Contacts of the strand formed by residues 33 - 40 (chain B) in PDB entry 2XN9
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 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 4.1 0.7 - - - +
32B ASP* 1.3 78.9 - - + +
34B MET* 1.3 64.3 + - - +
35B TYR* 3.4 26.9 - - + +
51B SER 3.2 9.2 - - - +
52B GLN* 4.1 16.4 - - - +
95B SER* 3.1 24.3 - - - -
96B SER* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 5.3 0.2 - - + -
25B CYS* 3.5 38.1 - - - +
27B GLN* 3.6 37.0 - - + +
33B ALA* 1.3 80.7 - - - +
35B TYR* 1.3 64.1 + - - +
50B TYR* 3.3 4.0 - - - +
51B SER 2.9 30.8 + - - -
70B ARG* 3.6 23.3 - - - +
73B LYS 3.6 15.7 - - - +
74B GLU 4.4 0.7 - - - +
75B SER 4.3 3.1 - - - -
76B PHE* 3.5 32.7 - - + +
93B CYS* 3.8 4.0 - - - -
94B ALA 3.1 8.5 - - - +
95B SER* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 3.3 30.4 + - - -
33B ALA* 3.4 17.8 - - + +
34B MET* 1.3 84.7 - - - +
36B TRP* 1.3 62.9 + - - +
37B TYR* 3.7 20.2 - - + -
47B LEU* 4.1 9.0 - - + -
49B TYR 3.5 6.1 - - - -
50B TYR* 3.5 22.2 - + + -
52B GLN* 5.0 2.9 + - - -
76B PHE* 3.7 2.9 - - - -
92B LEU 4.5 0.2 - - - -
93B CYS* 3.2 9.9 - - - -
94B ALA* 2.8 41.3 + - + +
96B SER* 2.8 30.9 + - - -
103B GLN* 3.5 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.5 29.8 - - - -
23B LEU* 3.6 33.7 - - + -
24B SER 4.2 3.4 - - - -
25B CYS* 3.5 24.4 - - + +
35B TYR* 1.3 74.8 - - - +
37B TYR* 1.3 62.0 + - - +
47B LEU* 3.4 8.0 - - - +
48B ILE* 2.9 39.0 + - + +
49B TYR* 2.9 12.1 + - + +
68B VAL* 4.1 9.2 - - + -
76B PHE* 2.6 50.0 + + - +
78B LEU* 3.4 35.4 - - + +
91B TYR* 3.9 18.4 - - + -
92B LEU 3.3 24.7 - - - -
93B CYS* 4.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.2 9.5 + - - +
100A PHE* 3.8 25.2 - + - -
35B TYR* 3.7 17.8 - - + -
36B TRP* 1.3 74.9 - - - +
38B ARG* 1.3 60.4 + - - +
45B LEU* 3.9 27.8 - - + -
46B ARG 3.3 9.2 - - - +
47B LEU* 3.6 41.1 - - + +
48B ILE* 3.8 5.3 - - - +
91B TYR* 3.5 7.8 - - - +
92B LEU* 2.6 42.7 + - + +
94B ALA* 4.2 2.2 - - + -
103B GLN* 2.7 43.8 + - - -
105B PHE* 3.6 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 1.3 76.3 - - - +
39B GLN* 1.3 60.4 + - - +
40B ASP* 2.9 37.9 + - - +
44B GLY 3.6 0.9 - - - +
45B LEU* 3.4 3.1 - - - -
46B ARG* 2.9 48.8 + - - +
48B ILE* 3.7 3.4 - - + +
62B ILE* 3.7 26.5 - - + -
66B TYR* 2.7 34.2 + - - -
84B GLN* 3.4 12.3 - - - +
86B ASN* 2.7 36.7 + - - +
88B THR 3.3 11.7 + - - -
89B ALA* 3.6 8.4 - - + +
90B PHE 3.6 4.5 - - - +
91B TYR* 3.8 19.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 2.7 44.5 + - - -
86A LEU* 3.7 17.0 - - - +
38B ARG* 1.3 74.6 - - - +
40B ASP* 1.3 75.7 + - - +
41B PRO* 4.7 0.3 - - - +
44B GLY* 3.3 15.5 + - - +
45B LEU* 3.7 20.8 - - + +
89B ALA* 3.8 1.0 - - - +
90B PHE* 2.9 54.1 + - + +
92B LEU* 3.9 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 2.9 35.6 + - - +
39B GLN* 1.3 82.3 + - - +
41B PRO* 1.3 77.2 - - + +
42B GLY 3.1 0.9 + - - -
43B GLN* 2.9 36.9 + - + +
44B GLY 3.7 7.7 + - - +
46B ARG* 2.6 30.8 + - - -
88B THR 3.8 4.0 - - - +
89B ALA* 3.7 9.2 - - - +
----------------------------------------------------------
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