Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 1YI2
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 VAL 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26700 G 3.9 7.2 - - - +
26710 U 3.2 37.0 + - - +
23B THR* 4.3 3.1 + - - +
25B ARG* 3.2 17.5 + - - -
109B LEU* 4.6 2.9 - - + -
112B THR* 4.5 8.9 - - + +
113B LEU* 4.3 28.3 - - + -
143B ILE* 3.8 24.2 - - + -
144B THR 3.1 9.9 - - - +
145B HIS* 3.9 14.1 - - + -
159B PRO 3.7 9.6 + - - +
160B ASP* 1.3 74.3 - - - +
162B MET* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26710 U 4.0 1.6 - - - -
23B THR* 3.6 7.0 - - + -
25B ARG* 3.7 14.6 - - - +
42B ALA* 3.7 16.6 - - + -
79B MET* 4.7 7.2 - - + +
143B ILE* 4.9 0.2 - - - -
144B THR* 2.5 43.7 + - + +
146B THR* 4.6 5.2 - - - -
160B ASP 4.0 12.1 - - - +
161B VAL* 1.3 76.2 - - - +
163B GLU* 1.3 59.8 + - - +
164B THR* 4.0 2.9 + - - +
308B LEU* 3.2 35.9 - - + -
310B ARG* 3.2 56.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26710 U 2.7 17.4 + - - +
26720 C 2.8 32.9 + - - +
29B TRP* 3.8 8.4 - - - -
85B ARG* 2.7 37.8 + - - -
87B TYR* 2.4 27.7 + - - -
141B ARG* 3.0 35.2 + - + +
142B LEU 3.6 9.6 - - - +
143B ILE* 3.7 10.3 - - + +
162B MET* 1.3 72.2 - - - +
164B THR* 1.3 62.4 + - - +
310B ARG* 3.3 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.8 9.4 - - + -
38B VAL* 3.6 20.4 - - + -
39B GLN 3.7 5.6 - - - -
40B GLY* 3.5 38.4 - - - +
41B PHE 5.2 0.2 + - - -
79B MET* 5.5 2.4 - - - +
141B ARG* 3.0 5.0 - - - +
142B LEU* 2.6 43.5 + - - +
144B THR* 4.3 9.0 + - - +
162B MET* 4.0 7.8 + - - +
163B GLU* 1.3 72.9 - - - +
165B ARG* 1.3 62.5 + - - +
166B VAL* 4.4 0.6 - - - +
310B ARG* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.5 48.8 - - + -
30B PRO 4.0 8.0 + - - -
32B ASP* 2.9 40.6 + - - -
39B GLN* 2.8 54.9 + - - +
139B ASP* 3.0 45.0 + - - +
140B LEU 3.9 3.8 - - - +
141B ARG* 3.5 12.1 - - + +
164B THR* 1.3 79.2 - - - +
166B VAL* 1.3 68.6 + - - +
167B GLY* 3.7 2.2 - - - -
174B ARG* 4.0 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.5 26.7 - - - +
38B VAL* 4.3 7.2 - - + -
84B LEU* 5.3 0.2 - - + -
140B LEU* 2.8 29.1 + - + +
141B ARG* 4.5 0.4 - - - -
142B LEU* 3.6 40.2 - - + +
164B THR 4.4 0.7 - - - +
165B ARG* 1.3 86.6 + - - +
167B GLY* 1.3 59.3 + - - +
174B ARG* 3.1 36.1 + - + +
177B HIS* 4.3 13.9 - - + -
178B ALA* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.1 23.3 - - - -
33B ASP 5.7 0.2 - - - -
35B GLN 3.8 2.3 - - - +
37B GLY* 2.9 28.3 + - - +
39B GLN* 3.6 15.4 + - - +
165B ARG* 3.7 5.4 - - - -
166B VAL* 1.3 76.4 - - - +
168B GLY* 1.3 57.9 + - - -
174B ARG* 3.6 4.0 - - - -
----------------------------------------------------------
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