Contacts of the helix formed by residues 192 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLY* 6.6 0.2 - - - -
162A ASP* 5.7 3.6 - - - +
164A GLU* 4.6 34.1 + - - -
165A ASP* 5.5 0.4 - - - -
166A GLY* 4.2 30.9 - - - -
169A ALA* 5.6 1.8 - - + -
190A TYR* 4.8 13.5 - + + -
191A ALA* 1.3 78.6 - - + +
193A ASN* 1.3 67.9 + - - +
195A PRO* 3.3 4.6 - - - +
196A ALA* 3.3 26.9 + - - +
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Residues in contact with ASN 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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129A GLY* 3.0 36.2 + - - +
130A THR* 3.6 9.5 - - - -
131A GLY* 4.0 1.2 + - - -
162A ASP* 3.4 24.5 + - - +
169A ALA* 4.2 10.3 - - - +
188A GLY* 3.5 10.8 - - - -
190A TYR* 3.3 30.4 + - - +
191A ALA 3.1 1.8 - - - -
192A TYR* 1.3 79.7 - - - +
194A GLY* 1.3 58.1 + - - +
195A PRO 3.3 1.8 - - - -
196A ALA* 3.2 3.3 + - - +
197A GLN* 2.8 43.8 + - - +
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Residues in contact with GLY 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 TYR 4.2 2.0 + - - -
191A ALA 4.3 0.2 + - - -
193A ASN* 1.3 75.4 - - - +
195A PRO* 1.3 63.7 - - - +
197A GLN* 3.3 12.1 + - - +
198A ALA* 2.7 29.6 + - - +
212A ILE* 4.4 2.6 - - - +
214A CYS* 3.7 32.1 - - - +
215A PHE 5.8 0.2 + - - -
221A ILE* 5.6 0.4 - - - +
230A ILE* 3.7 9.8 - - - +
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Residues in contact with PRO 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 ALA 3.2 23.8 - - - +
192A TYR* 3.3 10.8 - - - +
194A GLY* 1.3 86.7 - - - +
196A ALA* 1.3 53.9 + - - +
198A ALA* 3.5 0.5 - - - +
199A LEU* 2.8 36.4 + - - +
218A THR* 4.8 0.9 - - - +
220A ASP* 4.4 17.3 - - + +
221A ILE* 3.6 23.8 - - + +
224A TYR* 3.5 27.1 - - + -
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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
----------------------------------------------------------
166A GLY* 4.8 2.0 - - - +
169A ALA* 3.9 27.6 - - + +
170A VAL* 4.2 18.7 - - + +
173A ALA* 5.1 1.3 - - - -
192A TYR 3.3 18.0 + - - +
193A ASN* 3.2 5.6 + - - +
195A PRO* 1.3 79.8 - - - +
197A GLN* 1.3 63.2 + - + +
199A LEU* 3.4 8.3 + - - +
200A VAL* 3.2 25.8 + - - +
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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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129A GLY* 3.6 14.0 - - - +
173A ALA* 4.5 13.4 - - + +
186A PHE* 3.0 51.1 - - + +
187A PHE 3.2 21.0 + - - -
188A GLY* 3.3 19.6 + - - -
193A ASN* 2.8 27.8 + - - +
194A GLY* 3.6 8.0 - - - +
196A ALA* 1.3 74.4 - - + +
198A ALA* 1.3 58.0 + - - +
200A VAL* 3.2 3.6 + - - +
201A VAL* 2.9 32.9 + - - +
212A ILE* 3.7 16.3 - - + +
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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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194A GLY 2.7 18.6 + - - +
195A PRO 3.5 3.4 - - - +
197A GLN* 1.3 73.6 - - - +
199A LEU* 1.3 65.9 + - - +
201A VAL* 3.8 0.9 - - - +
202A LYS* 2.9 27.7 + - - +
212A ILE* 3.5 13.5 - - + -
224A TYR* 3.5 36.8 - - + -
229A VAL* 3.7 12.4 - - + +
230A ILE* 4.1 4.7 - - + -
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Residues in contact with LEU 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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170A VAL* 4.1 31.4 - - + -
195A PRO 2.8 19.7 + - - +
196A ALA* 3.5 6.5 - - - +
198A ALA* 1.3 74.9 - - - +
200A VAL* 1.3 56.9 + - - +
202A LYS* 3.7 4.7 - - + +
203A ASN* 2.9 66.8 + - - +
224A TYR* 3.5 17.6 + - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.4 37.9 - - + +
173A ALA* 3.7 13.0 - - + -
174A GLU* 3.7 29.4 - - + +
177A LEU* 3.4 24.9 - - + -
186A PHE* 5.1 0.9 - - + -
196A ALA 3.2 13.4 + - - +
197A GLN 3.2 7.6 + - - +
199A LEU* 1.3 77.8 - - + +
201A VAL* 1.3 58.9 + - - +
203A ASN* 3.5 7.4 + - - +
204A ALA* 3.0 27.4 + - + +
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Residues in contact with VAL 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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177A LEU* 4.6 3.6 - - + -
186A PHE* 3.9 22.2 - - + -
197A GLN 2.9 21.2 + - - +
198A ALA* 3.3 3.6 + - - +
200A VAL* 1.3 75.4 - - - +
202A LYS* 1.3 65.2 + - - +
204A ALA* 3.1 11.3 + - - +
205A GLY 3.2 0.2 + - - -
206A LYS* 3.0 54.5 + - + +
207A VAL* 3.8 8.5 - - + +
210A VAL* 4.0 21.1 - - + +
212A ILE* 3.7 19.3 - - + -
229A VAL* 4.8 7.2 - - + +
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Residues in contact with LYS 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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198A ALA 2.9 18.3 + - - +
199A LEU* 3.7 5.8 - - + +
201A VAL* 1.3 77.4 - - - +
203A ASN* 1.3 59.9 + - - +
205A GLY* 2.9 20.6 + - - -
207A VAL* 4.1 23.6 - - + +
224A TYR* 4.4 16.9 + - + +
227A GLU* 3.0 34.1 + - - +
229A VAL* 4.8 7.2 - - + +
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Residues in contact with ASN 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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174A GLU* 5.4 6.6 + - - +
199A LEU* 2.9 47.3 + - - +
200A VAL* 3.7 7.8 - - - +
202A LYS* 1.3 80.6 - - - +
204A ALA* 1.3 58.4 + - - +
205A GLY 3.1 1.3 + - - -
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Residues in contact with ALA 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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177A LEU* 3.6 23.3 - - + -
200A VAL* 3.0 18.0 + - + +
201A VAL 3.1 6.2 + - - +
203A ASN* 1.3 75.6 - - - +
205A GLY* 1.3 63.7 + - - +
206A LYS* 4.0 20.4 + - + +
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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