Contacts of the helix formed by residues 215 - 223 (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 ASN 215 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU 3.9 0.5 - - - +
11D ASP* 2.8 26.1 + - - -
12D THR 3.3 11.0 - - - +
179D THR* 3.2 31.4 + - - +
182D ARG* 3.7 0.2 - - - +
188D GLN* 3.6 9.9 + - - +
213D THR* 3.1 18.3 + - - +
214D SER* 1.3 78.1 + - - +
216D ILE* 1.3 62.8 + - - +
217D LEU* 3.0 13.9 + - - +
218D PHE* 2.9 37.0 + - + -
219D ALA* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 3.4 24.2 - - + +
12D THR* 3.1 18.2 + - + +
14D MSE 3.8 33.2 - - + -
17D ILE* 3.6 33.0 - - + -
72D TYR* 3.7 27.8 - - + -
73D LEU* 4.2 13.9 - - + -
77D ILE* 5.0 1.8 - - + -
214D SER 4.0 0.4 - - - +
215D ASN* 1.3 71.4 - - - +
217D LEU* 1.3 63.3 + - - +
219D ALA* 3.2 7.6 + - - +
220D LYS* 3.0 22.0 + - - +
226D PRO* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 5.6 5.4 - - + +
8D SER* 4.0 21.3 - - - +
10D LEU* 3.0 32.9 + - + +
11D ASP* 4.0 23.6 - - + +
69D GLU* 5.2 2.0 - - + +
185D LEU* 5.9 3.8 - - + -
215D ASN* 3.0 9.7 + - - +
216D ILE* 1.3 77.4 - - - +
218D PHE* 1.3 65.1 + - + +
220D LYS* 3.3 15.2 + - + +
221D LYS* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 5.0 0.7 - - - -
185D LEU* 3.7 27.8 - - + -
188D GLN* 3.3 36.8 - - + -
189D ASP* 3.5 44.6 - - + -
192D MSE 4.0 15.8 - - + +
213D THR* 4.0 8.5 - - + -
215D ASN* 2.9 37.1 + - + +
217D LEU* 1.3 80.2 - - + +
219D ALA* 1.3 65.1 + - - +
221D LYS* 4.2 10.5 - - + -
222D TYR* 2.9 46.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 3.5 9.8 + - - +
213D THR* 3.5 13.1 - - + +
215D ASN 2.9 14.2 + - - +
216D ILE 3.5 8.7 - - - +
218D PHE* 1.3 75.7 - - - +
220D LYS* 1.3 56.6 + - - +
223D GLY* 2.9 26.7 + - - -
224D VAL* 3.1 29.3 + - - +
225D LYS 3.9 1.1 - - - +
226D PRO* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.2 12.8 - - + -
68D GLU* 2.5 45.7 + - - +
69D GLU* 5.0 4.6 - - + +
72D TYR* 3.4 52.6 + - + -
216D ILE 3.0 13.5 + - - +
217D LEU* 3.6 17.7 - - + +
219D ALA* 1.3 79.2 - - - +
221D LYS* 1.3 62.3 + - - +
223D GLY* 3.7 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ASP* 2.7 30.1 + - - +
217D LEU* 2.9 19.8 + - + +
218D PHE* 3.8 14.0 - - + +
219D ALA 3.3 0.2 - - - -
220D LYS* 1.3 77.7 - - - +
222D TYR* 1.3 90.3 + - + +
223D GLY 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ASP* 2.7 28.7 + - - -
192D MSE 3.4 40.4 - - + -
193D GLN* 3.2 34.7 + - + +
196D MSE 3.8 42.1 - - + +
218D PHE* 2.9 25.3 + + - +
221D LYS* 1.3 102.6 + - + +
223D GLY* 1.3 63.0 + - - +
224D VAL* 3.4 3.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA 2.9 8.1 + - - -
220D LYS* 3.7 4.9 + - - -
221D LYS 3.4 4.0 + - - -
222D TYR* 1.3 79.2 - - - +
224D VAL* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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