Contacts of the strand formed by residues 160 - 168 (chain B) in PDB entry 3ORH
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 LEU 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 3.4 9.4 - - - -
129B PHE 3.4 14.4 - - - +
131B GLY* 4.2 3.6 - - - -
132B ILE* 3.8 21.3 - - + -
156B ALA 3.2 21.3 + - - +
157B PHE 3.6 0.2 + - - -
158B ARG 3.4 0.8 - - - -
159B LEU* 1.3 77.3 - - - +
161B LYS* 1.3 65.2 + - - +
162B PRO* 4.6 0.2 - - - +
164B GLY* 3.8 15.9 - - - +
165B VAL 3.8 28.5 - - - +
166B LEU* 4.0 19.7 - - + +
202B PHE* 4.0 25.1 - - + -
235B LYS* 2.9 35.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY* 5.8 0.8 - - - -
63B ARG* 3.8 25.1 - - - +
127B GLY* 3.3 23.3 - - - +
128B HIS* 3.8 5.4 - - - +
129B PHE 2.9 18.9 + - - +
130B ASP* 3.3 39.5 + - - +
159B LEU 3.7 0.2 + - - -
160B LEU* 1.3 77.2 - - - +
162B PRO* 1.4 79.4 - - + +
163B GLY 3.2 0.2 + - - -
164B GLY* 2.8 17.8 + - - +
235B LYS* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 5.5 2.7 - - - +
160B LEU 4.0 1.1 - - - +
161B LYS* 1.4 90.1 - - + +
163B GLY* 1.3 60.5 + - - +
164B GLY 3.4 0.3 + - - -
235B LYS* 4.4 9.8 - - + +
236B GLY 3.7 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 4.0 20.1 - - - +
161B LYS 3.2 0.2 + - - -
162B PRO* 1.3 71.2 - - - +
164B GLY* 1.3 64.3 + - - +
165B VAL* 3.9 1.2 + - - +
234B THR* 3.7 14.3 - - - +
235B LYS 2.9 21.4 + - - -
236B GLY 4.0 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 5.0 0.7 - - - -
129B PHE 4.5 0.9 - - - -
130B ASP* 3.2 17.7 - - - -
160B LEU* 3.8 14.6 - - - +
161B LYS* 2.8 19.9 + - - +
162B PRO 3.2 1.8 + - - -
163B GLY* 1.3 79.5 - - - +
165B VAL* 1.3 60.2 + - - -
233B VAL 3.8 0.3 - - - +
234B THR* 3.3 2.8 - - - -
235B LYS 2.9 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.2 31.9 - - + +
57B ALA* 4.3 9.3 - - - +
59B SER* 3.5 13.2 - - - +
60B LYS* 3.8 17.5 - - + -
130B ASP 3.0 9.2 + - - +
131B GLY* 3.2 4.3 - - - -
132B ILE 2.9 25.8 + - - +
160B LEU* 3.8 4.0 - - - +
163B GLY 5.0 0.7 - - - +
164B GLY* 1.3 73.2 - - - +
166B LEU* 1.3 73.1 + - - +
232B LEU* 4.4 15.7 - - + -
233B VAL 3.6 12.6 - - - +
234B THR* 4.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.6 25.1 - - + +
134B TYR* 4.8 4.0 - - + -
151B PHE* 4.9 0.4 - - + -
152B ILE* 3.8 31.2 - - + -
156B ALA* 3.8 24.0 - - + -
160B LEU* 4.0 15.4 - - + +
165B VAL* 1.3 74.9 - - - +
167B THR* 1.4 82.3 + - - +
168B TYR* 4.6 11.7 - - + -
197B LEU* 4.9 0.9 - - + -
202B PHE* 4.2 10.1 - - + -
231B PRO 3.8 0.3 - - - +
232B LEU* 3.7 3.1 - - - -
233B VAL* 2.7 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.3 45.8 - - + +
56B ALA* 3.9 9.2 - - - -
57B ALA* 3.8 13.5 - - + +
132B ILE 2.9 19.1 + - - +
133B LEU* 3.9 11.0 - - + -
134B TYR 3.0 20.8 + - - -
165B VAL 4.2 0.2 + - - -
166B LEU* 1.4 76.7 - - - +
168B TYR* 1.3 66.4 + - - +
230B THR* 3.8 4.5 - - - +
231B PRO* 2.7 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.8 7.7 - - - +
133B LEU* 5.5 0.4 - - - -
134B TYR* 3.1 29.4 - - + +
148B GLN* 3.7 26.7 - - + -
149B PHE* 4.5 0.9 - - - -
152B ILE* 3.8 24.2 - - + -
166B LEU* 4.6 10.8 - - + -
167B THR* 1.3 81.3 + - - +
169B CYS* 1.3 71.2 + - - +
174B TRP* 3.6 13.4 - + - -
189B PHE* 3.6 10.9 - + - -
193B GLN* 2.9 44.3 + - - +
197B LEU* 4.0 18.7 - - + +
231B PRO* 3.2 45.4 - - + +
233B VAL* 4.8 2.7 - - + -
----------------------------------------------------------
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