Contacts of the helix formed by residues 154 - 162 (chain B) in PDB entry 1YA8
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 GLY 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.4 29.3 - - - +
152B TYR 3.6 2.6 + - - -
153B ASP* 1.3 72.5 + - - +
155B LEU* 1.3 64.5 + - - +
156B ALA 3.6 0.9 - - - -
157B LEU* 4.2 7.4 - - - -
158B ALA* 3.2 24.8 + - - +
165B VAL* 3.9 22.3 - - - +
167B THR* 5.4 0.2 - - - +
476B PHE* 4.8 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.8 32.8 - - + +
39B SER 5.0 0.7 - - - +
40B LEU* 4.0 25.1 - - + -
47B VAL* 3.8 31.4 - - + +
49B ILE* 4.5 8.3 - - + -
122B TYR* 3.7 4.2 - - + -
153B ASP* 2.8 26.7 + - - +
154B GLY* 1.3 78.8 - - - +
156B ALA* 1.3 64.9 + - - +
158B ALA* 3.7 2.5 - - - +
159B ALA* 3.1 20.3 + - - +
481B LEU* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.0 8.3 - - + -
153B ASP 4.7 1.4 + - - -
154B GLY 3.6 0.2 - - - -
155B LEU* 1.3 79.3 - - - +
157B LEU* 1.3 55.8 + - - +
159B ALA* 3.2 1.2 + - - -
160B HIS* 2.7 57.6 + - + +
476B PHE 4.1 10.1 - - - +
477B GLY* 4.0 25.4 - - - +
480B PHE* 4.3 10.1 - - + -
481B LEU* 4.6 8.3 - - + +
497B MET* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B MET* 4.6 13.2 - - + -
154B GLY* 3.9 7.8 + - - +
155B LEU 3.4 0.2 - - - -
156B ALA* 1.3 76.9 - - - +
158B ALA* 1.3 57.6 + - - +
161B GLU* 3.0 36.8 + - + +
163B VAL* 3.7 8.6 - - + +
165B VAL* 3.6 25.4 - - + -
218B PHE* 4.2 26.0 - - + -
475B VAL* 3.7 26.0 - - + +
476B PHE* 4.5 17.0 + - + -
497B MET* 3.7 33.1 - - + +
500B TRP* 5.7 2.7 - - + -
501B ALA* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.4 5.4 - - + -
122B TYR* 3.7 20.9 - - + +
124B PRO* 3.4 16.0 - - + +
154B GLY 3.2 18.7 + - - +
155B LEU 3.7 3.1 - - - +
157B LEU* 1.3 78.7 - - - +
159B ALA* 1.3 58.1 + - - +
162B ASN* 2.8 32.1 + - - -
163B VAL* 3.3 24.3 + - - +
165B VAL* 4.0 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.1 17.3 - - + -
43B PHE* 3.0 40.0 - - + -
45B GLN 5.8 0.4 - - - +
47B VAL* 4.1 14.8 - - + -
124B PRO* 4.3 9.1 - - - +
155B LEU 3.1 13.4 + - - +
156B ALA 3.9 1.3 - - - +
158B ALA* 1.3 79.4 - - - +
160B HIS* 1.3 63.1 + - - +
161B GLU 3.5 0.7 + - - -
162B ASN* 3.8 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.9 15.8 - - + +
41B GLU 5.5 0.6 + - - -
43B PHE* 3.6 23.7 - + - -
156B ALA* 2.7 46.7 + - + +
157B LEU 4.3 0.9 - - - +
159B ALA* 1.3 76.0 - - - +
161B GLU* 1.3 70.4 + - + +
162B ASN 3.7 0.2 - - - -
480B PHE* 3.3 47.0 - + - -
494B LYS* 4.6 14.1 - - - +
497B MET* 4.3 18.9 - - + +
498B LYS* 5.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.0 16.8 + - + +
160B HIS* 1.3 85.4 - - - +
162B ASN* 1.3 72.6 + - - +
163B VAL* 3.3 6.7 + - + +
494B LYS 4.5 2.6 - - - +
497B MET* 3.5 24.4 - - + +
498B LYS* 3.5 45.0 + - - +
501B ALA* 3.3 22.0 - - + -
505B ARG* 3.1 44.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 4.0 16.2 + - - +
125B ALA* 5.6 0.8 - - - +
133B LEU* 3.0 42.2 - - - +
134B PRO* 4.2 5.2 - - - +
158B ALA 2.8 15.1 + - - -
159B ALA 3.8 5.6 + - - +
160B HIS 3.7 1.8 - - - -
161B GLU* 1.3 80.0 - - - +
163B VAL* 1.3 60.2 + - - +
505B ARG* 4.8 1.1 + - - +
----------------------------------------------------------
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