Contacts of the helix formed by residues 200 - 217 (chain A) in PDB entry 4WNO
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 GLY 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ILE* 3.6 24.2 - - - +
172A LEU* 4.6 1.2 - - - +
199A ASP* 1.3 78.7 - - - +
201A LYS* 1.3 61.3 + - - +
202A ALA 3.1 0.2 - - - -
203A ASP* 3.0 19.1 + - - +
204A LEU 3.5 5.9 + - - -
269A PHE* 3.5 28.6 - - - -
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Residues in contact with LYS 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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199A ASP* 2.9 20.1 + - - +
200A GLY* 1.3 76.9 - - - +
202A ALA* 1.3 61.8 + - - +
204A LEU* 3.1 14.8 + - + +
205A TRP 3.1 14.7 + - - -
263A HIS* 2.9 38.2 + - + +
264A LYS* 3.6 13.1 + - - +
266A ARG* 3.0 49.0 + - + +
267A MET 3.8 13.0 - - - +
268A ASP* 3.6 26.0 - - - +
269A PHE* 4.4 3.1 - - + -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 6.5 0.9 - - + -
189A ALA* 3.8 16.4 + - + +
191A GLU* 3.9 7.8 + - - +
192A VAL* 3.9 18.2 - - + -
198A TYR* 3.8 21.5 - - + -
199A ASP 3.0 15.2 + - - +
201A LYS* 1.3 78.8 - - - +
203A ASP* 1.3 63.8 + - - +
205A TRP* 3.2 5.9 + - - +
206A SER* 3.2 23.4 + - - -
266A ARG* 3.9 0.6 - - - +
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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
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126A MET* 3.9 20.6 - - + +
134A ILE 4.7 0.2 - - - +
135A ILE* 3.5 15.3 - - - +
136A HIS* 2.8 26.4 + - - +
137A ARG* 2.9 29.1 + - - +
139A LEU* 3.8 21.1 - - + +
199A ASP 4.4 0.4 + - - -
200A GLY 3.0 11.6 + - - +
202A ALA* 1.3 78.8 - - - +
204A LEU* 1.3 58.1 + - - +
206A SER* 3.2 7.8 + - - -
207A ILE* 2.9 32.8 + - - +
269A PHE* 5.0 1.0 - - + -
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Residues in contact with LEU 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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200A GLY 3.5 3.5 + - - +
201A LYS* 3.1 15.5 + - + +
203A ASP* 1.3 74.7 - - - +
205A TRP* 1.3 65.3 + - - +
207A ILE* 3.3 16.1 + - + +
208A GLY 2.9 18.0 + - - -
258A LEU* 3.7 23.8 - - + +
266A ARG* 4.7 2.2 - - - -
267A MET 3.3 25.6 - - - +
268A ASP* 3.7 22.2 - - - +
269A PHE* 3.7 38.6 - - + +
272A PHE* 3.8 29.8 - - + -
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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
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186A MET 5.3 0.8 + - - -
187A TYR* 3.4 13.7 + - - +
188A MET 3.2 11.5 + - - -
189A ALA* 3.4 24.0 - - + -
190A PRO* 3.5 30.1 - - + -
201A LYS 3.1 6.7 + - - -
202A ALA 3.2 8.5 + - - +
204A LEU* 1.3 76.1 - - - +
206A SER* 1.3 65.6 + - - +
208A GLY* 3.0 4.2 + - - -
209A THR* 3.0 32.1 + - + +
221A PHE* 3.6 30.5 - + - -
233A TYR* 3.6 21.5 + - - -
239A LEU* 3.8 8.5 - - + -
258A LEU 3.7 11.7 - - - -
259A LEU* 3.5 44.0 - - + +
260A GLN 3.5 22.0 - - - -
261A ARG 4.1 0.9 - - - -
266A ARG* 3.9 10.6 - - - +
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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
----------------------------------------------------------
137A ARG 5.6 2.9 + - - -
139A LEU* 3.6 31.7 + - - +
187A TYR 2.8 27.2 + - - -
188A MET* 4.7 2.9 - - - -
189A ALA 4.7 0.2 + - - -
202A ALA 3.2 11.2 + - - -
203A ASP* 3.4 12.3 + - - -
205A TRP* 1.3 79.6 - - - +
207A ILE* 1.3 56.7 + - - +
209A THR* 2.5 22.2 + - - -
210A ILE* 2.9 18.5 + - - +
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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
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119A LEU* 3.8 28.9 - - + -
122A ILE* 4.2 13.9 - - + -
126A MET* 3.6 40.4 - - + -
139A LEU* 3.9 12.6 - - + -
203A ASP 2.9 17.4 + - - +
204A LEU* 3.6 22.0 - - + +
206A SER* 1.3 75.7 - - - +
208A GLY* 1.3 62.9 + - - +
210A ILE* 3.2 16.2 + - + +
211A VAL* 2.9 24.7 + - + +
258A LEU* 4.6 3.4 - - + -
272A PHE* 4.1 15.0 - - + -
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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
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204A LEU 2.9 11.1 + - - -
205A TRP 3.0 4.7 + - - -
207A ILE* 1.3 77.2 - - - +
209A THR* 1.3 56.2 + - - +
211A VAL* 3.3 2.3 + - - -
212A TYR* 2.9 28.4 + - - +
255A LEU* 3.5 8.3 - - - +
258A LEU* 3.8 29.8 - - - +
259A LEU* 3.9 11.4 - - - +
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Residues in contact with THR 209 (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 MET 4.5 7.0 - - - +
187A TYR* 3.1 30.1 - - - +
205A TRP* 3.0 38.0 + - + +
206A SER* 2.5 21.8 + - - -
208A GLY* 1.3 73.4 - - - +
210A ILE* 1.3 59.9 + - - +
212A TYR* 3.4 7.6 + - - +
213A GLN* 2.9 30.1 + - - +
220A PRO* 3.9 22.8 - - + +
259A LEU* 3.8 11.0 - - + -
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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
----------------------------------------------------------
100A LEU* 3.9 28.5 - - + -
122A ILE* 4.9 13.5 - - + -
139A LEU* 4.0 12.3 - - + -
140A LYS* 3.7 40.2 - - - +
141A PRO* 3.9 15.4 - - + +
144A ILE* 4.2 13.2 - - + -
206A SER 2.9 18.3 + - - +
207A ILE* 3.2 17.5 + - + +
209A THR* 1.3 78.5 + - - +
211A VAL* 1.3 60.3 - - + +
213A GLN* 3.2 2.8 + - - +
214A CYS* 2.9 32.1 + - - -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.0 18.0 - - + +
119A LEU* 3.8 37.2 - - + -
207A ILE* 2.9 23.0 + - + +
208A GLY* 3.7 5.4 - - - +
210A ILE* 1.3 77.5 - - + +
212A TYR* 1.3 64.2 + - - +
214A CYS* 3.1 9.6 + - - +
215A LEU* 3.1 21.4 + - + +
251A LEU* 3.9 24.2 - - + -
254A LEU* 5.7 1.8 - - + -
255A LEU* 3.5 20.4 - - + -
258A LEU* 5.1 4.0 - - + -
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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 2.9 17.9 + - - +
209A THR* 3.6 7.4 - - - +
210A ILE 3.3 0.2 - - - -
211A VAL* 1.3 77.1 - - - +
213A GLN* 1.3 61.1 + - - +
215A LEU* 3.2 6.2 + - + +
216A THR* 3.0 55.0 + - + +
218A LYS* 3.1 24.6 - - + +
219A ALA 3.6 3.8 + - - -
220A PRO* 3.2 36.7 + - + +
241A PRO* 3.8 19.3 - - + -
242A THR* 2.5 40.8 + - - -
243A ILE* 4.1 12.6 - - + -
244A PRO* 5.5 0.2 - - + -
255A LEU* 3.7 14.8 - - + +
259A LEU* 4.4 7.6 - - + -
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Residues in contact with GLN 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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101A ALA* 6.2 0.7 - - - -
104A LEU* 3.4 19.7 - - + +
105A HIS* 3.7 16.1 - - - -
141A PRO* 3.3 16.7 - - + +
142A GLN* 6.0 0.6 - - - +
186A MET* 5.5 2.6 - - - -
187A TYR* 2.6 33.8 + - + -
209A THR 2.9 17.5 + - - +
210A ILE 3.2 3.8 + - - +
212A TYR* 1.3 76.9 - - - +
214A CYS* 1.3 59.3 + - - +
216A THR* 4.2 0.2 - - - -
217A GLY* 2.8 51.7 + - - -
218A LYS* 3.4 21.7 - - - +
219A ALA* 4.6 3.9 - - - +
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Residues in contact with CYS 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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100A LEU* 3.9 31.2 - - - -
104A LEU* 4.2 13.7 - - - -
109A THR* 3.3 8.8 - - - -
110A LEU* 2.9 46.7 + - + -
115A ILE* 3.9 22.9 - - + -
118A PHE* 5.5 2.9 - - - -
210A ILE* 2.9 20.9 + - - -
211A VAL* 3.1 10.3 + - - +
213A GLN* 1.3 77.6 - - - +
215A LEU* 1.3 58.0 + - - +
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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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109A THR* 3.3 17.8 + - - +
110A LEU 4.5 6.2 - - - +
112A GLU* 4.6 10.1 - - + +
115A ILE* 3.9 20.2 - - + +
211A VAL* 3.1 12.1 + - + +
212A TYR* 3.5 8.7 - - + +
214A CYS* 1.3 79.5 - - - +
216A THR* 1.3 63.5 + - + +
243A ILE* 4.3 1.1 - - + -
244A PRO* 4.0 19.2 - - + +
247A THR* 3.6 35.9 - - + +
251A LEU* 4.2 12.6 - - + -
255A LEU* 3.9 21.3 - - + -
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Residues in contact with THR 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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108A ARG* 5.3 2.6 + - - -
109A THR* 3.4 12.6 - - - +
212A TYR* 3.0 43.6 + - + +
215A LEU* 1.3 82.1 - - + +
217A GLY* 1.3 57.4 + - - +
218A LYS* 3.0 33.8 + - - +
242A THR 4.5 0.4 - - - +
244A PRO* 3.8 31.4 - - + -
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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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104A LEU* 4.0 12.3 - - - -
105A HIS* 3.3 18.6 + - - -
108A ARG* 5.8 2.5 - - - -
109A THR* 3.5 8.4 - - - +
213A GLN* 2.8 40.7 + - - -
216A THR* 1.3 71.6 - - - +
218A LYS* 1.3 62.2 + - - +
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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
------------------------------------------------------------
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