Contacts of the strand formed by residues 44 - 53 (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 GLY 44 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 5.5 0.9 - - - -
88A LEU* 4.1 8.7 - - - -
101A GLY 3.6 14.8 - - - -
102A LYS 3.6 14.8 + - - -
38B ARG 3.6 1.0 - - - +
39B GLN* 3.3 31.9 - - - +
40B ASP 3.7 4.8 + - - -
42B GLY* 4.6 0.4 - - - -
43B GLN* 1.3 80.6 - - - +
45B LEU* 1.3 64.8 + - - -
46B ARG* 5.4 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 4.3 5.4 - - + -
88A LEU* 4.4 12.1 - - + +
100A PHE* 3.5 47.7 + - + +
101A GLY 4.1 4.9 + - - -
37B TYR* 3.9 22.6 - - + -
38B ARG 3.4 2.5 - - - -
39B GLN* 3.7 37.9 - - + +
43B GLN 4.6 1.2 - - - +
44B GLY* 1.3 74.2 - - - +
46B ARG* 1.3 65.8 + - - +
47B LEU 4.3 0.2 + - - -
92B LEU* 3.8 16.2 - - + -
105B PHE* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.3 3.6 - - - -
38B ARG* 2.9 52.4 + - - +
40B ASP* 2.6 31.3 + - - -
43B GLN* 3.3 47.4 + - - +
44B GLY 5.4 0.4 + - - +
45B LEU* 1.3 77.6 - - - +
47B LEU* 1.3 64.9 + - - +
48B ILE* 3.5 3.5 + - - +
61B ASP* 5.7 3.4 - - + +
62B ILE* 3.7 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 3.9 29.6 - - + +
98A LEU 4.6 11.4 - - - +
35B TYR* 4.1 13.2 - - + -
36B TRP 3.4 16.2 - - - +
37B TYR* 3.6 32.9 - - + +
45B LEU 4.3 0.2 + - - -
46B ARG* 1.3 71.0 - - - +
48B ILE* 1.3 58.5 + - - +
49B TYR 3.6 19.5 - - - +
50B TYR* 3.9 14.6 - - + -
60B GLY* 4.4 8.5 - - - -
61B ASP* 3.3 25.5 + - - +
62B ILE* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 2.9 12.0 + - + +
37B TYR* 3.8 8.3 - - - +
38B ARG* 3.7 21.3 - - + +
46B ARG 3.9 11.0 - - - +
47B LEU* 1.3 73.4 - - - +
49B TYR* 1.3 74.9 + - + +
60B GLY* 2.9 22.0 + - - -
62B ILE* 4.2 18.6 - - + +
63B ALA* 3.6 7.8 - - - +
66B TYR* 3.6 41.7 - - + -
78B LEU* 4.1 16.8 - - + -
91B TYR* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 3.5 0.7 - - - -
36B TRP* 2.9 29.3 + - + +
47B LEU* 3.6 3.8 - - - +
48B ILE* 1.3 98.7 - - + +
50B TYR* 1.3 64.9 + - - +
57B PHE* 4.3 5.6 - + - -
58B GLN 3.4 20.4 - - - -
59B LYS* 3.3 49.6 + - - +
60B GLY 4.1 1.6 - - - +
63B ALA* 3.6 19.2 + - + +
66B TYR* 3.2 33.7 + - + -
67B SER* 4.0 6.8 - - - -
68B VAL* 3.6 44.6 - - + -
76B PHE* 4.1 2.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY* 5.6 3.8 + - - -
97A ASN* 3.4 33.8 - - + +
34B MET 3.3 13.7 - - - +
35B TYR* 3.5 17.9 - + + -
47B LEU* 3.9 16.2 - - + -
49B TYR* 1.3 76.5 - - - +
51B SER* 1.3 65.8 + - - +
52B GLN* 3.8 22.1 + - - -
57B PHE* 3.3 4.9 - - - +
58B GLN* 2.9 72.4 + - + +
59B LYS 3.6 16.8 - - - -
60B GLY* 4.8 0.7 - - - -
76B PHE* 3.8 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.2 4.3 - - - +
34B MET 2.9 30.0 + - - -
35B TYR* 6.4 0.2 - - - -
50B TYR* 1.3 82.1 - - - +
52B GLN* 1.3 59.5 + - - +
53B ILE 3.4 2.6 + - - -
56B ASP 2.7 26.3 + - - -
57B PHE* 3.9 1.6 - - - -
58B GLN* 3.8 3.6 - - - -
70B ARG* 2.7 33.7 + - - +
76B PHE* 3.7 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 4.3 8.0 + - - +
32B ASP* 3.4 20.5 - - - +
33B ALA* 3.9 15.2 + - - +
35B TYR* 5.0 2.6 + - - -
50B TYR* 3.8 21.5 + - + -
51B SER* 1.3 72.5 - - - +
53B ILE* 1.3 64.7 + - + +
56B ASP* 3.9 9.6 + - - +
58B GLN* 3.4 32.7 + - - +
98B ARG* 4.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.7 32.1 + - - +
51B SER* 3.3 4.1 + - - -
52B GLN* 1.3 82.1 - - + +
54B VAL* 1.3 86.2 + - + +
56B ASP* 3.1 37.9 + - + +
70B ARG* 3.7 4.9 - - - -
98B ARG* 4.4 9.6 - - - +
----------------------------------------------------------
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