Contacts of the helix formed by residues 162 - 175 (chain A) in PDB entry 1VPW
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 ALA 162 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 3.0 23.1 + - - +
161A ASN* 1.3 76.5 - - - +
163A PHE* 1.3 57.5 + - - +
165A GLY* 3.7 1.5 - - - -
166A GLY 3.2 18.2 + - - -
191A ASN* 3.6 26.5 - - - +
192A THR* 4.7 1.6 - - - -
195A GLY* 3.7 4.0 - - - -
196A ARG* 3.3 31.8 - - + +
274A TYR* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASN* 3.0 2.3 - - - -
162A ALA* 1.3 75.3 - - - +
164A GLU* 1.3 71.6 + - + +
165A GLY 2.9 5.5 + - - -
166A GLY 3.0 10.7 + - - -
167A TYR* 3.0 15.9 + + + -
195A GLY* 3.3 15.1 + - - +
198A ALA* 3.9 14.8 - - + -
199A GLY* 3.1 34.2 - - - -
202A LYS* 4.2 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASN* 3.4 16.4 + - + +
163A PHE* 1.3 86.9 - - + +
165A GLY* 1.3 59.1 + - - +
167A TYR* 3.8 8.0 - - - +
168A MET* 2.9 47.7 + - + +
322A HIS* 2.6 37.8 + - - +
323A PRO* 3.5 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASN 3.2 8.3 + - - -
162A ALA 3.8 0.2 - - - -
163A PHE 2.9 1.6 - - - -
164A GLU* 1.3 75.5 - - - +
166A GLY* 1.3 65.2 + - - +
168A MET* 2.9 17.0 + - - +
169A ALA* 3.0 13.5 + - - +
274A TYR* 3.3 30.3 - - - -
290A ILE* 4.2 4.6 - - - +
323A PRO* 3.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 3.2 8.1 + - - -
163A PHE 3.0 6.4 + - - -
165A GLY* 1.3 74.4 - - - +
167A TYR* 1.3 61.4 + - - +
169A ALA* 3.2 4.4 + - - +
170A GLY 3.1 18.4 + - - -
196A ARG* 3.1 29.4 - - - -
200A PHE* 3.2 17.3 - - - +
244A PHE* 4.7 5.8 - - - -
274A TYR* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.0 17.6 + + + +
164A GLU* 3.9 10.3 - - - +
166A GLY* 1.3 72.3 - - - +
168A MET* 1.3 71.3 + - + +
170A GLY* 3.3 1.4 + - - -
171A ARG* 3.0 49.7 + - + +
199A GLY* 3.1 14.3 - - - +
202A LYS* 2.9 34.5 - - + -
203A ALA* 3.5 14.7 - - + +
206A GLU* 2.6 45.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 2.9 37.2 + - + +
165A GLY* 2.9 9.4 + - - +
167A TYR* 1.3 80.2 - - + +
169A ALA* 1.3 65.0 + - - +
171A ARG* 3.2 8.4 - - - +
172A TYR* 3.1 22.5 + - - +
290A ILE* 4.4 9.2 - - + -
323A PRO* 3.8 25.1 - - - +
324A ARG* 3.9 7.0 - - + -
325A LEU* 3.3 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 3.0 10.5 + - - +
166A GLY 3.5 8.1 - - - +
167A TYR 3.2 0.4 - - - -
168A MET* 1.3 75.7 - - - +
170A GLY* 1.3 70.9 + - - +
172A TYR* 3.3 4.7 + - - +
173A LEU* 3.2 22.4 + - - +
200A PHE* 4.8 0.7 - - - -
244A PHE* 4.0 30.1 - - + -
272A ILE* 3.8 25.8 - - + +
290A ILE* 4.1 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 3.1 9.6 + - - -
167A TYR 3.3 2.0 + - - -
169A ALA* 1.3 75.5 - - - +
171A ARG* 1.3 63.5 + - - +
173A LEU* 2.8 18.0 + - - +
174A ILE* 2.9 18.9 + - - +
200A PHE* 3.7 23.3 - - - -
203A ALA* 4.4 6.3 - - - -
204A MET* 3.8 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.0 50.9 + - + +
168A MET* 3.2 13.0 - - - +
170A GLY* 1.3 72.3 - - - +
172A TYR* 1.3 52.9 + - - +
174A ILE* 2.9 31.8 + - - +
175A GLU* 2.7 79.1 + - - +
203A ALA* 4.0 12.1 + - - +
206A GLU* 4.1 12.5 + - - +
207A ALA* 5.0 4.6 - - - +
340A ARG* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A MET 3.1 8.1 + - - +
169A ALA* 3.4 11.2 - - - +
171A ARG* 1.3 79.1 - - - +
173A LEU* 1.3 68.4 + - + +
175A GLU* 3.1 12.7 + - + +
176A ARG* 2.8 57.2 + - + +
272A ILE* 4.5 15.3 - - + -
288A THR* 4.2 11.9 + - + +
325A LEU* 4.0 21.1 - - + -
327A GLU* 2.8 49.6 + - + +
331A VAL* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA 3.4 12.3 - - - +
170A GLY 2.8 10.2 + - - +
172A TYR* 1.3 81.0 - - + +
174A ILE* 1.3 63.5 + - - +
176A ARG* 3.2 7.5 + - - -
178A HIS* 3.1 30.7 + - + +
181A ILE* 4.0 40.2 - - + -
200A PHE* 4.2 11.9 - - + -
242A ALA* 4.4 16.8 - - + -
243A VAL 4.6 0.9 - - - +
244A PHE* 4.3 5.8 - - + +
270A SER* 5.4 1.1 - - - +
272A ILE* 4.0 28.0 - - + +
331A VAL* 4.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLY 2.9 20.8 + - - +
171A ARG* 3.1 29.6 - - - +
173A LEU* 1.3 71.1 - - - +
175A GLU* 1.3 66.2 + - - +
176A ARG 2.9 6.3 + - - -
177A GLY* 3.0 14.6 + - - -
178A HIS 3.7 12.2 + - - +
179A ARG* 6.4 0.4 - - + -
181A ILE* 5.0 1.1 - - + -
203A ALA 4.3 7.9 - - - +
204A MET* 4.8 11.0 - - + -
207A ALA* 3.1 35.7 - - + -
209A ILE* 3.9 19.5 - - + -
340A ARG* 4.4 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.7 57.3 + - - +
172A TYR* 3.5 11.1 - - + +
174A ILE* 1.3 73.6 - - - +
176A ARG* 1.3 60.7 + - + +
177A GLY 3.3 1.0 + - - -
337A ARG* 4.3 9.0 + - - +
340A ARG* 3.3 45.3 + - - +
----------------------------------------------------------
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