Contacts of the helix formed by residues 155 - 169 (chain A) in PDB entry 1VOM
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 ILE 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.3 32.1 - - + +
123A LEU* 3.8 8.2 - - + +
135A TYR* 4.0 1.3 - - + -
154A HIS* 1.3 88.6 + - + +
156A PHE* 1.4 65.5 + - + +
158A ILE* 3.2 20.8 + - + +
159A SER* 2.9 28.7 + - - +
177A ILE* 4.9 0.7 - - + -
188A ASN* 3.7 18.2 - - + +
191A LYS* 3.6 24.5 - - + -
192A VAL* 3.7 28.9 - - + +
653A VAL* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE 3.8 11.2 - - - -
135A TYR* 3.9 21.8 - + - -
139A MET 4.1 0.4 - - - -
140A VAL* 3.3 46.7 - - + -
143A PHE* 3.8 17.3 - + + -
154A HIS* 2.6 36.5 + + - +
155A ILE* 1.4 76.5 - - + +
157A ALA* 1.3 62.0 + - - +
159A SER* 3.4 6.0 + - - -
160A ASP* 3.0 23.6 + - - +
191A LYS* 3.6 30.5 - - + -
194A GLN* 3.9 9.4 - - - -
195A TYR* 3.6 34.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.3 22.9 - - - +
143A PHE* 3.8 23.3 - - + -
146A ARG 5.5 2.6 - - - +
148A ARG* 5.2 4.3 - - + -
151A VAL* 4.6 8.1 - - + -
152A ALA 4.2 2.7 - - - +
154A HIS* 3.0 14.2 + - - +
156A PHE* 1.3 79.9 - - - +
158A ILE* 1.3 66.0 + - - +
160A ASP* 3.3 6.8 + - - +
161A VAL* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.5 10.0 + - + -
121A LEU 4.6 10.8 - - - +
122A PHE 4.7 0.2 - - - -
123A LEU* 4.0 25.1 - - + +
148A ARG* 6.3 0.4 - - - +
154A HIS 3.2 3.6 + - - +
155A ILE* 3.2 35.0 + - + +
157A ALA* 1.3 77.8 - - - +
159A SER* 1.3 61.7 + - - +
161A VAL* 3.4 9.4 + - + +
162A ALA* 3.0 23.7 + - - +
175A LEU* 3.9 9.8 - - + +
651A HIS* 4.0 29.6 - - + +
652A PHE 3.6 26.7 - - - +
653A VAL* 3.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE 2.9 21.4 + - - -
156A PHE* 3.6 6.2 - - - -
158A ILE* 1.3 80.0 - - - +
160A ASP* 1.3 55.8 + - - +
162A ALA* 3.3 3.3 + - - +
163A TYR* 2.9 28.2 + - - +
175A LEU* 4.4 9.8 - - - +
192A VAL* 3.4 39.0 - - - +
195A TYR* 3.6 23.1 - - - -
196A LEU* 4.1 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE 3.8 6.5 - - - +
145A GLY* 3.2 18.7 + - - -
146A ARG 4.0 8.1 - - - +
156A PHE 3.0 13.1 + - - +
157A ALA* 3.3 7.4 + - - +
159A SER* 1.3 72.1 - - - +
161A VAL* 1.3 56.3 + - - +
163A TYR* 3.2 5.5 + - - +
164A ARG* 2.6 87.4 + - - +
195A TYR* 2.4 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG 5.4 3.4 - - - +
147A ARG* 6.1 0.2 - - - -
148A ARG* 4.2 32.3 - - + +
157A ALA 3.1 15.7 + - - +
158A ILE* 3.5 12.1 - - + +
160A ASP* 1.3 76.3 - - + +
162A ALA* 1.3 60.2 + - - +
164A ARG* 3.0 7.7 + - - +
165A SER* 2.7 35.1 + - - +
651A HIS* 4.1 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE 3.0 10.2 + - - +
159A SER 3.6 8.1 - - - +
161A VAL* 1.3 79.1 - - - +
163A TYR* 1.3 65.3 + - - +
165A SER* 3.2 0.9 + - - -
166A MET* 2.9 19.9 + - - +
173A GLN* 3.4 20.1 - - + +
175A LEU* 3.9 17.7 - - + -
450A ILE* 4.2 5.4 - - + -
651A HIS* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 2.9 14.4 + - - +
160A ASP* 3.3 9.6 - - - +
162A ALA* 1.3 79.0 - - - +
164A ARG* 1.3 96.8 + - - +
166A MET* 3.2 25.1 + - + +
167A LEU* 3.2 43.9 + - + +
196A LEU* 4.3 9.2 - - + -
199A VAL* 4.3 16.1 + - + -
200A ALA* 3.5 22.2 - - + +
247A PHE* 3.8 7.0 - + - -
251A GLY* 2.7 33.2 + - - -
450A ILE* 3.8 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 4.2 11.5 - - - +
145A GLY* 3.3 26.2 - - - +
146A ARG 5.9 0.2 - - - +
160A ASP* 2.6 63.0 + - - +
161A VAL* 3.8 5.6 - - - +
163A TYR* 1.3 99.9 - - - +
165A SER* 1.3 55.8 + - - +
167A LEU* 3.2 7.5 + - - +
168A ASP* 2.6 54.4 + - - +
199A VAL* 4.8 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 2.7 30.3 + - - +
162A ALA* 3.6 2.0 - - - -
164A ARG* 1.3 72.9 - - - +
166A MET* 1.3 63.2 + - - +
168A ASP* 4.4 4.3 - - - +
169A ASP* 2.9 42.4 + - - +
171A GLN* 4.0 1.8 - - - -
173A GLN* 3.5 25.2 + - - -
649A ASN* 4.1 7.0 + - - -
651A HIS* 4.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 2.9 13.2 + - - +
163A TYR* 3.3 30.1 - - + +
164A ARG 3.1 0.2 - - - -
165A SER* 1.3 77.0 - - - +
167A LEU* 1.3 79.4 + - + +
170A ARG* 2.7 34.7 + - - -
171A GLN 3.4 21.3 + - - +
173A GLN* 3.4 8.7 - - + +
247A PHE* 3.2 51.1 - - + -
251A GLY* 4.6 0.2 - - - -
448A TYR* 3.7 26.6 - - + -
449A PHE 4.4 3.1 - - - +
450A ILE* 3.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.2 46.3 + - + +
164A ARG* 3.9 11.2 - - - +
166A MET* 1.3 101.1 - - + +
168A ASP* 1.3 67.5 + - - +
170A ARG* 3.6 14.7 + - - +
249A ASN 4.4 10.5 - - - +
250A ALA 4.5 4.3 - - - +
251A GLY* 3.7 20.0 - - - +
448A TYR* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 2.6 38.9 + - - +
165A SER* 4.3 3.0 - - - +
167A LEU* 1.3 79.3 - - - +
169A ASP* 1.3 67.4 + - - +
170A ARG* 4.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER* 2.9 25.9 + - - +
168A ASP* 1.3 81.6 - - - +
170A ARG* 1.3 71.3 + - - +
171A GLN* 2.7 40.1 + - - +
649A ASN* 4.9 0.5 + - - -
----------------------------------------------------------
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