Contacts of the helix formed by residues 215 - 223 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.8 0.3 - - - +
11A ASP* 3.0 25.3 + - - +
12A THR 3.2 12.5 - - - +
179A THR* 3.0 32.3 + - - +
182A ARG* 3.8 0.2 - - - +
188A GLN* 3.7 12.3 + - - +
213A THR* 3.0 14.1 + - - +
214A SER* 1.3 76.2 + - - +
216A ILE* 1.3 58.9 + - - +
217A LEU* 3.1 13.2 + - - +
218A PHE* 2.9 38.8 + - + -
219A ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.5 29.2 - - + +
12A THR* 3.2 12.4 + - + +
14A MSE 3.8 36.3 - - + +
17A ILE* 3.7 32.5 - - + -
72A TYR* 3.6 27.5 - - + -
73A LEU* 4.3 9.9 - - + -
77A ILE* 4.9 1.8 - - + -
214A SER 4.1 0.7 - - - +
215A ASN* 1.3 71.8 - - - +
217A LEU* 1.3 56.8 + - - +
219A ALA* 3.3 7.1 + - - +
220A LYS* 3.0 28.5 + - - +
226A PRO* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 5.6 5.6 - - + +
8A SER* 3.9 28.7 - - - +
10A LEU* 2.8 27.1 + - + +
11A ASP* 3.9 23.8 - - + +
69A GLU* 4.8 4.0 - - + +
185A LEU* 5.9 4.7 - - + -
215A ASN* 3.1 8.4 + - - +
216A ILE* 1.3 76.8 - - - +
218A PHE* 1.3 63.4 + - + +
220A LYS* 3.3 13.8 + - + +
221A LYS* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 4.9 0.7 - - - -
182A ARG* 4.3 1.8 - - - -
185A LEU* 3.7 29.2 - - + -
188A GLN* 3.3 34.8 - - + -
189A ASP* 3.4 44.2 - - + -
192A MSE 3.9 18.0 - - + +
213A THR* 4.0 6.7 - - + -
215A ASN* 2.9 36.5 + - + +
217A LEU* 1.3 79.4 - - + +
219A ALA* 1.3 66.8 + - - +
221A LYS* 4.1 11.0 - - + -
222A TYR* 3.0 45.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.5 10.0 + - - +
213A THR* 3.4 16.2 - - + +
215A ASN 2.8 17.7 + - - +
216A ILE 3.4 8.5 - - - +
218A PHE* 1.3 71.6 - - - +
220A LYS* 1.3 62.3 + - - +
223A GLY* 3.0 20.6 + - - -
224A VAL* 3.0 29.7 + - - +
225A LYS 3.9 0.2 - - - -
226A PRO* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.4 11.2 - - + -
68A GLU* 2.7 47.8 + - - +
69A GLU* 4.9 5.2 - - + +
72A TYR* 3.3 52.6 + - + -
216A ILE 3.0 13.0 + - - +
217A LEU* 3.5 16.8 - - + +
219A ALA* 1.3 77.6 - - - +
221A LYS* 1.3 62.5 + - - +
223A GLY* 3.6 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 2.8 30.3 + - - +
217A LEU* 2.9 19.0 + - + +
218A PHE* 3.7 14.0 - - + +
220A LYS* 1.3 79.2 - - - +
222A TYR* 1.3 87.2 + - + +
223A GLY 3.4 0.7 + - - -
204C ASP* 5.5 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 2.6 31.0 + - - -
192A MSE 3.6 40.4 - - + -
193A GLN* 3.3 34.8 + - + +
196A MSE 3.8 33.2 - - + +
218A PHE* 3.0 27.0 + + - +
221A LYS* 1.3 100.8 + - + +
223A GLY* 1.3 62.1 + - - +
224A VAL* 3.4 10.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA 3.0 7.7 + - - -
220A LYS* 3.6 6.1 + - - -
221A LYS 3.4 4.2 + - - -
222A TYR* 1.3 79.4 - - - +
224A VAL* 1.3 61.9 + - - +
----------------------------------------------------------
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