Contacts of the helix formed by residues 200 - 219 (chain B) in PDB entry 1VHQ
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 ASN 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 3.9 13.0 - - - +
195B TYR* 3.6 10.1 + - - -
198B ALA* 3.4 6.4 - - - +
199B GLN* 1.3 82.1 + - - +
201B ILE* 1.3 66.1 + - - +
202B ALA* 3.1 9.3 + - - +
203B GLU* 2.8 50.9 + - - +
204B ALA 3.2 15.8 + - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.8 32.1 - - + +
29A LEU* 3.5 18.8 - - + +
30A LEU* 3.8 15.5 - - + +
33A SER* 3.4 24.2 - - - -
23B HIS* 3.4 36.8 - - + +
27B LEU* 3.9 15.7 - - + -
195B TYR* 3.3 13.8 + - - +
200B ASN* 1.3 75.8 - - - +
202B ALA* 1.3 65.2 + - - +
204B ALA* 3.2 2.5 + - - +
205B ALA* 2.9 21.5 + - - +
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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
----------------------------------------------------------
30A LEU* 4.3 10.3 - - - -
33A SER* 3.3 18.1 + - - +
34A ARG* 4.0 26.5 - - + +
200B ASN* 3.1 6.1 + - - +
201B ILE* 1.3 80.6 - - - +
203B GLU* 1.3 63.1 + - + +
205B ALA* 3.3 3.4 + - - +
206B SER* 3.1 22.7 + - - -
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 3.7 28.6 - - + +
197B LEU 4.2 1.2 - - - +
198B ALA* 3.5 9.9 - - + -
199B GLN* 2.8 46.8 + - - +
200B ASN* 2.8 30.4 + - - +
202B ALA* 1.3 75.1 - - + +
204B ALA* 1.3 66.1 + - - +
206B SER* 2.7 25.6 + - - -
207B GLY 3.6 2.6 + - - -
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.2 9.6 - - + -
178B VAL* 4.5 3.8 - - - -
194B ALA* 4.8 7.8 - - - +
195B TYR* 3.7 31.6 - - + -
198B ALA* 3.6 14.7 - - + +
200B ASN 3.2 4.2 + - - +
201B ILE 3.4 8.3 - - - +
203B GLU* 1.3 81.4 - - - +
205B ALA* 1.3 61.7 + - - +
207B GLY* 3.4 1.9 + - - -
208B ILE* 3.0 34.4 + - + +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 13.7 - - + -
34A ARG* 5.9 2.0 - - + -
27B LEU* 3.8 29.5 - - + +
201B ILE 2.9 16.4 + - - +
202B ALA* 3.6 5.4 - - - +
203B GLU 3.2 0.2 - - - -
204B ALA* 1.3 76.6 - - - +
206B SER* 1.3 55.7 + - - +
208B ILE* 4.5 2.5 - - - -
209B ASP* 2.8 45.4 + - - +
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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
----------------------------------------------------------
178B VAL* 4.9 0.3 - - - +
179B ASP* 3.5 27.5 + - - +
202B ALA 3.1 12.1 + - - -
203B GLU* 2.7 22.8 + - - -
205B ALA* 1.3 75.7 - - - +
207B GLY* 1.3 61.5 + - - +
209B ASP* 3.8 6.2 - - - +
210B LYS* 3.3 26.8 + - - +
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Residues in contact with GLY 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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178B VAL 3.3 19.5 - - - -
179B ASP* 4.3 7.9 - - - -
180B ASP 4.6 0.4 - - - -
181B ILE* 4.0 0.3 - - - +
192B THR* 3.9 18.1 + - - -
194B ALA* 6.1 0.7 - - - -
203B GLU 3.6 1.8 + - - -
204B ALA 3.4 4.7 + - - -
206B SER* 1.3 78.5 + - - +
208B ILE* 1.3 66.7 + - - +
210B LYS* 3.2 6.0 + - - +
211B LEU* 2.9 22.5 + - - +
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Residues in contact with ILE 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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24B GLU* 3.8 35.9 - - + -
27B LEU* 4.0 22.0 - - + +
28B THR* 3.6 35.2 - - - +
137B MSE 3.9 23.1 - - + -
192B THR* 4.6 3.1 - - + -
194B ALA* 4.4 10.3 - - + -
204B ALA* 3.0 21.6 + - + +
205B ALA* 4.0 4.9 - - - +
207B GLY* 1.3 75.0 - - - +
209B ASP* 1.3 57.1 + - - +
211B LEU* 3.1 7.1 + - - +
212B VAL* 2.9 35.5 + - + +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.6 5.5 - - - +
30B LEU* 5.9 0.5 - - - +
31B ALA* 3.5 15.7 - - - +
34B ARG* 2.8 35.7 + - - +
205B ALA* 2.8 33.4 + - - +
206B SER* 3.8 6.2 - - - +
208B ILE* 1.3 72.4 - - - +
210B LYS* 1.3 58.3 + - - +
212B VAL* 3.5 1.4 + - - +
213B SER* 3.0 30.4 + - - -
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 2.8 30.6 + - - +
180B ASP* 4.0 20.5 + - - +
181B ILE* 3.9 20.0 - - + -
206B SER* 3.3 12.7 + - - +
207B GLY* 3.2 9.7 + - - +
209B ASP* 1.3 76.9 - - - +
211B LEU* 1.3 58.5 + - - +
213B SER* 3.3 6.3 + - - -
214B ARG* 3.0 29.6 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.1 18.2 - - + -
135B GLY* 4.3 2.5 - - - -
136B PHE 3.7 24.9 - - - +
137B MSE 4.2 15.9 - - + -
181B ILE* 3.6 12.0 - - + +
190B VAL* 3.7 26.2 - - + +
191B THR 4.0 2.5 - - - -
192B THR* 3.6 28.7 - - + +
207B GLY 2.9 13.0 + - - +
208B ILE* 3.1 6.9 + - - +
210B LYS* 1.3 76.3 - - - +
212B VAL* 1.3 77.9 + - + +
214B ARG* 3.2 2.3 + - - +
215B VAL* 2.9 32.9 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.3 11.4 - - + +
31B ALA* 3.8 32.3 - - + +
32B ILE* 4.1 21.1 - - + +
35B SER* 5.0 0.9 - - - +
93B ILE* 3.9 20.2 - - + -
208B ILE* 2.9 32.6 + - + +
209B ASP 4.0 1.6 - - - +
211B LEU* 1.3 78.4 - - + +
213B SER* 1.3 64.3 + - - +
215B VAL* 3.3 5.1 + - - +
216B LEU* 2.9 38.8 + - + +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 5.9 0.9 - - - -
209B ASP 3.0 18.7 + - - -
210B LYS* 3.6 7.0 - - - -
211B LEU 3.3 0.2 - - - -
212B VAL* 1.3 78.6 - - - +
214B ARG* 1.3 62.3 + - - +
216B LEU* 3.2 10.3 + - - +
217B VAL* 3.0 31.2 + - - +
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Residues in contact with ARG 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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181B ILE* 3.7 24.2 - - + -
183B VAL* 4.0 19.2 - - + +
185B GLU* 2.8 32.9 + - - -
190B VAL* 4.1 10.5 - - + -
210B LYS 3.0 16.5 + - - +
211B LEU 3.9 2.7 - - - +
213B SER* 1.3 74.3 - - - +
215B VAL* 1.3 64.5 + - - +
217B VAL* 3.2 34.6 + - - +
218B LEU* 2.9 48.4 + - + +
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Residues in contact with VAL 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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7B ILE* 5.2 2.9 - - + -
91B ALA* 3.5 29.2 - - + -
92B LEU 5.0 0.2 - - - +
93B ILE* 4.4 15.3 - - + -
133B PRO* 3.5 17.2 - - + +
134B LEU 4.4 1.6 - - - +
135B GLY* 4.1 19.3 - - - +
190B VAL* 3.9 24.0 - - + -
211B LEU* 2.9 26.0 + - + +
212B VAL* 3.7 6.5 - - - +
214B ARG* 1.3 75.7 - - - +
216B LEU* 1.3 59.0 + - + +
218B LEU* 3.3 6.5 + - - -
219B ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 216 (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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5B LYS* 4.8 11.4 - - + +
7B ILE* 3.5 36.6 - - + -
31B ALA 5.0 0.2 - - - +
32B ILE* 5.2 1.6 - - + -
35B SER* 3.4 36.8 - - - +
37B ALA* 4.2 13.2 - - + -
212B VAL* 2.9 33.9 + - + +
213B SER* 3.2 7.4 + - - +
215B VAL* 1.3 76.3 - - + +
217B VAL* 1.3 63.8 + - + +
219B ALA* 2.9 24.3 + - + +
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Residues in contact with VAL 217 (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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213B SER* 3.0 24.7 + - - +
214B ARG* 3.5 33.9 - - - +
216B LEU* 1.3 75.9 - - + +
218B LEU* 1.3 64.5 + - + +
219B ALA 3.1 9.5 - - - +
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Residues in contact with LEU 218 (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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133B PRO* 3.7 22.8 - - + +
183B VAL* 4.5 5.6 - - + -
185B GLU* 4.9 2.0 - - - +
188B LYS* 3.5 55.2 + - + +
190B VAL* 3.8 29.2 - - + -
214B ARG* 2.9 54.4 + - + +
215B VAL 3.5 7.6 - - - +
217B VAL* 1.3 79.4 - - + +
219B ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 4.1 40.9 + - + -
7B ILE* 5.3 0.4 - - + -
90B ASP* 3.9 22.2 - - + +
91B ALA* 4.6 3.6 - - + -
133B PRO* 3.7 10.7 - - + +
215B VAL 2.9 14.2 + - - +
216B LEU* 2.9 27.0 + - + +
217B VAL 3.1 8.2 - - - +
218B LEU* 1.3 81.3 - - - +
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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
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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