Contacts of the strand formed by residues 13 - 20 (chain B) in PDB entry 1OXC
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 ARG 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR 5.3 2.8 + - - -
46A ASN* 2.5 32.7 + - - +
11B ASN 5.7 0.4 - - - +
12B THR* 1.3 85.4 - - - +
14B PHE* 1.3 60.8 + - - +
54B VAL* 3.4 20.2 - - + +
55B LEU 3.1 10.8 - - - +
56B ASN* 4.0 19.7 - - + +
111B TRP* 3.8 5.7 - - - +
112B PRO* 4.6 0.2 - - - +
113B LEU* 3.8 33.0 + - + +
114B GLY* 5.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.4 27.6 - - + -
12B THR 3.7 8.5 - - - -
13B ARG* 1.3 75.7 - - - +
15B GLY* 1.3 64.9 + - - +
16B VAL* 4.3 10.3 - - + -
30B VAL* 4.7 0.4 - - + -
32B VAL* 4.2 3.8 - - + -
54B VAL* 3.4 3.5 - - - +
55B LEU* 2.8 74.9 + - + -
56B ASN 3.8 1.8 - - - -
57B SER* 3.6 23.3 - - - -
63B VAL* 3.8 31.6 - - + -
109B ILE* 3.6 21.5 - - + -
110B ASN 3.5 14.1 - - - +
111B TRP* 3.9 5.6 - - + -
113B LEU* 3.6 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.8 22.9 - - - -
14B PHE* 1.3 78.7 - - - +
16B VAL* 1.3 60.9 + - - +
17B THR 4.3 0.2 - - - -
53B GLN 3.5 7.2 - - - -
54B VAL* 4.5 1.8 - - - -
109B ILE* 3.1 5.0 - - - -
110B ASN* 2.9 39.7 + - - -
113B LEU* 3.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.3 5.8 - - + -
15B GLY* 1.3 74.8 - - - +
17B THR* 1.3 64.7 + - - +
30B VAL* 3.7 26.9 - - + -
38B ALA* 4.8 0.4 - - + -
40B PHE* 3.7 20.5 - - + -
52B THR* 3.2 3.7 + - - -
53B GLN* 3.0 34.0 + - + +
55B LEU* 4.1 24.2 - - + -
107B VAL* 3.7 21.5 - - + -
108B VAL 3.4 2.9 - - - -
109B ILE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.4 27.9 - - + -
47A ASN* 4.8 2.6 + - - -
15B GLY 5.0 0.3 - - - -
16B VAL* 1.3 74.7 + - - +
18B ALA* 1.3 60.4 + - - +
19B PHE* 4.0 18.4 - - + -
40B PHE* 4.6 1.3 - - - -
49B VAL* 3.2 35.2 - - + -
51B GLY 3.4 6.7 - - - +
52B THR* 2.8 20.3 + - - +
106B VAL 3.8 0.3 - - - +
107B VAL* 3.3 7.0 - - - +
108B VAL* 2.9 37.1 + - - -
110B ASN* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 1.3 75.0 - - - +
19B PHE* 1.3 64.0 + - - +
28B VAL* 4.0 16.2 - - + -
40B PHE* 3.8 20.4 - - + -
49B VAL* 3.2 10.0 - - - +
50B ILE* 3.0 45.1 + - + -
51B GLY 3.0 7.9 + - - +
106B VAL 3.3 7.0 - - - +
107B VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.4 35.7 - - + -
19A PHE* 4.5 5.4 - + - -
108A VAL* 5.1 8.3 - - + -
110A ASN* 4.8 7.4 - - - -
17B THR* 4.0 25.6 - - + -
18B ALA* 1.3 74.4 - - - +
20B ALA* 1.3 60.7 + - - +
21B ASN* 4.6 0.9 - - - +
47B ASN* 3.5 42.8 - - - +
48B ALA 3.2 6.3 - - - +
49B VAL* 3.7 18.4 - - + -
50B ILE* 4.7 3.6 - - - +
103B ASN 4.6 0.3 - - - +
104B ASP 4.4 0.2 - - - -
105B ALA* 3.2 6.8 - - - +
106B VAL* 2.8 57.7 + - + +
108B VAL* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 1.3 74.7 - - - +
21B ASN* 1.3 63.5 + - - +
22B SER 5.1 0.2 - - - +
26B GLN* 4.1 15.5 - - + -
42B GLY 4.6 2.5 - - - +
44B SER* 3.2 26.0 - - - +
47B ASN* 3.0 24.9 + - - -
48B ALA 3.0 9.8 + - - -
50B ILE* 3.8 24.2 - - + -
104B ASP 3.4 7.9 - - - +
----------------------------------------------------------
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