Contacts of the helix formed by residues 184 - 202 (chain B) in PDB entry 1VLP
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B GLU* 3.3 26.7 - - - -
151B TRP* 5.2 1.8 - - - -
153B TYR* 2.7 28.3 + - - -
182B ARG* 3.2 16.3 - - - +
183B ARG* 1.3 81.0 - - - +
185B LEU* 1.3 64.4 + - - +
186B LYS* 3.3 4.1 + - - -
187B ALA* 2.8 21.7 + - - +
188B GLN 3.2 15.4 + - - -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.7 29.2 - - + +
7B LYS* 5.5 6.1 - - + +
11B ASP* 3.8 11.4 - - - +
141B GLU* 2.9 16.1 + - - +
182B ARG* 3.6 34.1 - - - +
184B SER* 1.3 71.8 - - - +
186B LYS* 1.3 65.5 + - - +
188B GLN* 3.1 4.2 + - - -
189B ASP* 3.0 20.5 + - + +
217B LEU* 5.6 6.5 - - + -
218B PHE* 3.5 29.8 - - + -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 5.4 1.0 + - - +
153B TYR* 3.6 43.6 - - + +
184B SER* 3.2 8.5 + - - +
185B LEU* 1.3 80.4 - - - +
187B ALA* 1.3 55.3 + - - +
189B ASP* 3.2 9.0 + - + +
190B LEU* 2.9 44.3 + - + +
99D GLU* 5.0 15.1 - - - +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TYR* 3.9 10.3 - - + -
156B GLN* 5.3 2.4 - - - +
183B ARG* 4.2 0.7 - - + -
184B SER* 2.8 30.1 + - - +
186B LYS* 1.3 74.8 - - - +
188B GLN* 1.3 63.6 + - - +
190B LEU* 3.3 5.5 + - - +
191B ILE* 3.2 27.2 + - - +
358B THR* 4.0 13.9 - - - +
361B PHE* 3.9 27.6 - - + -
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Residues in contact with GLN 188 (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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176B GLU* 3.2 32.1 + - - +
179B THR* 3.0 32.6 + - - +
182B ARG* 3.0 39.6 + - + +
184B SER 3.2 2.2 + - - -
185B LEU 3.1 8.9 + - - +
187B ALA* 1.3 79.5 - - - +
189B ASP* 1.3 63.1 + - - +
191B ILE* 3.4 7.8 - - + +
192B MSE 3.1 25.2 + - + +
215B ASN* 3.8 5.7 - - - +
218B PHE* 3.3 22.0 - - + -
358B THR* 3.9 17.5 - - + -
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.0 13.3 + - + +
186B LYS* 3.2 11.8 + - - +
188B GLN* 1.3 77.9 - - - +
190B LEU* 1.3 56.8 + - - +
192B MSE 3.3 3.9 + - - +
193B GLN* 2.8 52.0 + - - +
218B PHE* 3.4 21.2 - - + -
221B LYS* 2.8 23.1 + - - -
222B TYR* 2.5 24.7 + - - -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TYR* 3.7 41.5 - - + +
156B GLN* 4.3 18.8 - - + -
157B LEU* 3.7 24.8 - - + +
186B LYS* 2.9 32.7 + - + +
187B ALA 3.3 4.7 + - - +
189B ASP* 1.3 76.8 - - - +
191B ILE* 1.3 58.9 + - - +
193B GLN* 3.4 25.7 + - - +
194B GLY 3.0 20.6 + - - -
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Residues in contact with ILE 191 (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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156B GLN* 4.0 23.6 - - + +
159B GLN* 6.2 0.2 - - - +
160B ALA* 3.5 25.0 - - + +
176B GLU* 3.7 35.9 - - + +
187B ALA 3.2 12.7 + - - +
188B GLN* 3.4 18.2 - - + +
190B LEU* 1.3 74.1 - - - +
192B MSE 1.3 63.1 + - + +
194B GLY* 3.2 0.7 + - - -
195B ILE* 2.8 42.0 + - + +
357B PHE* 3.2 35.7 - - + +
358B THR* 4.1 4.9 - - + -
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Residues in contact with MSE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 4.2 21.1 - - - +
188B GLN* 3.1 19.3 + - + +
189B ASP 3.4 8.3 - - - +
191B ILE* 1.3 78.4 - - + +
193B GLN* 1.3 63.0 + - - +
195B ILE* 3.3 10.7 + - + +
196B MSE 3.0 63.6 + - + +
210B LEU* 5.7 0.9 - - + -
212B GLY 5.9 0.4 - - - -
213B THR* 4.1 37.2 - - + -
218B PHE* 4.0 25.6 - - + +
222B TYR* 3.7 26.7 - - + -
224B VAL* 4.4 2.2 - - + -
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.7 22.8 - - + +
189B ASP* 2.8 36.4 + - - +
190B LEU* 3.4 24.0 - - - +
192B MSE 1.3 76.0 - - - +
194B GLY* 1.3 56.8 + - - +
196B MSE 3.8 3.3 - - - +
197B LYS* 2.9 30.1 + - - +
222B TYR* 3.2 27.2 + - + +
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.5 36.3 - - - +
160B ALA* 4.4 0.2 - - - -
161B GLU* 3.2 20.3 - - - +
190B LEU 3.0 11.4 + - - -
191B ILE 3.2 3.9 + - - -
193B GLN* 1.3 74.3 - - - +
195B ILE* 1.3 63.1 + - - +
197B LYS* 3.4 1.0 + - - +
198B ALA 3.1 17.7 + - - -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA 4.7 1.3 - - - +
161B GLU 4.4 0.2 - - - +
164B ALA* 4.2 17.5 - - + -
174B PHE* 4.5 4.7 - - + -
176B GLU* 4.1 15.3 - - + -
191B ILE* 2.8 37.3 + - + +
192B MSE 3.7 11.9 - - + +
194B GLY* 1.3 76.3 - - - +
196B MSE 1.3 60.4 + - + +
198B ALA* 3.1 5.9 + - - +
199B VAL* 2.9 27.9 + - + +
210B LEU* 3.7 37.0 - - + -
357B PHE* 3.8 41.5 - - + -
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Residues in contact with MSE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B MSE 3.0 49.1 + - + +
193B GLN* 3.9 5.8 - - - +
195B ILE* 1.3 76.1 - - + +
197B LYS* 1.3 57.0 + - - +
199B VAL* 3.4 9.1 + - - +
200B ASN* 2.8 44.5 + - - +
210B LEU* 3.8 21.1 - - + -
222B TYR* 3.3 35.0 - - + +
224B VAL* 3.1 33.9 - - + -
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Residues in contact with LYS 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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157B LEU* 3.9 16.8 - - + +
158B GLU* 5.8 3.0 + - - +
161B GLU* 3.3 32.1 + - - +
193B GLN 2.9 17.9 + - - +
194B GLY* 3.6 7.2 - - - +
195B ILE 3.1 0.2 - - - -
196B MSE 1.3 74.2 - - - +
198B ALA* 1.3 64.6 + - - +
200B ASN* 3.4 6.8 + - - +
201B GLY* 3.2 18.7 + - - -
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Residues in contact with ALA 198 (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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161B GLU* 3.6 20.7 - - + +
164B ALA* 3.5 26.2 - - + -
165B GLU* 3.9 19.3 - - + +
168B PHE* 3.9 4.3 - - + -
194B GLY 3.1 9.3 + - - +
195B ILE 3.4 8.5 - - - +
197B LYS* 1.3 73.9 - - - +
199B VAL* 1.3 65.4 + - - +
201B GLY* 3.2 10.8 + - - -
206B ASN* 3.0 17.4 + - - -
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Residues in contact with VAL 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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168B PHE* 3.7 20.8 - - + -
195B ILE 2.9 18.5 + - - +
196B MSE 3.5 15.9 - - - +
197B LYS 3.3 0.2 - - - -
198B ALA* 1.3 74.2 - - - +
200B ASN* 1.3 72.6 + - - +
202B ASN 3.1 15.8 + - - -
203B PRO* 3.1 12.6 - - - +
206B ASN* 3.6 9.5 - - - +
207B LYS* 3.7 35.0 - - + +
210B LEU* 3.7 28.0 - - + -
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Residues in contact with ASN 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 MSE 2.8 31.5 + - - +
197B LYS* 4.0 6.2 - - - +
198B ALA 3.2 0.2 - - - -
199B VAL* 1.3 87.7 - - - +
201B GLY* 1.3 60.6 + - - +
202B ASN 3.2 0.8 + - - -
203B PRO* 3.6 20.8 - - - +
207B LYS* 5.6 0.7 - - - +
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Residues in contact with GLY 201 (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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197B LYS 3.2 12.1 + - - -
198B ALA* 3.2 6.7 + - - -
199B VAL 3.1 2.2 - - - -
200B ASN* 1.3 77.7 - - - +
202B ASN* 1.3 61.1 + - - +
203B PRO* 3.9 1.4 - - - +
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Residues in contact with ASN 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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199B VAL 3.1 4.9 + - - -
201B GLY* 1.3 81.9 - - - +
203B PRO* 1.3 61.7 - - - +
204B ASP* 4.0 7.6 + - - +
205B ARG* 3.6 44.2 + - - +
206B ASN* 2.8 37.2 + - - +
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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