Contacts of the helix formed by residues 186 - 198 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B ILE* 5.2 0.4 - - + -
185B GLN* 1.3 87.0 - - + +
187B ASP* 1.3 56.6 + - - +
188B TYR* 3.0 26.7 - - + +
189B ARG* 2.6 45.8 + - + -
190B ARG* 3.1 9.0 + - - +
284B PHE* 3.4 21.1 - - + -
285B ALA* 3.1 40.2 - - + +
328B PHE 5.4 0.4 - - - +
329B GLY* 4.3 7.0 - - - -
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Residues in contact with ASP 187 (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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185B GLN* 2.5 20.0 + - - +
186B PRO* 1.3 70.3 - - - +
188B TYR* 1.3 58.9 + - + +
189B ARG 3.4 0.3 + - - -
190B ARG* 2.6 53.5 + - - +
191B ASN* 2.6 31.0 + - - +
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Residues in contact with TYR 188 (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 22.4 - - + +
187B ASP* 1.3 80.4 - - + +
189B ARG* 1.3 85.2 - - + +
191B ASN* 3.3 24.7 + - - +
192B GLU* 2.6 23.8 + - - +
327B PRO* 6.0 0.3 - - - +
328B PHE 4.8 1.2 + - - -
329B GLY* 3.3 32.4 - - - -
330B GLN* 3.5 21.8 + - + +
4D G 5.5 3.9 + - - +
5D G 5.8 8.3 - - - -
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 3.8 4.7 - - + -
186B PRO* 2.6 44.1 + - + +
188B TYR* 1.3 86.8 - - + +
190B ARG* 1.3 64.9 + - - +
191B ASN 3.0 2.4 + - - -
192B GLU* 2.9 37.1 + - - +
193B ILE* 3.4 19.4 + - - +
258B LYS* 3.2 47.6 - - - +
261B LEU* 3.8 19.0 - - + +
285B ALA* 4.4 11.3 + - + +
329B GLY 4.6 11.3 + - - -
331B ASP* 5.1 1.4 + - - -
70D G 3.1 24.7 + - - -
71D C 4.4 4.2 + - - -
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Residues in contact with ARG 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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177B TYR* 5.0 7.3 + - - -
181B PRO* 2.8 48.6 + - - +
184B ILE* 3.1 47.4 + - + +
185B GLN* 3.9 0.8 + - - -
186B PRO 3.1 6.6 + - - +
187B ASP* 2.6 51.3 + - - +
189B ARG* 1.3 77.8 - - - +
191B ASN* 1.3 68.4 + - - +
193B ILE* 3.5 3.0 + - - +
194B ILE* 3.0 43.2 + - + +
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Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 2.6 24.8 + - - +
188B TYR* 3.3 17.9 - - - +
189B ARG 3.0 1.0 - - - -
190B ARG* 1.3 84.6 + - - +
192B GLU* 1.3 58.4 + - + +
193B ILE 3.0 1.1 - - - -
194B ILE* 2.8 23.1 - - + +
195B SER* 2.7 37.6 + - - -
4D G 4.4 26.0 + - - +
5D G 5.8 2.4 - - - -
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Residues in contact with GLU 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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188B TYR* 2.6 26.3 - - - +
189B ARG* 2.9 51.2 + - - +
191B ASN* 1.3 76.6 - - + +
193B ILE* 1.3 59.2 + - + +
195B SER* 3.6 5.8 - - - -
196B PHE* 2.7 34.2 + - - +
261B LEU* 5.2 2.8 - - - +
70D G 3.9 14.7 + - - +
71D C 3.4 47.8 + - - +
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Residues in contact with ILE 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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177B TYR* 3.7 18.6 - - + +
184B ILE* 4.6 4.5 - - + -
189B ARG 3.4 14.8 - - - +
190B ARG* 3.5 8.7 + - - +
191B ASN 3.0 0.8 - - - -
192B GLU* 1.3 81.2 - - + +
194B ILE* 1.3 57.2 + - - +
196B PHE* 3.2 8.1 - - + +
197B VAL* 2.7 33.8 + - - +
261B LEU* 3.5 30.7 - - + -
262B ARG* 4.3 18.4 - - + +
265B THR* 3.9 14.8 - - - +
266B VAL* 3.7 26.2 - - + -
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Residues in contact with ILE 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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174B LEU* 4.5 2.7 - - + -
177B TYR* 3.9 38.6 - - + -
190B ARG* 3.0 34.2 + - - +
191B ASN* 2.8 33.2 - - + +
193B ILE* 1.3 75.2 - - - +
195B SER* 1.3 69.2 + - - +
197B VAL* 3.2 1.6 + - - +
198B LYS* 2.8 58.2 + - + +
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Residues in contact with SER 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 ASN 2.7 13.9 + - - -
192B GLU* 3.6 7.6 - - - -
194B ILE* 1.3 87.7 - - - +
196B PHE* 1.3 65.4 + - - +
198B LYS* 3.2 16.8 + - - +
199B GLN* 3.3 12.3 - - - +
2D G 4.9 6.5 + - - -
3D C 4.1 25.1 + - - -
71D C 5.7 1.3 - - - -
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Residues in contact with PHE 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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192B GLU 2.7 23.1 + - - +
193B ILE* 3.2 13.9 - - + +
195B SER* 1.3 72.3 - - - +
197B VAL* 1.3 62.8 + - + +
199B GLN* 2.7 37.2 - - - +
200B GLY* 4.0 2.4 + - - -
201B LEU* 4.1 21.9 - - + +
262B ARG* 3.7 44.4 - - + -
266B VAL* 4.2 20.2 - - + -
267B TYR* 5.1 3.6 - + - -
71D C 5.5 0.4 + - - -
72D C 3.9 39.3 - - - -
73D A 4.8 5.4 - - - -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLN* 3.4 33.3 - - + +
173B LEU* 4.3 15.3 - - + -
174B LEU* 3.3 32.5 - - + -
177B TYR* 3.8 22.4 - - + +
193B ILE 2.7 22.3 + - - +
194B ILE 3.7 2.9 - - - +
196B PHE* 1.3 77.9 - - + +
198B LYS* 1.3 51.6 + - - +
199B GLN 2.5 20.2 + - - -
200B GLY* 3.3 10.0 + - - -
201B LEU* 4.2 13.0 - - + +
266B VAL* 4.3 6.3 - - + -
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Residues in contact with LYS 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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170B GLN* 4.6 6.1 - - - +
174B LEU* 3.5 35.0 - - + -
194B ILE* 2.8 38.2 + - + +
195B SER* 3.2 9.1 + - - +
197B VAL* 1.3 67.1 - - - +
199B GLN* 1.3 62.9 + - - +
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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