Contacts of the helix formed by residues 160 - 171 (chain A) in PDB entry 1YVP
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 ASP 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR 4.2 0.6 + - - -
159A LYS* 1.3 72.9 - - - +
161A ALA* 1.3 63.1 + - - +
162A LEU* 3.3 15.7 + - - +
163A ASN* 3.1 46.4 + - - +
164A LEU* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS 3.3 5.4 + - - -
160A ASP* 1.3 74.6 + - - +
162A LEU* 1.3 57.8 + - - +
164A LEU* 3.2 7.6 + - - +
165A ALA* 2.9 28.8 + - - +
192A ASN* 4.6 3.7 + - - +
194A GLY* 3.5 40.4 - - - +
195A LEU* 4.1 7.5 - - + +
198A VAL* 3.8 5.4 - - - +
225A VAL* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 3.3 14.2 + - - +
161A ALA* 1.3 79.1 - - - +
163A ASN* 1.3 65.3 + - - +
165A ALA* 3.2 6.4 + - + +
166A MET* 3.2 19.1 + - - +
221A GLU 5.8 0.2 - - - +
224A LYS* 4.2 33.7 - - + +
225A VAL* 3.7 17.3 - - + +
228A TYR* 3.8 37.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 5.7 3.6 - - + -
160A ASP* 3.1 38.3 + - + +
162A LEU* 1.3 76.1 - - - +
164A LEU* 1.3 66.3 + - - +
166A MET* 3.1 15.1 + - + +
167A ALA* 3.0 20.8 + - - +
9G G 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TRP* 4.3 13.2 - - + -
156A TYR* 3.9 34.5 - - + +
159A LYS* 4.4 20.1 - - + +
160A ASP 2.8 13.4 + - - +
161A ALA* 3.5 10.8 - - - +
163A ASN* 1.3 75.8 - - - +
165A ALA* 1.3 58.2 + - - +
167A ALA* 3.0 8.3 + - + -
168A VAL* 2.8 45.2 + - + +
195A LEU* 4.2 18.2 - - + +
198A VAL* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 2.9 13.4 + - - +
162A LEU* 3.4 13.5 - - + +
164A LEU* 1.3 77.4 - - - +
166A MET* 1.3 58.2 + - - +
168A VAL* 3.6 8.5 - - - +
169A THR* 2.8 32.9 + - - +
198A VAL* 4.5 5.1 - - + +
225A VAL* 4.3 13.0 - - + -
228A TYR* 3.7 18.5 - - + -
229A LEU* 4.0 15.7 - - + -
----------------------------------------------------------
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 LEU 3.2 8.8 + - - +
163A ASN* 3.1 16.7 + - + +
165A ALA* 1.3 78.0 - - - +
167A ALA* 1.3 72.7 + - + +
169A THR* 3.3 2.3 + - - -
170A LYS* 3.0 44.6 + - + +
171A TYR* 5.2 1.1 - - + -
228A TYR* 3.5 26.6 + - + +
254A VAL* 5.9 2.7 - - + -
257A HIS* 5.1 2.9 - - - +
9G G 3.6 76.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 3.7 23.5 - - + +
155A TRP* 5.0 4.3 - - + -
159A LYS* 5.9 2.7 - - + -
163A ASN 3.0 13.2 + - - +
164A LEU* 3.0 19.0 + - + +
166A MET* 1.3 89.6 - - + +
168A VAL* 1.3 57.7 + - + +
171A TYR* 3.1 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.7 1.8 - - + -
164A LEU* 2.8 45.3 + - + +
165A ALA* 3.6 12.8 - - - +
167A ALA* 1.3 72.3 - - - +
169A THR* 1.3 69.4 + - + +
171A TYR 4.2 0.9 - - - -
172A LYS* 3.5 24.3 - - - +
179A HIS* 3.6 33.9 + - + +
198A VAL* 4.2 9.4 - - + -
201A TYR* 4.4 12.0 - - + -
202A VAL* 4.1 26.2 - - + -
229A LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA 2.8 23.2 + - - +
166A MET 3.3 3.5 + - - -
168A VAL* 1.3 76.8 - - + +
170A LYS* 1.3 64.5 + - - +
172A LYS* 4.4 10.3 + - - +
201A TYR* 3.6 35.4 - - + +
228A TYR* 3.7 5.0 + - - -
229A LEU* 4.2 6.7 - - + -
232A THR* 3.8 19.3 - - + +
256A GLU 4.6 6.8 - - - +
257A HIS* 2.9 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 3.0 32.6 + - - +
169A THR* 1.3 81.3 + - - +
171A TYR* 1.3 85.1 + - + +
172A LYS 3.9 1.4 + - - -
174A ARG* 3.1 17.7 + - - -
254A VAL* 3.9 15.7 - - + +
256A GLU* 3.2 45.9 - - + +
257A HIS* 4.3 9.2 - - - +
277A PRO* 4.3 8.1 - - - +
8G C 2.5 31.4 + - - -
9G G 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.0 8.2 - - + +
122A PRO* 3.5 38.1 - - + -
123A THR* 3.4 19.3 - - - -
126A PHE* 4.0 1.2 - - - -
166A MET* 5.2 1.1 - - + -
167A ALA* 3.1 15.6 + - - +
168A VAL 3.9 2.5 - - - -
170A LYS* 1.3 103.7 - - + +
172A LYS* 1.3 56.4 + - - +
173A GLN 3.3 2.6 + - - -
174A ARG* 3.6 30.1 - - + +
179A HIS* 2.7 30.5 - - - -
256A GLU* 4.9 1.6 - - - -
7G C 3.5 24.0 - - - -
8G C 2.8 22.2 - - - -
9G G 2.6 27.1 + - - -
----------------------------------------------------------
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