Contacts of the strand formed by residues 164 - 170 (chain F) in PDB entry 1B06
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 PRO 164 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D GLU* 3.4 13.0 - - + +
139F TYR* 3.3 23.7 - - - -
140F TYR* 3.3 34.4 + - + +
142F ASN* 4.1 9.0 - - - +
162F GLU 3.6 6.0 - - - +
163F LEU* 1.3 84.6 - - - +
165F VAL* 1.3 63.6 + - - +
166F ILE* 4.2 3.7 - - + +
203F ARG* 6.3 0.2 - - + -
207F TYR* 3.5 56.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ALA* 4.9 2.9 - - + -
162D GLU* 2.6 30.8 + - + +
83F LEU* 4.8 11.4 - - + -
86F ILE* 4.1 25.8 - - + -
137F VAL* 3.5 30.7 - - + -
138F LEU 3.8 3.1 - - - -
139F TYR* 4.1 13.0 - - + -
159F HIS* 6.0 0.7 - - + +
164F PRO* 1.3 75.0 - - - +
166F ILE* 1.3 62.6 + - - +
167F LEU 3.8 9.9 - - - +
168F ILE* 3.9 16.4 - - + -
203F ARG* 3.4 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASN* 3.4 9.2 - - - +
105F LEU* 4.3 22.4 - - + -
138F LEU* 2.8 25.5 + - + +
139F TYR 4.2 1.8 - - - +
140F TYR* 3.8 31.4 - - + +
147F LEU* 4.6 4.5 - - + -
164F PRO* 4.2 7.6 - - + +
165F VAL* 1.3 80.4 - - - +
167F LEU* 1.3 60.3 + - + +
200F ALA* 3.4 40.0 - - + +
203F ARG* 3.9 11.8 - - + +
204F LEU* 3.6 35.2 - - + +
207F TYR* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASN* 3.4 20.0 - - - +
119F PHE* 4.0 24.7 - - + -
123F PHE* 4.2 11.9 - - + -
136F THR 4.8 0.2 - - - -
137F VAL* 3.4 5.4 - - - +
138F LEU* 2.9 39.9 + - + -
165F VAL* 4.2 0.9 - - - -
166F ILE* 1.3 80.5 - - + +
168F ILE* 1.3 66.8 + - - +
191F TRP* 4.0 22.7 - - + -
192F TRP* 4.5 2.2 - - + -
195F VAL* 3.6 28.3 - - + -
197F TRP* 3.9 29.2 - - + -
200F ALA* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 3.8 30.1 - - + +
86F ILE* 3.9 22.4 - - + -
87F TYR* 3.9 28.0 - - + -
90F ASN* 2.9 21.4 + - - +
91F MET* 5.8 0.2 - - - +
135F TRP* 3.5 31.0 - - + -
136F THR 3.5 11.2 - - - +
137F VAL* 3.9 17.0 - - + -
165F VAL* 3.9 10.3 - - + -
167F LEU* 1.3 78.7 - - - +
169F VAL* 1.3 67.5 + - - +
191F TRP* 3.5 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F TYR* 4.4 1.3 - - - -
123F PHE* 3.4 23.3 - - + -
127F ALA* 5.5 0.2 - - + -
135F TRP* 3.3 12.3 - - - +
136F THR* 3.1 30.6 + - - +
168F ILE* 1.3 73.5 - - - +
170F ASP* 1.3 65.3 + - - +
171F GLU* 3.6 3.2 + - + +
187F TYR* 4.0 10.8 - - + +
188F LEU* 3.9 25.4 - - + -
191F TRP* 3.3 58.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F HIS* 2.8 12.1 + - - -
84F HIS* 3.4 2.1 + - - -
87F TYR* 3.7 25.6 - - + +
134F GLY 3.9 0.3 - - - +
135F TRP* 3.3 28.8 - - + -
169F VAL* 1.3 72.9 - - - +
171F GLU* 1.3 63.9 + - - +
172F PHE* 3.1 22.2 + - - +
174F HIS* 3.6 0.2 + - - -
175F ALA* 3.7 11.6 - - + +
187F TYR* 2.9 29.3 + - - -
327F FE 2.0 33.7 - - - -
----------------------------------------------------------
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