 2.8 18.1 + - - +
198D ALA* 1.3 67.1 - - - +
200D VAL* 1.3 58.7 + - + +
201D VAL 3.0 1.8 - - - -
202D LYS* 2.8 31.7 + - + +
203D ASN* 2.9 34.8 + - - +
224D TYR* 3.3 21.9 - - + +
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 3.2 36.6 - - + +
173D ALA* 3.5 37.0 - - + +
174D GLU* 3.6 19.7 - - + +
177D LEU* 3.7 22.1 - - + +
186D PHE* 5.0 3.6 - - + -
196D ALA 3.1 8.2 + - - +
197D GLN 3.8 6.3 - - - +
199D LEU* 1.3 79.3 - - - +
201D VAL* 1.3 58.8 + - - +
203D ASN* 3.8 11.6 + - - +
204D ALA* 3.5 15.4 + - - +
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU* 4.8 3.4 - - + -
186D PHE* 3.9 22.2 - - + -
197D GLN 2.9 22.4 + - - +
198D ALA 3.8 3.8 - - - +
200D VAL* 1.3 75.0 - - + +
202D LYS* 1.3 66.3 + - - +
203D ASN 3.4 0.2 + - - -
204D ALA 3.4 4.4 + - - +
206D LYS* 3.1 56.6 + - + +
207D VAL* 3.7 7.6 + - - +
208D GLY 5.1 0.2 - - - +
210D VAL* 3.9 21.3 - - + +
212D ILE* 3.7 17.5 - - + -
229D VAL* 4.7 6.3 - - + +
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Residues in contact with LYS 202 (chain D).
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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198D ALA 2.9 14.4 + - - +
199D LEU* 2.8 15.8 + - + +
201D VAL* 1.3 77.4 - - - +
203D ASN* 1.3 64.3 + - - +
205D GLY* 3.4 10.7 + - - -
207D VAL* 4.3 19.3 - - + +
224D TYR* 3.9 21.6 - - + +
227D GLU* 3.4 28.5 + - - +
229D VAL* 4.9 3.4 - - + -
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Residues in contact with ASN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 6.0 1.4 - - - +
174D GLU* 5.0 11.1 + - - +
199D LEU* 2.9 37.3 + - - +
200D VAL* 3.8 14.7 - - - +
202D LYS* 1.3 75.5 - - - +
204D ALA* 1.3 59.2 + - + +
205D GLY* 2.9 10.4 + - - -
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU* 3.6 31.0 - - + -
200D VAL 3.5 3.7 + - - +
201D VAL 3.4 3.9 + - - +
203D ASN* 1.3 77.2 - - - +
205D GLY* 1.3 63.1 + - - +
206D LYS* 3.6 26.3 + - + +
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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