Contacts of the helix formed by residues 184 - 202 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D GLU* 3.3 24.2 - - - -
151D TRP* 4.7 2.6 - - - -
153D TYR* 2.6 29.8 + - - -
182D ARG* 3.2 17.7 - - - +
183D ARG* 1.3 80.2 - - - +
185D LEU* 1.3 64.7 + - - +
186D LYS* 3.4 4.2 + - - -
187D ALA* 2.9 20.7 + - - +
188D GLN 3.1 17.5 + - - -
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 3.5 32.5 - - + +
7D LYS* 5.5 8.1 - - + +
11D ASP* 3.7 11.9 - - - +
141D GLU* 2.9 17.6 + - - +
182D ARG* 3.4 37.2 - - - +
184D SER* 1.3 72.0 - - - +
186D LYS* 1.3 63.0 + - - +
188D GLN* 3.1 4.9 + - - +
189D ASP* 2.9 21.3 + - + +
217D LEU* 5.9 4.0 - - + -
218D PHE* 3.7 24.9 - - + -
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D GLU* 5.5 0.2 + - - -
153D TYR* 3.5 52.2 - - + +
184D SER* 3.2 2.5 + - - +
185D LEU* 1.3 79.1 - - - +
187D ALA* 1.3 63.8 + - - +
189D ASP* 3.2 9.4 + - + +
190D LEU* 2.9 39.5 + - + +
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR* 3.7 16.8 - - + -
156D GLN* 5.2 2.0 - - - +
183D ARG* 4.3 0.9 - - + -
184D SER* 2.9 30.8 + - - +
186D LYS* 1.3 77.8 - - - +
188D GLN* 1.3 62.0 + - - +
190D LEU* 3.3 4.9 + - - +
191D ILE* 3.2 29.5 + - + +
358D THR 4.0 14.1 - - - +
361D PHE* 4.0 20.2 - - + -
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Residues in contact with GLN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLU* 3.2 29.9 + - - +
179D THR* 3.0 32.2 + - - +
182D ARG* 2.9 41.8 + - + +
184D SER 3.1 4.0 + - - +
185D LEU 3.1 7.2 + - - +
187D ALA* 1.3 81.1 - - - +
189D ASP* 1.3 60.6 + - - +
191D ILE* 3.4 9.9 - - + +
192D MSE 3.1 30.0 + - + +
215D ASN* 3.6 6.5 + - - +
218D PHE* 3.3 22.3 - - + -
358D THR* 3.8 15.9 - - + -
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 2.9 12.8 + - + +
186D LYS* 3.6 11.7 - - - +
188D GLN* 1.3 77.6 - - - +
190D LEU* 1.3 62.5 + - - +
192D MSE 3.3 4.0 + - - +
193D GLN* 2.9 46.6 + - - +
218D PHE* 3.5 23.2 - - + -
221D LYS* 2.7 25.6 + - - -
222D TYR* 2.7 19.5 + - - -
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR* 3.6 43.3 - - + +
156D GLN* 4.3 18.8 - - + -
157D LEU* 3.8 23.0 - - + +
186D LYS* 2.9 36.3 + - + +
187D ALA 3.3 4.7 + - - +
189D ASP* 1.3 74.7 - - - +
191D ILE* 1.3 58.2 + - - +
193D GLN* 3.3 28.0 - - - +
194D GLY 3.0 21.8 + - - -
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D GLN* 3.9 24.2 - - + +
159D GLN* 6.2 0.7 - - - +
160D ALA* 3.5 25.5 - - + +
176D GLU* 3.9 29.8 - - + +
187D ALA* 3.2 14.3 + - + +
188D GLN* 3.4 17.0 - - + +
190D LEU* 1.3 75.2 - - - +
192D MSE 1.4 60.3 + - + +
194D GLY* 3.6 0.5 - - - -
195D ILE* 2.8 47.0 + - + +
357D PHE* 3.3 31.9 - - + +
358D THR* 4.1 13.5 - - + -
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Residues in contact with MSE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLU* 4.3 17.9 - - - +
188D GLN* 3.1 21.4 + - + +
189D ASP 3.5 4.9 - - - +
191D ILE* 1.4 74.6 - - + +
193D GLN* 1.3 58.0 + - - +
195D ILE* 3.3 11.5 + - + +
196D MSE 2.9 44.7 + - - +
210D LEU* 6.0 1.1 - - + -
212D GLY 6.1 0.4 - - - -
213D THR* 4.1 37.7 - - + -
218D PHE* 4.0 24.9 - - + +
222D TYR* 3.4 45.1 - - + -
224D VAL* 4.5 7.9 - - + -
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 3.4 23.7 - - + +
189D ASP* 2.9 29.8 + - - +
190D LEU* 3.3 25.6 - - - +
192D MSE 1.3 76.0 - - - +
194D GLY* 1.3 56.5 + - - +
196D MSE 3.5 3.0 + - - +
197D LYS* 2.9 29.6 + - - +
222D TYR* 3.2 26.7 + - + +
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Residues in contact with GLY 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 3.4 35.4 - - - +
160D ALA* 4.3 0.4 - - - -
161D GLU* 3.3 19.2 - - - +
190D LEU 3.0 12.6 + - - -
191D ILE 3.2 3.3 + - - -
193D GLN* 1.3 72.1 - - - +
195D ILE* 1.3 65.8 + - - +
197D LYS* 3.3 1.3 + - - -
198D ALA 3.1 17.7 + - - -
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ALA* 4.5 1.7 - - - +
164D ALA* 4.2 17.9 - - + +
174D PHE* 4.6 4.0 - - + -
176D GLU* 4.1 15.0 - - + -
191D ILE* 2.8 37.0 + - + +
192D MSE 3.8 12.8 - - + +
194D GLY* 1.3 74.7 - - - +
196D MSE 1.3 60.0 + - - +
198D ALA* 3.2 6.8 + - - +
199D VAL* 3.0 26.7 + - + +
210D LEU* 3.9 36.8 - - + -
357D PHE* 3.8 41.5 - - + -
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Residues in contact with MSE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D MSE 2.9 26.9 + - + +
193D GLN* 3.9 4.0 - - - +
195D ILE* 1.3 74.6 - - - +
197D LYS* 1.3 60.8 + - - +
199D VAL* 3.2 17.1 + - + +
200D ASN* 2.9 52.8 + - - +
207D LYS* 5.5 3.6 - - - +
210D LEU* 3.8 17.3 - - + -
222D TYR* 3.8 40.6 - - + +
224D VAL* 3.7 32.8 - - + -
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Residues in contact with LYS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 4.2 19.4 - - + +
158D GLU* 5.9 2.6 + - - +
161D GLU* 2.8 33.6 + - - +
193D GLN 2.9 18.4 + - - +
194D GLY* 3.6 5.6 - - - +
196D MSE 1.3 75.7 - - - +
198D ALA* 1.3 60.6 + - - +
200D ASN* 3.4 5.9 + - - +
201D GLY* 3.2 18.2 + - - -
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D GLU* 3.7 21.4 - - + +
164D ALA* 3.6 26.2 - - + -
165D GLU* 3.9 11.9 - - + +
168D PHE* 3.8 7.8 - - + -
194D GLY 3.1 9.1 + - - +
195D ILE 3.3 9.2 - - - +
197D LYS* 1.3 74.5 - - - +
199D VAL* 1.3 66.1 + - - +
201D GLY* 3.3 10.1 + - - -
206D ASN* 2.9 15.4 + - - -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D PHE* 3.6 27.3 - - + -
195D ILE* 3.0 20.4 + - + +
196D MSE 3.2 17.9 + - + +
198D ALA* 1.3 76.6 - - - +
200D ASN* 1.3 60.6 + - - +
202D ASN 3.1 7.6 + - - -
203D PRO* 3.1 24.3 - - - +
206D ASN* 3.3 3.5 + - - +
207D LYS* 3.8 46.7 - - + +
210D LEU* 3.8 26.7 - - + -
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Residues in contact with ASN 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D MSE 2.9 37.8 + - - +
197D LYS* 3.4 4.9 + - - +
198D ALA 3.2 0.2 - - - -
199D VAL* 1.3 75.5 - - - +
201D GLY* 1.3 62.1 + - - +
202D ASN 3.3 0.4 - - - -
203D PRO* 3.5 17.1 - - - +
207D LYS* 3.2 26.3 + - - -
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Residues in contact with GLY 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LYS 3.2 12.5 + - - -
198D ALA 3.3 6.3 + - - -
199D VAL 3.2 1.8 - - - -
200D ASN* 1.3 76.9 - - - +
202D ASN* 1.3 59.9 + - - +
203D PRO* 3.9 1.4 - - - +
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Residues in contact with ASN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D VAL 3.1 4.6 + - - -
201D GLY* 1.3 80.3 - - - +
203D PRO* 1.3 63.2 - - - +
204D ASP* 3.9 7.1 + - - +
205D ARG* 3.4 44.1 + - - +
206D ASN* 2.9 38.4 + - - +
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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