Contacts of the helix formed by residues 186 - 197 (chain A) in PDB entry 2CT8
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 PRO 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ILE* 4.8 1.1 - - + -
185A GLN* 1.3 87.2 - - + +
187A ASP* 1.3 54.7 + - - +
188A TYR* 3.2 22.4 - - + +
189A ARG* 2.5 58.2 + - + +
190A ARG 3.1 4.6 + - - -
283A VAL 4.4 0.4 - - - +
284A PHE* 3.4 23.3 - - + -
285A ALA* 3.1 41.7 - - + +
328A PHE 5.6 0.2 - - - +
329A GLY* 4.8 1.1 - - - -
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Residues in contact with ASP 187 (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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185A GLN* 2.3 27.6 + - - +
186A PRO* 1.3 66.1 - - - +
188A TYR* 1.3 70.1 + - + +
190A ARG* 3.1 30.9 + - - +
191A ASN* 2.9 33.4 + - - +
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Residues in contact with TYR 188 (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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186A PRO* 4.1 15.9 - - + +
187A ASP* 1.3 80.4 - - + +
189A ARG* 1.3 94.4 + - + +
191A ASN* 3.5 11.7 + - - +
192A GLU* 2.8 38.2 + - + +
328A PHE 4.7 2.3 + - - -
329A GLY* 3.3 33.2 + - - -
330A GLN* 3.9 12.7 + - + +
70C G 5.7 0.7 - - - -
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Residues in contact with ARG 189 (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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184A ILE* 4.1 3.8 - - + -
186A PRO* 2.5 49.2 + - + +
188A TYR* 1.3 91.5 - - + +
190A ARG* 1.3 66.2 + - - +
192A GLU* 2.7 53.3 + - - +
193A ILE* 3.2 16.8 + - - +
258A LYS* 2.7 51.0 - - - +
261A LEU* 3.7 20.6 - - + +
285A ALA* 4.3 5.8 + - + +
329A GLY 5.0 2.4 + - - -
331A ASP* 5.1 2.0 + - - -
70C G 3.0 20.4 + - - -
71C C 3.9 8.3 - - - -
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Residues in contact with ARG 190 (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 TYR* 4.3 10.9 + - + +
181A PRO* 2.9 48.5 + - - +
182A GLU* 5.4 1.2 - - - +
183A PHE* 6.4 0.2 - - - -
184A ILE* 3.6 42.0 + - + +
185A GLN* 4.3 4.2 + - - -
186A PRO 3.1 6.9 + - - +
187A ASP* 3.1 32.5 + - - +
189A ARG* 1.3 75.2 - - - +
191A ASN* 1.3 70.6 + - - +
193A ILE* 2.8 9.0 + - - +
194A ILE* 2.6 56.1 + - + +
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Residues in contact with ASN 191 (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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187A ASP* 2.9 28.2 + - - +
188A TYR* 3.8 9.9 - - - +
190A ARG* 1.3 90.0 + - - +
192A GLU* 1.3 62.8 + - - +
194A ILE* 3.2 27.6 - - + +
195A SER* 2.9 23.6 + - - -
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Residues in contact with GLU 192 (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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188A TYR* 2.8 32.9 + - + +
189A ARG* 2.7 37.4 + - - +
190A ARG 3.0 0.2 - - - -
191A ASN* 1.3 75.8 - - - +
193A ILE* 1.3 62.6 + - + +
195A SER* 3.2 6.5 - - - -
196A PHE* 2.8 26.0 + - - +
261A LEU* 5.0 3.8 - - - +
70C G 2.5 35.9 + - - +
71C C 2.9 41.9 + - - +
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Residues in contact with ILE 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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177A TYR* 3.6 30.5 - - + +
184A ILE* 4.2 6.3 - - + -
189A ARG 3.2 5.8 + - - +
190A ARG 2.8 7.6 + - - +
192A GLU* 1.3 77.5 - - + +
194A ILE* 1.3 52.4 + - - +
195A SER 2.6 15.8 + - - -
196A PHE* 3.9 11.4 - - + -
197A VAL* 2.8 25.7 + - + +
261A LEU* 3.3 37.9 - - + +
262A ARG* 4.4 8.3 - - + +
265A THR* 2.8 31.2 - - - +
266A VAL* 3.7 16.4 - - + -
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Residues in contact with ILE 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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174A LEU* 4.0 7.1 - - + +
177A TYR* 3.4 45.1 - - + -
184A ILE* 4.4 0.7 - - + -
190A ARG* 2.6 38.7 + - + +
191A ASN* 3.2 41.5 - - + +
193A ILE* 1.3 68.8 - - - +
195A SER* 1.3 56.3 + - - +
198A LYS* 3.2 36.2 + - - +
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Residues in contact with SER 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 ASN 2.9 20.0 - - - -
192A GLU* 3.2 6.1 - - - -
193A ILE 2.6 1.8 - - - -
194A ILE* 1.3 81.4 - - - +
196A PHE* 1.3 62.6 + - - -
197A VAL 3.4 0.9 - - - -
198A LYS* 3.0 27.3 - - - +
199A GLN* 3.2 7.3 - - - +
3C C 5.0 9.9 + - - -
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Residues in contact with PHE 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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192A GLU 2.8 16.6 + - - +
193A ILE* 3.7 11.0 - - + +
195A SER* 1.3 74.0 - - - +
197A VAL* 1.3 80.9 + - + +
199A GLN* 2.6 40.1 - - - +
200A GLY 3.9 0.3 + - - -
201A LEU* 4.3 18.7 - - + +
262A ARG* 3.3 55.6 - - + -
266A VAL* 4.1 15.3 - - + -
267A TYR* 5.0 6.3 - + - -
71C C 4.9 0.7 - - - +
72C C 4.0 33.4 - - - -
73C A 4.0 15.5 - - - -
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Residues in contact with VAL 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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170A GLN* 3.6 35.1 - - + +
173A LEU* 4.4 12.8 - - + -
174A LEU* 3.6 22.4 - - + -
177A TYR* 4.0 13.0 - - + +
193A ILE 2.8 14.8 + - - +
196A PHE* 1.3 78.1 - - + +
198A LYS* 1.3 53.3 + - - +
199A GLN 2.8 14.6 + - - -
200A GLY 3.4 7.6 + - - -
201A LEU* 3.5 22.1 - - + +
266A VAL* 3.5 35.0 - - + -
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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