Contacts of the helix formed by residues 200 - 217 (chain A) in PDB entry 2JC6
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 LYS 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS* 3.2 78.3 + - + +
139A GLY* 4.2 18.5 - - - -
141A VAL* 4.0 18.1 - - + +
199A SER* 1.3 75.7 - - - +
201A ALA* 1.3 61.7 + - - +
203A ASP* 3.1 12.4 + - - +
204A CYS* 3.7 2.6 + - - -
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 4.3 0.7 - - - +
199A SER* 3.0 15.1 + - - +
200A LYS* 1.3 75.8 - - - +
202A VAL* 1.3 64.7 + - - +
204A CYS* 3.0 21.7 + - - +
205A TRP 3.1 5.7 + - - -
264A PRO* 3.8 26.2 - - + +
267A ARG* 3.1 29.9 + - + +
268A TYR 5.7 0.4 - - - +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 4.2 5.2 - - + -
143A ARG* 4.2 29.8 - - + +
189A ALA* 4.0 10.2 - - + +
191A GLU* 3.4 20.5 + - - +
192A VAL* 3.7 29.2 - - + -
198A TYR* 3.9 14.8 - - + -
199A SER 3.3 17.0 + - - +
201A ALA* 1.3 76.6 - - - +
203A ASP* 1.3 63.6 + - - +
205A TRP* 3.4 5.5 - - - +
206A SER* 3.3 22.4 + - - +
267A ARG* 4.2 2.5 - - - +
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.8 3.5 - - + +
135A LEU* 5.7 0.3 - - - +
136A HIS* 2.8 35.3 + - + +
141A VAL* 3.5 10.1 - - - +
142A HIS* 3.0 25.0 + - - +
143A ARG* 3.0 27.4 + - - -
145A LEU* 3.8 23.0 + - + +
200A LYS 3.1 2.2 + - - +
202A VAL* 1.3 74.0 - - - +
204A CYS* 1.3 62.1 + - - +
206A SER* 3.3 7.0 + - - -
207A ILE* 3.0 31.4 + - - +
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Residues in contact with CYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A HIS* 4.0 4.9 - - - -
200A LYS 4.0 11.9 - - - -
201A ALA* 3.0 12.4 + - - +
203A ASP* 1.3 76.0 - - - +
205A TRP* 1.3 61.7 + - - +
207A ILE* 3.2 7.6 + - - +
208A GLY 3.2 16.8 + - - -
259A LEU* 3.4 22.2 - - + +
267A ARG* 4.1 5.6 - - - -
268A TYR 3.2 28.0 - - - +
269A THR* 3.9 3.6 - - - -
270A CYS* 3.7 35.7 - - - -
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY 5.0 1.0 + - - -
187A TYR* 3.5 20.9 + - - +
188A VAL 3.4 12.1 + - - -
189A ALA* 3.6 14.6 - - + -
190A PRO* 3.6 33.7 - - + -
201A ALA 3.1 5.3 + - - -
202A VAL 3.4 9.2 - - - +
204A CYS* 1.3 75.7 - - - +
206A SER* 1.3 63.0 + - - +
208A GLY* 3.1 12.6 + - - -
209A VAL* 3.1 27.8 + - + +
221A PHE* 3.7 31.0 - + - -
233A ILE* 4.2 6.5 - - + +
236A ALA* 3.9 16.6 - - + -
238A TYR* 5.3 0.7 - + - -
259A LEU 3.6 10.8 - - - -
260A MET* 3.5 43.8 - - + +
261A GLU 3.7 19.5 - - - -
267A ARG* 3.7 18.3 - - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG 5.6 2.6 + - - -
145A LEU* 3.6 36.7 + - - +
187A TYR* 3.6 18.1 + - - +
202A VAL* 3.3 13.1 + - - +
203A ASP* 3.3 12.2 + - - -
205A TRP* 1.3 82.4 - - - +
207A ILE* 1.3 58.5 + - - +
209A VAL* 3.3 6.6 + - - +
210A ILE* 3.0 34.5 + - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.9 25.5 - - + +
128A VAL* 3.9 20.0 - - + -
129A LEU* 3.8 35.0 - - + -
132A VAL* 3.9 31.4 - - + -
145A LEU* 4.1 7.0 - - + -
203A ASP 3.0 15.6 + - - +
204A CYS* 3.7 9.0 - - - +
205A TRP 3.2 0.4 - - - -
206A SER* 1.3 75.7 - - - +
208A GLY* 1.3 57.1 + - - +
210A ILE* 3.3 7.8 + - + +
211A ALA* 2.9 27.5 + - - +
259A LEU* 4.1 8.3 - - + -
270A CYS* 4.1 7.6 - - - -
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A CYS 3.2 7.5 + - - -
205A TRP 3.1 8.2 + - - -
207A ILE* 1.3 77.2 - - - +
209A VAL* 1.3 54.8 + - - +
211A ALA* 3.5 6.1 + - - +
212A TYR* 3.0 27.4 + - - +
256A ILE* 3.8 6.9 - - - +
259A LEU* 3.6 25.7 - - - +
260A MET* 3.6 15.6 - - - +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY 4.8 2.5 - - - +
187A TYR* 3.6 36.1 - - + +
205A TRP* 3.1 37.3 + - + +
206A SER* 3.7 8.5 - - - +
207A ILE 3.3 0.2 - - - -
208A GLY* 1.3 73.2 - - - +
210A ILE* 1.3 67.4 + - + +
212A TYR* 3.3 3.4 + - - +
213A ILE* 3.1 28.1 + - + +
220A PRO* 3.9 21.1 - - + -
221A PHE* 4.9 2.0 - - + -
260A MET* 3.9 23.8 - - + -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.7 17.0 - - + -
128A VAL* 4.8 12.3 - - + -
145A LEU* 4.2 10.5 - - + +
146A LYS* 4.1 23.3 - - - +
147A PRO* 3.8 25.1 - - + -
150A LEU* 4.3 22.7 - - + -
206A SER 3.0 23.3 + - - +
207A ILE* 3.5 10.5 - - + +
209A VAL* 1.3 78.3 - - + +
211A ALA* 1.3 61.3 + - - +
213A ILE* 3.3 8.8 + - - +
214A LEU* 2.9 36.2 + - + +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.7 24.2 - - + +
207A ILE 2.9 16.4 + - - +
208A GLY* 3.7 7.0 - - - +
209A VAL 3.3 0.2 - - - -
210A ILE* 1.3 77.7 - - - +
212A TYR* 1.3 62.5 + - - +
214A LEU* 3.5 3.8 + - - +
215A LEU* 3.4 27.7 + - - +
255A PHE* 4.2 16.6 - - + -
256A ILE* 4.0 17.5 - - + -
278A TRP* 4.9 6.5 - - + -
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Residues in contact with TYR 212 (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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208A GLY 3.0 15.0 + - - +
209A VAL* 3.4 12.3 - - - +
210A ILE 3.2 0.2 - - - -
211A ALA* 1.3 76.7 - - - +
213A ILE* 1.3 59.3 - - - +
215A LEU 3.3 8.1 + - - -
216A CYS* 3.3 29.2 + - - -
218A TYR* 3.5 26.4 - + - -
220A PRO* 3.4 43.5 + - + +
238A TYR* 4.1 9.2 - + - -
239A GLU 2.5 29.8 + - - -
240A PHE* 3.9 19.3 - + - -
241A ASP* 3.4 14.9 + - - -
245A TRP* 3.6 26.2 + + - -
256A ILE* 3.8 13.2 - - + +
260A MET* 4.3 3.1 - - - -
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Residues in contact with ILE 213 (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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107A PHE* 3.8 30.0 - - + -
147A PRO* 4.1 17.7 - - + -
187A TYR* 3.9 28.3 - - + -
209A VAL* 3.1 24.4 + - + +
210A ILE* 3.3 4.5 + - - +
212A TYR* 1.3 74.8 - - - +
214A LEU* 1.3 59.6 + - + +
215A LEU 3.1 0.2 - - - -
217A GLY* 2.7 33.5 + - - -
218A TYR 3.5 19.5 - - - +
219A PRO* 3.8 10.3 - - + -
220A PRO* 4.4 1.1 - - + -
293A VAL* 4.7 1.0 - - - +
297A ILE* 5.5 0.9 - - - +
301A PHE* 3.8 22.9 - - + -
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Residues in contact with LEU 214 (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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106A LEU* 3.9 25.4 - - + -
107A PHE* 5.0 10.1 - - + -
110A ILE* 4.0 19.3 - - + -
116A TYR* 2.7 38.5 + - - +
121A ALA* 4.1 10.5 - - + +
124A LEU* 4.0 31.0 - - + -
125A ILE* 4.1 15.7 - - + -
147A PRO* 5.2 3.1 - - + -
150A LEU* 5.8 0.7 - - + -
210A ILE* 2.9 36.9 + - + +
211A ALA* 3.9 6.3 - - - +
212A TYR 3.4 0.6 - - - -
213A ILE* 1.3 75.6 - - + +
215A LEU* 1.3 60.3 + - - +
293A VAL* 4.2 4.7 - - - +
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Residues in contact with LEU 215 (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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117A THR 4.9 0.2 - - - +
118A GLU* 3.7 27.8 - - + -
121A ALA* 3.5 26.9 - - + -
211A ALA 3.6 15.9 - - - +
212A TYR 3.3 2.0 + - - -
213A ILE 3.1 1.0 - - - -
214A LEU* 1.3 79.5 - - - +
216A CYS* 1.3 57.4 + - - +
244A TYR 4.5 2.9 - - - +
245A TRP* 4.0 13.9 - - + -
248A ILE* 3.8 20.3 - - + +
252A ALA* 3.9 27.8 - - + -
256A ILE* 4.2 13.9 - - + -
278A TRP* 3.9 12.3 - - + -
289A ILE* 3.8 19.1 - - + +
293A VAL* 3.7 12.5 - - - +
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Residues in contact with CYS 216 (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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212A TYR* 3.3 32.1 + - - -
215A LEU* 1.3 80.6 - - - +
217A GLY* 1.3 56.9 + - - +
218A TYR* 3.4 46.7 + - + -
244A TYR* 4.4 8.9 - - + +
245A TRP* 3.6 19.1 - - + +
292A SER* 4.1 2.4 + - - +
293A VAL* 3.8 15.4 - - - -
296A GLN* 3.1 25.6 - - - +
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Residues in contact with GLY 217 (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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213A ILE* 2.7 24.5 + - - -
216A CYS* 1.3 72.7 - - - +
218A TYR* 1.3 56.5 + - - +
293A VAL* 3.8 14.8 - - - +
296A GLN* 3.1 30.9 - - - +
297A ILE* 3.3 11.9 + - - -
300A ASN* 3.7 0.3 + - - -
301A PHE* 3.6 15.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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