Contacts of the helix formed by residues 189 - 213 (chain B) in PDB entry 3V3E
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 GLU 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.6 1.8 - - + +
100B SER* 3.9 21.6 + - - -
103B ASP* 3.0 13.1 + - - +
187B LEU* 4.6 1.1 - - - -
188B GLN* 1.3 92.0 - - + +
190B PRO* 1.3 66.3 - - - +
191B ARG 3.2 3.1 - - - +
192B ARG* 3.0 58.8 + - + +
193B VAL* 3.2 13.5 + - - +
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Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASP* 3.9 21.0 - - - +
187B LEU* 3.8 29.7 - - + +
188B GLN 3.2 9.4 - - - +
189B GLU* 1.3 89.7 - - - +
191B ARG* 1.3 65.3 + - + +
193B VAL* 3.5 3.5 + - - +
194B GLU* 3.0 26.7 + - - +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU 3.1 1.4 + - - -
190B PRO* 1.3 84.3 - - + +
192B ARG* 1.3 56.5 + - + +
194B GLU* 3.3 21.1 + - - +
195B GLU* 2.7 46.6 + - + +
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY 5.5 0.2 + - - -
98B GLU* 2.9 41.6 + - - +
99B LEU* 3.9 16.6 - - + +
189B GLU* 3.0 51.2 + - + +
191B ARG* 1.3 77.4 - - + +
193B VAL* 1.3 64.3 + - - +
195B GLU* 3.2 22.5 + - - +
196B LEU* 3.0 23.9 + - - +
199B ARG* 4.9 2.4 + - - +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.1 14.7 - - + +
103B ASP* 4.5 4.7 - - + +
107B LEU* 4.0 14.1 - - + -
181B ILE* 3.7 12.7 - - + +
182B THR* 3.4 44.0 - - - +
183B ASP* 4.4 1.1 - - - +
187B LEU* 3.7 33.4 - - + -
189B GLU 3.2 11.2 + - - +
190B PRO 3.6 7.2 - - - +
192B ARG* 1.3 72.8 - - - +
194B GLU* 1.3 59.0 + - - +
196B LEU 3.2 1.2 + - - -
197B GLN* 2.9 31.7 + - + +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PRO 3.0 15.5 + - - +
191B ARG* 3.4 25.0 - - - +
192B ARG 3.2 0.2 - - - -
193B VAL* 1.3 78.5 - - - +
195B GLU* 1.3 63.5 + - - +
197B GLN* 3.6 19.0 - - - +
198B ASN* 2.9 42.3 + - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG* 2.7 32.4 + - - +
192B ARG* 3.2 25.8 + - - +
194B GLU* 1.3 72.1 - - + +
196B LEU* 1.3 58.7 + - - +
198B ASN* 3.8 7.4 - - - +
199B ARG* 3.0 50.0 + - - +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.9 2.9 - - + -
93B ILE* 4.8 1.1 - - + -
94B PRO 3.0 23.6 - - - +
95B GLY* 3.8 27.4 - - - +
96B PHE* 3.9 6.1 - - + +
99B LEU* 4.4 8.7 - - + -
181B ILE* 3.9 28.9 - - + -
192B ARG 3.0 15.5 + - - +
193B VAL* 3.9 3.4 - - - +
195B GLU* 1.3 72.0 - - - +
197B GLN* 1.3 61.9 + - - +
199B ARG* 3.2 41.4 + - + +
200B ILE* 2.9 41.2 + - + +
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Residues in contact with GLN 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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178B LEU* 3.6 19.8 + - + +
181B ILE* 3.4 32.2 + - - +
182B THR* 3.6 22.2 + - - +
183B ASP 4.5 2.9 + - - +
193B VAL* 2.9 18.3 + - - +
194B GLU* 3.6 22.4 - - - +
196B LEU* 1.3 76.9 - - - +
198B ASN* 1.3 58.1 + - - +
200B ILE* 3.0 4.2 + - - +
201B ALA* 2.7 35.7 + - + +
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Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 2.9 45.3 + - - +
195B GLU* 3.8 6.2 - - - +
197B GLN* 1.3 78.3 - - - +
199B ARG* 1.3 67.8 + - - +
201B ALA* 4.0 7.1 - - - +
202B SER* 2.9 30.9 + - - +
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Residues in contact with ARG 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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33B LEU* 3.6 17.5 - - + +
95B GLY* 4.9 6.3 - - - -
192B ARG* 4.9 2.2 + - - +
195B GLU* 3.0 43.7 + - - +
196B LEU* 3.2 48.2 - - + +
198B ASN* 1.3 77.7 - - - +
200B ILE* 1.3 61.4 + - - +
202B SER* 3.6 5.8 - - - -
203B CYS* 3.1 21.5 + - - +
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Residues in contact with ILE 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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33B LEU* 4.2 19.5 - - + -
37B LEU* 4.3 11.0 - - + -
93B ILE* 4.2 20.9 - - + -
174B CYS* 3.6 24.5 - - + +
177B ALA* 4.2 13.7 - - + +
178B LEU* 3.6 23.8 - - + -
181B ILE* 4.3 10.3 - - + -
196B LEU* 2.9 42.9 + - + +
197B GLN* 3.0 6.5 + - - +
199B ARG* 1.3 73.9 - - - +
201B ALA* 1.3 63.9 + - - +
203B CYS* 3.2 3.3 + - - +
204B LEU* 3.0 20.6 + - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.9 21.3 - - + +
197B GLN* 2.7 22.4 + - + +
198B ASN* 4.0 8.3 - - - +
200B ILE* 1.3 74.5 - - - +
202B SER* 1.3 56.3 + - - +
204B LEU* 3.2 4.9 + - + +
205B LYS* 2.8 32.8 + - - +
221B LEU* 5.4 0.9 - - - +
225B LEU* 6.3 3.4 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASN* 2.9 21.3 + - - +
199B ARG* 3.6 6.7 - - - -
201B ALA* 1.3 75.7 - - - +
203B CYS* 1.3 63.6 + - - +
205B LYS* 3.3 8.6 + - - +
206B GLU* 2.9 27.9 + - - +
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Residues in contact with CYS 203 (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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30B PRO 3.7 22.7 - - - +
31B ALA 4.2 0.4 - - - -
33B LEU* 4.0 15.3 - - + -
34B LEU* 3.6 49.1 - - - -
37B LEU* 4.5 1.1 - - + -
174B CYS* 4.1 5.4 - - - -
199B ARG 3.1 10.3 + - - +
200B ILE* 3.3 10.8 - - - +
202B SER* 1.3 78.8 - - - +
204B LEU* 1.3 65.0 + - - +
206B GLU* 3.8 4.5 - - - +
207B HIS* 2.9 24.1 + - - +
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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
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171B ALA* 3.6 43.3 - - + +
174B CYS* 3.7 22.2 - - + -
175B LEU* 4.9 6.3 - - + +
178B LEU* 4.1 13.7 - - + -
200B ILE 3.0 9.0 + - - +
201B ALA* 3.6 8.3 - - - +
203B CYS* 1.3 76.8 - - - +
205B LYS* 1.3 65.3 + - - +
207B HIS* 2.9 7.3 + - + +
208B VAL* 2.9 29.7 + - + +
221B LEU* 4.0 15.5 - - + -
224B LEU* 4.1 10.3 - - + -
225B LEU* 3.8 29.2 - - + -
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Residues in contact with LYS 205 (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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201B ALA 2.8 20.6 + - - +
202B SER* 3.7 7.9 - - - +
204B LEU* 1.3 73.7 - - - +
206B GLU* 1.3 65.0 + - + +
208B VAL* 3.4 2.9 + - - +
209B ALA* 3.0 25.3 + - + +
215B PRO 5.7 2.8 + - - -
216B GLN* 6.2 1.4 - - - +
218B ALA* 6.1 2.7 - - + -
221B LEU* 4.0 35.0 - - + +
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Residues in contact with GLU 206 (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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30B PRO 5.4 5.8 - - - +
202B SER 2.9 18.7 + - - +
203B CYS* 3.9 4.4 - - - +
205B LYS* 1.3 79.5 - - + +
207B HIS* 1.3 52.6 + - - +
209B ALA* 3.1 7.8 + - - +
210B ALA* 2.6 42.2 + - + +
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Residues in contact with HIS 207 (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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34B LEU* 3.8 30.2 - - + +
168B ASP* 2.8 39.0 + - - -
170B PRO* 3.7 19.4 - - + +
171B ALA* 3.9 20.4 - - + -
174B CYS* 6.1 0.2 - - - -
203B CYS 2.9 21.5 + - - +
204B LEU* 3.5 5.2 - - + +
206B GLU* 1.3 73.9 - - - +
208B VAL* 1.3 63.5 + - + +
210B ALA* 3.7 6.9 - - - +
211B VAL* 3.0 47.6 + - + +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA* 4.4 4.3 - - + -
204B LEU* 2.9 30.9 + - + +
205B LYS* 3.9 5.4 - - - +
207B HIS* 1.3 81.1 - - + +
209B ALA* 1.3 58.2 + - - +
211B VAL* 5.1 1.8 - - - -
212B ALA* 3.2 27.8 + - + +
216B GLN 6.0 1.1 - - - +
218B ALA* 5.6 4.5 - - - +
220B CYS* 3.4 33.0 - - + -
221B LEU* 4.2 17.0 - - + +
224B LEU* 3.9 25.1 - - + -
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Residues in contact with ALA 209 (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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205B LYS* 3.0 16.2 + - + +
206B GLU* 3.6 9.2 - - - +
208B VAL* 1.3 75.6 - - - +
210B ALA* 1.3 59.4 + - - +
211B VAL 3.2 5.3 + - - -
213B GLY 3.1 37.6 + - - +
214B GLU* 4.1 4.5 + - - +
215B PRO* 4.6 9.4 - - + +
216B GLN* 4.2 19.3 - - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 2.6 30.5 + - + +
207B HIS* 3.3 8.7 + - - +
209B ALA* 1.3 71.6 - - - +
211B VAL* 1.3 61.5 + - - +
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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
----------------------------------------------------------
168B ASP* 4.3 9.6 - - - +
207B HIS* 3.0 39.9 + - + +
208B VAL* 4.7 1.6 - - - +
210B ALA* 1.3 84.4 - - - +
212B ALA* 1.3 66.0 + - + +
213B GLY 3.5 4.2 + - - -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.2 24.2 + - + +
211B VAL* 1.3 83.3 - - + +
213B GLY* 1.3 58.1 + - - +
220B CYS* 5.2 11.7 - - + -
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Residues in contact with GLY 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA* 3.1 24.5 + - - +
211B VAL 3.5 4.2 + - - -
212B ALA* 1.3 79.2 - - - +
214B GLU* 1.3 62.9 + - - -
216B GLN 3.8 13.7 + - - -
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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