Contacts of the helix formed by residues 188 - 205 (chain B) in PDB entry 4D2W
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 SER 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B HIS* 3.2 48.7 + - - +
128B TYR 4.7 1.6 - - - -
129B ALA* 4.2 13.0 - - - -
157B PRO* 4.3 8.2 - - - +
187B GLY* 1.3 73.4 - - - -
189B GLU* 1.3 73.9 + - - +
190B ALA 3.1 2.2 - - - +
191B ASP* 3.2 11.2 + - - +
192B VAL* 3.8 3.6 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 4.5 0.7 - - - +
187B GLY* 3.9 8.6 - - - -
188B SER* 1.3 91.4 + - - +
190B ALA* 1.4 61.7 + - - +
192B VAL* 3.2 23.2 + - + +
193B TRP 3.3 5.0 + - - -
248B PRO* 3.7 33.3 - - + +
251B ARG* 2.9 28.0 + - + +
252B ILE 5.9 2.0 - - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 5.9 3.6 - - + -
176B ALA* 3.8 14.1 - - + +
178B GLU* 3.5 19.5 + - + +
179B LEU* 3.9 29.4 - - + -
187B GLY 4.6 10.9 - - - +
188B SER* 3.1 1.4 - - - +
189B GLU* 1.4 77.2 - - - +
191B ASP* 1.3 58.6 + - - +
193B TRP* 3.3 5.7 + - - +
194B SER* 3.1 29.3 + - - -
251B ARG* 3.5 3.7 - - - +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 4.1 4.7 - - + +
123B VAL* 5.1 0.2 - - - +
124B HIS* 2.7 35.2 + - + +
129B ALA* 3.6 6.9 - - - -
130B HIS* 2.8 24.2 + - - +
131B ARG* 3.0 29.0 + - - +
133B LEU* 3.6 21.9 - - + +
188B SER 3.2 5.5 + - - +
190B ALA* 1.3 77.0 - - - +
192B VAL* 1.3 59.0 + - - +
194B SER* 3.3 7.0 + - - -
195B MET* 3.0 33.0 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B HIS* 4.8 1.6 - - + -
188B SER 4.3 8.7 - - - +
189B GLU* 3.2 16.0 + - + +
191B ASP* 1.3 72.7 - - - +
193B TRP* 1.4 66.0 + - - +
195B MET* 3.3 19.4 + - + -
196B GLY* 3.0 18.2 + - - -
243B MET* 3.5 16.3 - - + +
251B ARG* 4.0 12.6 - - + -
252B ILE* 3.5 42.8 - - + +
254B MET* 4.3 23.6 - - + +
257B LEU* 5.2 2.2 - - + -
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Residues in contact with TRP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 5.0 0.8 + - - -
174B TYR 3.6 7.8 - - - -
175B ALA 3.4 13.1 + - - -
176B ALA* 3.5 20.9 - - + -
177B PRO* 3.6 30.1 - - + -
189B GLU 3.3 4.2 + - - -
190B ALA 3.3 8.7 + - - +
192B VAL* 1.4 77.7 - - - +
194B SER* 1.4 65.1 + - - +
196B GLY* 3.0 12.0 + - - -
197B ILE* 3.0 28.2 + - + +
209B PHE* 3.5 37.5 - + - -
221B ILE* 3.9 16.5 - - + +
224B GLY* 4.9 0.2 - - - -
243B MET 3.8 11.4 - - - -
244B LEU* 3.6 33.2 - - + +
245B GLN 3.5 29.2 - - - -
246B VAL* 4.0 6.7 - - + -
251B ARG* 3.7 18.5 - - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 5.6 3.3 + - - -
133B LEU* 3.8 32.4 + - - -
174B TYR* 2.7 29.6 + - - +
175B ALA* 4.8 1.2 - - - -
176B ALA 4.9 0.2 + - - -
190B ALA 3.1 15.3 + - - -
191B ASP* 3.3 11.0 + - - -
193B TRP* 1.4 76.5 - - - +
195B MET* 1.3 56.8 + - - +
197B ILE* 3.2 6.9 + - - +
198B LEU* 3.0 31.8 + - - +
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Residues in contact with MET 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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113B PHE* 3.1 17.0 - - + -
116B ILE* 4.1 20.4 - - + -
117B VAL* 4.3 18.4 - - - -
120B VAL* 3.8 26.9 - - + -
133B LEU* 4.0 13.2 - - + -
191B ASP 3.0 11.4 + - - +
192B VAL* 3.5 24.2 - - + +
193B TRP 3.2 0.2 - - - -
194B SER* 1.3 73.3 - - - +
196B GLY* 1.3 60.7 + - - +
198B LEU* 3.4 7.8 + - + +
199B LEU 2.9 23.9 + - - -
243B MET* 3.6 9.2 - - + -
254B MET* 3.6 30.3 - - + -
257B LEU* 3.9 14.1 - - + -
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL 3.0 10.3 + - - -
193B TRP 3.0 5.8 + - - -
195B MET* 1.3 74.0 - - - +
197B ILE* 1.4 62.8 + - - +
199B LEU* 3.5 4.2 + - - +
200B TYR* 3.1 19.4 + - - +
240B LEU* 3.5 10.5 - - - +
243B MET* 3.7 29.5 - - - +
244B LEU* 3.8 11.5 - - - +
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Residues in contact with ILE 197 (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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173B ALA 3.6 18.8 - - - +
174B TYR* 3.5 26.7 - - + -
193B TRP* 3.0 39.1 + - + +
194B SER* 3.2 9.1 + - - +
196B GLY* 1.4 75.7 - - - +
198B LEU* 1.3 57.6 + - - +
200B TYR* 3.3 4.0 + - - +
201B VAL* 2.9 27.7 + - - +
207B LEU* 3.8 16.8 - - + -
208B PRO* 3.6 27.6 - - + -
209B PHE* 3.8 15.5 - - + -
244B LEU* 3.7 13.9 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.3 16.6 - - + -
98B ILE* 5.5 0.2 - - + -
113B PHE* 4.7 4.7 - - + -
116B ILE* 4.3 18.2 - - + -
133B LEU* 4.2 21.5 - - + -
134B LYS* 4.0 4.3 - - - +
135B PRO* 3.8 39.5 - - + -
138B LEU* 4.2 15.3 - - + -
174B TYR* 4.0 8.3 - - + -
194B SER 3.0 16.6 + - - +
195B MET* 3.4 14.4 - - + +
196B GLY 3.3 0.2 - - - -
197B ILE* 1.3 75.9 - - - +
199B LEU* 1.3 55.8 + - - +
201B VAL* 3.2 9.0 - - + +
202B LEU* 2.9 39.2 + - + +
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Residues in contact with LEU 199 (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* 3.8 8.7 - - + -
113B PHE* 3.8 22.8 - - + -
195B MET 2.9 17.4 + - - +
196B GLY* 3.5 5.8 - - - +
197B ILE 3.3 0.2 - - - -
198B LEU* 1.3 74.5 - - - +
200B TYR* 1.3 62.7 + - - +
202B LEU* 3.8 5.0 - - - +
203B MET* 3.3 41.3 + - + +
236B SER 4.9 0.7 - - - +
239B LEU* 3.6 32.1 - - + -
240B LEU* 3.7 22.7 - - + +
243B MET* 4.0 10.1 - - - -
262B TRP* 3.6 31.6 - - + -
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Residues in contact with TYR 200 (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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196B GLY 3.1 14.3 + - - +
197B ILE 3.5 7.6 - - - +
199B LEU* 1.3 75.5 - - - +
201B VAL* 1.3 57.0 + - - +
203B MET* 3.3 3.0 + - - -
204B CYS* 2.9 58.1 + - + +
206B PHE* 3.3 41.1 - + - -
207B LEU 3.8 1.6 - - - -
208B PRO* 3.5 39.6 + - + +
226B TYR* 3.7 16.2 - + - -
227B ASP* 2.7 37.7 + - - +
229B PRO* 3.7 5.4 - - + +
232B LEU* 4.8 3.1 - - + -
240B LEU* 3.8 27.5 - - + +
244B LEU* 4.8 1.1 - - + -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 4.2 24.0 - - + +
135B PRO* 4.8 2.2 - - + -
174B TYR* 3.7 15.9 - - - +
197B ILE 2.9 19.4 + - - +
198B LEU* 3.2 19.3 - - + +
200B TYR* 1.3 75.2 - - - +
202B LEU* 1.4 58.5 + - + +
205B GLY* 2.7 29.8 + - - -
206B PHE 3.6 20.6 - - - +
207B LEU* 3.2 38.8 - - + -
208B PRO* 4.3 0.9 - - + -
1C MET* 4.7 11.9 - - + -
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Residues in contact with LEU 202 (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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94B LEU* 4.2 18.2 - - + -
98B ILE* 3.7 30.7 - - + -
103B ARG* 3.9 1.6 - - - -
104B LEU* 2.9 51.9 + - + +
109B THR* 3.7 31.9 - - + +
112B VAL* 4.0 19.7 - - + -
113B PHE* 4.4 13.9 - - + -
116B ILE* 4.5 7.0 - - + -
198B LEU* 2.9 30.4 + - + +
199B LEU 3.8 0.7 - - - +
200B TYR 3.3 0.2 - - - -
201B VAL* 1.4 79.5 - - + +
203B MET* 1.3 56.7 + - - +
204B CYS 3.7 0.3 + - - -
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 3.4 11.9 - - - +
104B LEU 3.7 10.3 - - - +
106B GLU* 4.2 14.6 - - - +
109B THR* 3.3 21.8 - - + +
199B LEU* 3.3 39.3 + - + +
200B TYR 3.3 4.0 + - - +
202B LEU* 1.3 76.2 - - - +
204B CYS* 1.3 59.2 + - - +
231B TRP* 3.0 21.7 + - - -
232B LEU* 3.8 16.6 - - + -
236B SER* 3.3 36.1 - - - +
240B LEU* 4.3 14.1 - - + -
262B TRP* 4.1 13.9 - - + -
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Residues in contact with CYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 3.7 11.8 - - - +
200B TYR* 2.9 54.4 + - + +
203B MET* 1.3 81.5 - - - +
205B GLY* 1.3 60.0 + - - +
206B PHE* 3.3 30.5 - - + +
229B PRO* 3.8 21.3 - - - -
231B TRP* 3.8 9.3 - - - -
232B LEU* 4.0 18.4 - - - -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 5.3 8.9 - - - +
102B ASP 5.7 0.4 - - - -
103B ARG* 4.0 14.2 - - - +
201B VAL 2.7 21.1 + - - -
203B MET 3.9 0.4 - - - -
204B CYS* 1.3 71.6 - - - +
206B PHE* 1.3 61.9 + - - +
1C MET* 5.0 14.3 + - - +
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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