Contacts of the helix formed by residues 200 - 217 (chain B) in PDB entry 4WNP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 3.5 28.0 - - - +
172B LEU* 4.3 1.8 - - - +
199B ASP* 1.3 79.6 - - - +
201B LYS* 1.3 59.7 + - - +
202B ALA 3.0 1.8 + - - -
203B ASP* 3.1 19.6 + - - +
204B LEU 3.9 0.7 + - - -
269B PHE* 3.3 30.3 - - - -
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Residues in contact with LYS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 2.9 20.4 + - - +
200B GLY* 1.3 73.9 - - - +
202B ALA* 1.3 64.4 + - - +
203B ASP 3.2 0.2 - - - -
204B LEU* 3.1 31.8 + - + +
205B TRP 3.4 4.3 + - - -
263B HIS* 2.9 29.7 + - + +
264B LYS* 3.5 18.8 + - - +
266B ARG* 2.7 53.6 + - + +
267B MET 4.1 2.0 - - - +
268B ASP* 3.5 33.8 + - + +
269B PHE* 4.2 6.2 - - + -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 6.6 0.2 - - + -
189B ALA* 3.8 10.1 + - + +
191B GLU* 3.7 14.2 + - - +
192B VAL* 3.8 29.2 - - + -
198B TYR* 4.0 9.0 - - + -
199B ASP* 3.0 16.4 + - - +
201B LYS* 1.3 78.3 - - - +
203B ASP* 1.3 62.9 + - - +
205B TRP* 3.2 15.1 + - - +
206B SER* 3.3 14.1 + - - -
266B ARG* 3.9 0.6 - - - +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B MET* 3.9 21.1 - - + +
135B ILE* 3.7 11.8 - - - +
136B HIS* 2.8 28.8 + - - +
137B ARG* 3.0 26.1 + - - +
139B LEU* 3.8 22.8 + - + +
200B GLY* 3.1 13.6 + - - +
202B ALA* 1.3 79.4 - - - +
204B LEU* 1.3 58.5 + - + +
206B SER* 3.1 11.2 + - - -
207B ILE* 2.9 30.6 + - - +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B MET* 5.3 0.2 - - + -
201B LYS* 3.1 21.6 + - + +
203B ASP* 1.3 74.2 - - - +
205B TRP* 1.3 62.1 + - - +
207B ILE* 3.3 21.8 + - + +
208B GLY* 2.9 22.9 + - - -
258B LEU* 3.5 25.8 - - + +
266B ARG* 4.3 6.7 - - - -
267B MET* 3.3 24.5 - - + +
268B ASP 4.1 10.5 - - - +
269B PHE* 3.8 41.1 - - + +
272B PHE* 4.0 23.3 - - + -
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Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B MET 5.1 1.2 + - - -
187B TYR* 3.7 5.1 + - - +
188B MET 3.3 25.1 + - - -
189B ALA* 3.5 16.6 - - + -
190B PRO* 3.5 26.7 - - + -
201B LYS 3.4 3.2 + - - -
202B ALA 3.2 10.6 + - - +
204B LEU* 1.3 78.4 - - - +
206B SER* 1.3 64.4 + - - +
208B GLY* 3.1 2.6 + - - -
209B THR* 3.0 46.3 + - + +
221B PHE* 3.6 29.8 - + - -
233B TYR* 3.5 22.8 + - - -
239B LEU* 3.9 9.6 - - + -
258B LEU 3.7 19.5 - - - -
259B LEU* 3.5 28.5 - - + +
260B GLN 3.6 23.3 - - - -
261B ARG 4.0 1.8 - - - -
266B ARG* 3.9 9.2 - - - +
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG 6.0 1.4 - - - -
139B LEU* 3.7 31.8 + - - +
187B TYR* 2.6 27.6 + - - -
188B MET* 4.7 0.5 - - - -
189B ALA 4.7 0.9 + - - -
202B ALA 3.3 10.8 + - - -
203B ASP* 3.1 13.0 + - - -
205B TRP* 1.3 79.8 - - - +
207B ILE* 1.3 60.5 + - - +
209B THR* 3.0 21.5 + - - -
210B ILE* 3.1 17.1 + - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.7 30.1 - - + -
122B ILE* 4.6 13.0 - - + -
126B MET* 3.7 34.1 - - + -
139B LEU* 4.1 12.6 - - + -
203B ASP 2.9 21.4 + - - +
204B LEU* 3.7 27.4 - - + +
206B SER* 1.3 76.0 - - - +
208B GLY* 1.3 62.2 + - - +
210B ILE* 3.2 11.4 + - + +
211B VAL* 3.0 24.5 + - + +
258B LEU* 4.7 3.6 - - + -
272B PHE* 4.2 15.5 - - + -
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Residues in contact with GLY 208 (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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204B LEU 2.9 12.9 + - - -
205B TRP 3.1 4.2 + - - -
207B ILE* 1.3 77.4 - - - +
209B THR* 1.3 57.3 + - - +
211B VAL* 3.4 2.7 + - - -
212B TYR* 3.0 27.2 + - - +
255B LEU* 3.6 8.9 - - - +
258B LEU* 3.8 28.0 - - - +
259B LEU* 3.8 11.3 - - - +
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B MET 4.6 9.0 - - - +
187B TYR* 3.1 26.8 - - - -
205B TRP* 3.0 42.4 + - + +
206B SER* 3.0 10.7 + - - -
208B GLY* 1.3 75.2 - - - +
210B ILE* 1.3 61.3 + - - +
212B TYR* 3.3 7.8 + - - +
213B GLN* 2.9 30.2 + - - +
220B PRO* 4.0 21.9 - - + +
259B LEU* 3.6 13.2 - - + -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.0 26.5 - - + -
122B ILE* 5.2 12.3 - - + -
139B LEU* 4.1 8.3 - - + -
140B LYS* 3.7 32.5 - - - +
141B PRO* 4.1 18.6 - - + -
144B ILE* 4.6 11.4 - - + -
187B TYR* 4.2 7.2 - - + -
206B SER 3.1 17.1 + - - +
207B ILE* 3.6 12.8 - - + +
209B THR* 1.3 79.2 + - - +
211B VAL* 1.3 68.1 + - + +
213B GLN* 3.2 9.3 + - - +
214B CYS* 3.0 26.0 + - - -
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.7 25.0 - - + +
119B LEU* 3.7 36.6 - - + -
122B ILE* 6.3 0.7 - - + -
207B ILE* 3.0 23.8 + - + +
208B GLY* 3.8 4.9 - - - +
210B ILE* 1.3 78.1 - - + +
212B TYR* 1.3 58.8 + - - +
214B CYS* 3.3 8.7 + - - +
215B LEU* 3.0 27.4 + - - +
251B LEU* 3.9 18.2 - - + -
254B LEU* 5.6 1.1 - - + -
255B LEU* 3.8 18.6 - - + -
258B LEU* 5.1 4.0 - - + -
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Residues in contact with TYR 212 (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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208B GLY 3.0 18.6 + - - +
209B THR* 3.4 9.4 - - - +
211B VAL* 1.3 77.8 - - - +
213B GLN* 1.3 56.5 + - - +
215B LEU* 3.7 3.3 - - + +
216B THR* 2.8 64.1 + - + +
218B LYS* 3.1 17.5 - - + -
219B ALA 3.9 3.5 + - - -
220B PRO* 3.5 29.0 + - + +
241B PRO* 4.1 15.0 - - + -
242B THR* 2.5 40.7 + - - -
243B ILE* 4.6 5.8 - - + -
244B PRO* 5.3 0.7 - - + -
255B LEU* 3.9 18.1 - - + +
259B LEU* 4.1 16.4 - - + -
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.9 23.7 - - + +
105B HIS* 6.2 2.0 - - - -
141B PRO* 3.4 13.8 - - + +
142B GLN* 6.1 0.6 - - - +
187B TYR* 2.8 35.0 + - - -
209B THR 2.9 15.4 + - - +
210B ILE* 3.2 5.3 + - - +
212B TYR* 1.3 76.7 - - - +
214B CYS* 1.3 58.5 + - - +
217B GLY* 2.6 42.1 + - - +
218B LYS 3.5 24.2 - - - +
219B ALA* 4.7 5.9 - - - +
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Residues in contact with CYS 214 (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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100B LEU* 4.1 23.8 - - - -
104B LEU* 3.9 18.6 - - - -
109B THR* 3.5 3.6 - - - -
110B LEU* 2.6 58.6 + - + +
115B ILE* 3.9 15.3 - - + -
118B PHE* 5.8 2.0 - - - -
210B ILE* 3.0 23.5 + - - -
211B VAL* 3.6 9.2 - - - +
213B GLN* 1.3 76.2 - - - +
215B LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 215 (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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109B THR* 3.6 13.6 + - - +
110B LEU 4.3 5.5 - - - +
112B GLU* 4.2 15.5 - - + +
115B ILE* 3.7 14.3 - - + +
211B VAL 3.0 16.5 + - - +
212B TYR* 3.7 4.3 - - + +
214B CYS* 1.3 80.9 - - - +
216B THR* 1.3 70.6 + - + +
243B ILE* 5.3 0.2 - - + -
244B PRO* 4.6 9.2 - - + -
247B THR* 3.7 26.9 - - + +
251B LEU* 3.9 20.6 - - + -
255B LEU* 3.7 27.6 - - + -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B THR* 3.3 13.8 - - - +
212B TYR* 2.8 56.8 + - + +
215B LEU* 1.3 87.1 - - + +
217B GLY* 1.3 58.6 + - - +
218B LYS* 2.9 34.2 + - - +
244B PRO* 4.4 18.6 - - + -
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 5.6 1.6 - - - -
108B ARG 3.6 20.9 - - - -
109B THR* 3.7 1.4 - - - +
213B GLN* 2.6 35.0 + - - +
216B THR* 1.3 72.5 + - - +
218B LYS* 1.3 61.5 + - - +
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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