Contacts of the strand formed by residues 15 - 22 (chain I) in PDB entry 1OZT
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 GLN 15 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LEU* 3.3 17.5 - - - +
9I LYS* 4.7 12.4 - - + -
12I GLY 5.8 0.4 + - - -
13I PRO* 3.5 18.2 + - - +
14I VAL* 1.3 76.6 - - - +
16I GLY* 1.3 58.8 + - - +
35I ILE* 4.2 5.6 - - - -
36I LYS* 2.8 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 3.6 4.0 - - - +
8I LEU* 2.8 36.9 + - - +
15I GLN* 1.3 78.2 - - - +
17I ILE* 1.3 69.3 + - - +
34I SER 3.3 14.1 - - - -
35I ILE* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I VAL* 4.0 18.2 - - + -
6I CYS 3.5 8.7 - - - +
7I VAL* 4.7 10.3 - - + -
8I LEU* 4.5 0.2 - - - +
16I GLY* 1.3 79.1 - - - +
18I ILE* 1.3 66.7 + - - +
19I ASN* 4.3 11.7 - - - +
33I GLY* 3.2 23.2 - - - -
34I SER 3.2 12.2 + - - -
54J THR* 4.2 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I VAL* 3.3 7.3 - - - +
6I CYS* 3.0 32.0 + - - +
8I LEU* 3.6 20.4 - - + -
17I ILE* 1.3 85.1 - - - +
19I ASN* 1.3 68.1 + - - +
20I PHE* 4.0 9.2 - - + -
31I VAL* 3.7 28.3 - - + -
32I TRP 3.6 3.1 - - - +
33I GLY* 4.2 5.4 - - - -
34I SER 4.2 8.1 - - - +
35I ILE* 4.2 19.3 - - + -
45I PHE* 4.1 14.6 - - + -
97I VAL* 4.2 9.9 - - + -
117I LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ALA 3.6 6.3 - - - +
5I VAL* 3.8 19.1 - - - +
17I ILE* 4.3 10.9 + - - +
18I ILE* 1.3 77.6 - - - +
20I PHE* 1.3 65.1 + - - +
31I VAL* 3.0 9.9 - - - +
32I TRP* 2.7 85.4 + - + +
33I GLY* 4.1 5.7 - - - -
54J THR* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LYS* 3.3 7.2 - - - +
4I ALA* 2.8 58.8 + - + +
5I VAL 4.2 0.2 - - - -
6I CYS* 4.2 15.0 - - + -
18I ILE* 4.0 16.2 - - + -
19I ASN* 1.3 75.3 - - - +
21I GLU* 1.3 61.8 + - - +
29I VAL* 4.1 10.8 - - + -
30I LYS 3.2 5.4 - - - -
31I VAL* 4.0 23.8 - - + -
32I TRP* 4.1 3.5 - - - -
47I VAL* 5.5 0.2 - - + -
84I LEU* 5.0 7.6 - - + -
104I ILE* 4.6 3.6 - - + -
106I LEU* 4.0 11.2 - - + -
112I ILE* 3.6 26.2 - - + -
117I LEU* 4.0 22.4 - - + -
149I ILE* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I ALA* 6.2 1.3 - - + -
2I THR 3.7 9.6 - - - +
3I LYS* 3.8 26.1 + - + +
20I PHE* 1.3 76.6 - - - +
22I GLN* 1.3 63.1 + - - +
23I LYS* 3.7 31.2 + - + +
28I PRO 3.9 0.9 - - - +
29I VAL* 3.3 2.3 - - - +
30I LYS* 2.7 53.5 + - + +
32I TRP* 3.6 24.8 - - + -
106I LEU* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I ALA* 3.5 0.7 + - - -
2I THR* 3.0 29.9 + - - +
21I GLU* 1.3 74.3 - - - +
23I LYS* 1.3 62.0 + - - +
24I GLU* 3.2 18.8 + - - +
25I SER* 3.4 14.6 + - - -
26I ASN 4.7 0.2 - - - -
27I GLY 3.0 19.8 + - - -
28I PRO 3.7 15.5 - - - +
29I VAL* 3.7 12.7 - - + +
104I ILE 4.7 0.6 + - - -
105I SER* 3.0 22.2 + - - -
106I LEU* 2.7 47.4 + - + +
107I SER* 3.9 3.5 + - - -
----------------------------------------------------------
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