Contacts of the strand formed by residues 32 - 40 (chain R) in PDB entry 2A3W
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 ASN 32 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R LEU* 3.7 10.0 - - - +
31R GLN* 1.3 102.9 - - - +
33R PHE* 1.3 66.4 + - - +
98R TRP 3.4 7.9 - - - +
99R GLU* 3.6 22.6 - - - +
100R SER* 3.8 2.6 + - - -
101R SER* 5.0 1.9 + - - -
161R ASP* 3.1 33.4 + - - +
162R SER* 3.8 12.0 - - - +
163R VAL* 4.1 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R LEU* 4.1 18.4 - - + -
32R ASN* 1.3 77.1 - - - +
34R THR* 1.3 73.2 + - - +
35R LEU* 4.0 9.9 - - + -
61R LEU* 3.5 38.1 - - + -
73R LEU* 4.2 8.1 - - + -
75R ILE* 3.6 19.3 - - + -
96R VAL* 3.8 20.9 - - + -
97R SER* 3.1 4.2 - - - -
98R TRP* 3.0 70.2 + + + +
125R VAL* 4.7 4.0 - - + -
159R MET* 4.1 14.4 - - + -
160R TRP 3.2 13.5 - - - +
162R SER 3.5 6.1 - - - +
163R VAL* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R PHE* 1.3 77.5 + - - +
35R LEU* 1.3 63.0 + - - +
36R CYS* 4.2 7.0 - - - -
95R CYS* 4.9 0.2 - - + -
96R VAL 3.3 10.3 - - - +
97R SER* 3.4 7.8 - - - -
159R MET* 3.2 4.0 - - - +
160R TRP* 2.8 45.9 + - + -
162R SER 2.7 22.3 + - - -
163R VAL* 3.4 1.9 - - - -
164R LEU* 2.9 26.6 + - + -
169R ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R PHE* 4.3 8.5 - - + -
34R THR* 1.3 74.3 - - - +
36R CYS* 1.3 62.1 + - - +
37R PHE* 3.7 20.8 - - + -
50R PHE* 3.5 46.2 - - + -
61R LEU* 5.4 0.4 - - + -
63R VAL* 3.8 14.8 - - + -
94R ILE 3.7 0.9 - - - +
95R CYS* 3.1 2.8 - - - -
96R VAL* 2.7 49.1 + - + +
157R LEU* 3.7 26.2 - - + -
158R TYR 3.4 15.0 - - - +
159R MET* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R THR* 4.2 8.1 - - - -
35R LEU* 1.3 75.5 - - - +
37R PHE* 1.3 66.0 + - - +
93R HIS* 4.1 8.5 - - - +
94R ILE 3.1 3.4 - - - -
95R CYS* 2.0 46.2 - - - -
156R ASP 3.9 3.4 - - - +
157R LEU* 3.3 1.4 - - - +
158R TYR* 2.7 39.2 + - + +
160R TRP* 3.7 29.1 - - + -
164R LEU* 4.7 0.2 - - - -
169R ILE* 4.3 3.4 - - - -
172R ALA* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R LEU* 3.7 28.0 - - + -
36R CYS* 1.3 80.0 - - - +
38R ARG* 1.3 69.6 + - - +
39R ALA* 4.4 2.2 - - + -
49R LEU* 3.6 44.9 - - + -
50R PHE* 4.6 5.6 - - + -
63R VAL* 4.2 7.9 - - + -
93R HIS* 3.7 8.7 + - - -
94R ILE* 2.8 69.8 + - + +
96R VAL* 5.5 0.2 - - + -
154R ILE* 4.5 8.3 - - + -
155R GLY 3.8 3.1 - - - +
156R ASP 3.3 11.0 - - - -
157R LEU* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 1.3 73.0 - - - +
39R ALA* 1.3 60.7 + - - +
92R VAL 3.4 12.3 - - - +
93R HIS* 3.8 24.2 - - + +
154R ILE* 3.3 9.5 - - - +
155R GLY* 2.8 39.6 + - - +
156R ASP* 2.8 32.4 + - + +
172R ALA 3.4 23.4 + - - -
173R TYR* 3.4 23.0 + - - -
174R GLN 4.8 0.2 - - - -
175R GLY* 4.0 13.1 - - - -
201R LEU* 4.8 10.6 - - + +
203R TRP* 3.7 28.5 - - + -
204R VAL* 5.4 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 4.3 8.0 - - + -
38R ARG* 1.3 75.6 - - - +
40R TYR* 1.3 60.1 + - - +
41R SER* 4.2 0.9 - - - -
47R TYR* 6.1 0.7 - - - +
49R LEU* 4.1 25.6 - - + -
90R ALA 4.2 0.9 - - - +
91R PRO* 3.5 2.1 - - - +
92R VAL* 2.9 48.4 + - + +
94R ILE* 4.6 1.1 - - + -
150R PHE* 4.5 4.5 - - + -
153R GLU 3.3 7.2 - - - +
154R ILE* 4.3 6.7 - - + -
203R TRP* 3.8 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R ALA* 1.3 74.7 - - - +
41R SER* 1.3 63.5 + - - +
89R PRO* 4.7 7.7 + - + +
90R ALA* 3.7 13.2 - - - -
91R PRO* 3.5 34.5 - - + +
150R PHE* 4.6 0.2 - - - -
152R GLY* 3.2 4.0 - - - -
153R GLU* 2.8 39.7 + - + +
203R TRP* 3.6 53.4 - + + +
83S LYS 5.0 4.2 + - - -
112S THR* 5.2 3.1 - - - +
113S PRO 3.0 27.9 + - - -
114S LEU* 3.6 13.8 - - - +
115S VAL* 3.5 37.4 + - + +
----------------------------------------------------------
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