Contacts of the strand formed by residues 164 - 170 (chain B) in PDB entry 3Q72
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 ALA 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS 3.2 4.8 + - - +
94B VAL* 3.6 4.0 - - + -
95B LEU* 3.0 26.9 + - - +
162B GLY 3.2 2.5 + - - -
163B ASP* 1.3 84.2 + - - +
165B TYR* 1.3 69.5 + - - +
166B VAL 4.1 0.4 + - - -
196B VAL* 5.0 0.4 - - - -
197B PRO* 3.6 17.9 - - + +
199B ILE* 5.0 2.0 - - + -
247B VAL* 3.6 31.2 - - + -
251B ILE* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 4.5 15.5 - - + +
95B LEU* 3.4 38.0 - - + +
97B LEU* 3.4 29.6 - - + -
160B ALA* 3.8 16.1 + - - +
162B GLY* 4.5 11.4 + - - -
164B ALA* 1.3 75.2 - - - +
166B VAL* 1.3 63.4 + - - +
167B ILE* 4.0 1.3 - - + -
187B LEU* 4.0 25.8 - - + -
191B ARG* 3.2 32.6 + - - -
196B VAL* 3.8 24.2 - - + -
197B PRO 3.1 6.6 + - - +
198B ILE* 3.4 14.3 - - + +
199B ILE* 3.0 26.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
94B VAL* 3.6 25.8 - - + -
95B LEU 2.8 13.8 + - - +
96B LEU* 3.7 18.1 - - + -
97B LEU* 2.8 29.5 + - - +
107B LEU* 6.0 0.2 - - + -
165B TYR* 1.3 76.5 - - - +
167B ILE* 1.3 59.7 + - - +
168B VAL* 4.1 11.4 - - + +
199B ILE* 3.7 7.0 - - + +
201B VAL* 3.9 25.4 - - + -
243B LEU* 4.3 11.0 - - + -
244B PHE* 4.9 2.0 - - + -
247B VAL* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.5 19.7 - - + +
165B TYR* 4.9 0.9 - - + -
166B VAL* 1.3 74.5 - - - +
168B VAL* 1.3 62.3 + - - +
180B ALA* 3.7 34.3 - - + +
183B LEU* 4.3 14.8 - - + -
184B ARG* 4.0 32.5 - - + +
187B LEU* 4.1 12.8 - - + -
198B ILE* 3.6 27.4 - - + -
199B ILE 2.9 12.6 + - - +
200B LEU* 3.6 12.1 - - + +
201B VAL 3.1 22.2 + - - -
227B CYS* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.8 5.6 - - + -
97B LEU 2.8 18.4 + - - +
98B GLY* 3.5 18.0 - - - -
99B ALA 4.0 1.7 + - - -
102B VAL* 3.5 32.1 - - + +
104B LYS* 3.9 14.8 - - + +
107B LEU* 4.0 22.0 - - + -
166B VAL* 4.1 20.4 - - + +
167B ILE* 1.3 78.7 - - - +
169B TYR* 1.3 73.4 + - - +
176B SER 4.7 1.9 - - - +
180B ALA* 4.9 0.5 - - - +
201B VAL* 3.6 9.6 - - + +
203B ASN* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.6 11.9 - - - -
168B VAL* 1.3 73.7 - - - +
170B SER* 1.3 70.4 + - - +
171B VAL* 4.0 14.6 - - + +
176B SER* 3.5 27.1 - - - +
177B PHE* 3.7 32.3 - + + -
180B ALA* 4.3 2.9 - - + -
200B LEU* 3.5 37.2 - - + -
201B VAL 2.9 18.3 + - - +
202B GLY* 3.3 24.9 - - - -
203B ASN* 2.8 29.8 + - - +
213B VAL* 4.1 12.8 - - + +
214B SER 4.7 0.2 + - - -
218B GLY* 3.7 10.2 - - - -
229B PHE* 3.1 25.9 - + - -
231B GLU* 4.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 4.9 0.7 - - - -
102B VAL* 3.5 21.6 - - - +
169B TYR* 1.3 80.8 - - - +
171B VAL* 1.3 56.8 + - - +
172B THR* 2.6 35.7 + - - -
173B ASP* 2.9 35.5 + - - +
176B SER* 3.1 6.4 + - - -
203B ASN 3.6 4.5 - - - -
204B LYS* 3.4 21.8 + - - +
213B VAL* 4.9 0.3 - - - +
----------------------------------------------------------
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