Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 2OTD
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 MSE 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.7 33.9 - - + -
7B PRO* 3.5 30.1 - - + +
9B ILE 3.8 15.4 + - - +
10B VAL* 3.5 27.5 - - + -
11B ALA* 2.8 27.0 + - - +
35B HIS* 3.5 5.5 + - - +
36B LYS* 1.3 82.0 - - - +
38B ILE* 1.3 67.8 + - - +
109B MSE 4.2 0.8 - - - +
110B MSE 3.3 11.9 - - - +
111B ALA 4.0 4.3 - - - +
112B ASN* 3.7 34.8 - - + +
144B LEU* 4.4 10.5 - - + -
231B CYS* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.7 4.5 - - - -
11B ALA* 3.4 20.0 - - + +
14B GLY* 3.9 15.0 - - - +
27B ILE* 3.7 37.0 - - + -
37B MSE 1.3 78.4 - - - +
39B GLU* 1.3 57.6 + - - +
40B PHE* 3.9 19.0 - - + -
100B VAL* 4.6 0.2 - - + -
104B CYS* 3.6 25.4 - - - -
109B MSE 3.9 24.9 - - + -
110B MSE 3.0 14.2 + - - +
111B ALA* 3.3 1.4 - - - +
112B ASN* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.5 14.8 - - + +
11B ALA 2.7 8.4 + - - +
12B HIS* 3.1 29.4 - - + -
13B ARG* 2.7 40.7 + - - +
14B GLY 3.1 5.7 + - - -
38B ILE* 1.3 72.6 - - - +
40B PHE* 1.3 80.4 + - - +
41B ASP* 2.7 26.4 - - - +
112B ASN* 3.2 36.3 - - + +
114B GLU* 3.5 8.2 - - + +
233B CYS* 5.0 5.4 - - + -
301B PO4 3.4 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 4.6 0.9 - - - -
14B GLY* 4.8 3.1 - - - +
22B ASN* 3.1 21.1 - - - +
27B ILE* 5.5 1.6 - - + -
38B ILE* 3.9 22.0 - - + -
39B GLU* 1.3 92.6 - - - +
41B ASP* 1.3 57.5 + - - +
42B ALA 3.5 0.9 + - - -
52B LEU* 3.6 28.5 - - + -
97B LEU* 3.6 27.8 - - + -
100B VAL* 3.6 24.7 - - + -
111B ALA* 3.7 24.0 - - + -
112B ASN 3.2 3.2 + - - -
113B ILE* 3.8 27.0 - - + -
114B GLU 3.1 20.3 + - - -
137B TRP* 4.5 2.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.1 23.9 + - - +
22B ASN* 2.8 27.8 - - - +
39B GLU* 2.7 23.3 - - - +
40B PHE* 1.3 70.1 - - - +
42B ALA* 1.3 58.2 + - - +
52B LEU* 3.2 8.2 - - - +
53B LEU 3.0 26.2 + - - +
54B HIS* 3.2 33.0 - - - +
114B GLU* 3.4 23.2 - - - +
116B LYS* 4.3 8.5 - - + -
301B PO4 3.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE 3.5 1.0 + - - +
41B ASP* 1.3 71.2 - - - +
43B LYS* 1.3 64.3 + - - +
50B ILE* 4.4 12.6 - - + -
51B PHE 3.6 5.8 - - - +
52B LEU* 4.2 13.5 - - + -
97B LEU* 4.5 3.1 - - + -
113B ILE* 3.7 28.7 - - + -
114B GLU 3.0 9.5 + - - +
115B ILE* 4.0 4.0 - - - +
116B LYS 3.0 27.9 + - - +
117B PRO 4.4 0.2 - - - -
129B VAL* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 1.3 75.1 - - - +
44B LEU* 1.3 67.9 + - - +
50B ILE* 3.2 11.8 - - - +
51B PHE* 2.9 57.1 + - + +
53B LEU* 2.6 21.3 + - + +
54B HIS 2.3 32.5 + - - -
55B ASP 2.5 17.2 + - - -
56B ASP* 4.1 20.4 + - - +
68B ALA* 5.3 1.6 - - + -
69B GLY 5.6 1.3 - - - +
116B LYS* 3.1 26.5 + - - +
117B PRO* 4.1 1.1 + - + -
118B THR* 4.1 20.9 - - - +
125B THR* 4.4 9.9 - - - -
129B VAL* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 5.2 0.2 - - + -
43B LYS* 1.3 80.3 - - - +
45B SER* 1.3 64.0 + - - +
48B GLY* 3.6 23.8 - - - +
49B GLU 3.3 14.6 - - - +
50B ILE* 3.7 19.1 - - + -
51B PHE* 3.8 6.5 - - - -
69B GLY* 3.4 19.1 - - - -
118B THR* 3.9 9.5 + - - +
121B THR* 5.6 6.3 - - + +
124B LEU* 3.7 44.9 - - + +
125B THR* 4.3 15.8 - - + +
128B MSE 3.9 23.1 - - + -
129B VAL* 5.8 0.9 - - + -
----------------------------------------------------------
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