Contacts of the strand formed by residues 2 - 8 (chain G) 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 THR 2 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA* 1.3 77.1 + - - +
3G LYS* 1.3 80.0 + - - +
21G GLU* 3.8 1.0 - - - +
22G GLN* 3.1 33.3 + - - -
106G LEU* 3.6 31.9 + - + +
107G SER* 5.5 4.2 - - - -
113G ILE* 4.4 10.8 - - + -
151G ILE* 5.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 3 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA* 4.1 9.0 - - + +
2G THR* 1.3 90.8 - - - +
4G ALA* 1.3 63.9 + - - +
20G PHE 3.3 13.2 - - - +
21G GLU* 4.0 27.4 + - + +
32G TRP* 4.9 10.0 - - - -
106G LEU* 4.1 2.9 - - - -
151G ILE* 4.0 3.3 - - - +
152G ALA* 3.2 33.5 + - + +
153G GLN* 3.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 4 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LYS* 1.3 77.5 - - - +
5G VAL* 1.3 63.8 + - - +
19G ASN* 3.6 3.1 - - - +
20G PHE* 2.8 42.7 + - + +
106G LEU* 4.1 11.9 - - + -
113G ILE* 4.2 7.9 - - + -
149G ILE* 3.9 18.6 - - + -
150G GLY 3.1 15.9 - - - +
152G ALA* 3.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ALA* 1.3 77.3 - - - +
6G CYS* 1.3 72.8 + - - +
7G VAL* 5.2 0.9 - - + -
17G ILE* 4.0 5.4 - - + -
18G ILE 3.4 15.3 - - - +
19G ASN* 3.8 14.1 - - - +
20G PHE* 4.4 3.1 - - - -
148G VAL 3.9 0.5 - - - +
149G ILE* 3.6 1.5 - - - -
150G GLY 2.9 32.2 + - - +
152G ALA* 3.7 20.2 - - + -
51H GLY 3.8 6.4 - - - +
52H ASP* 3.8 33.2 - - - +
53H ASN 5.0 0.7 - - - +
54H THR* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 6 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G VAL* 1.3 82.7 - - - +
7G VAL* 1.3 65.3 + - - +
8G LEU* 3.8 8.6 + - - +
17G ILE* 3.5 4.5 - - - +
18G ILE 3.0 30.0 + - - +
20G PHE* 4.3 7.9 - - + -
117G LEU* 3.8 23.6 - - + -
147G GLY* 3.3 42.0 - - - -
148G VAL 3.7 8.7 - - - +
149G ILE* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G VAL* 5.2 0.7 - - + -
6G CYS* 1.3 77.5 - - - +
8G LEU* 1.3 61.0 + - - +
9G LYS* 3.9 31.1 + - + +
16G GLY 3.7 9.0 - - - +
17G ILE* 4.6 8.7 - - + +
146G CYS 3.5 1.7 - - - +
147G GLY* 3.3 20.4 - - - -
148G VAL 4.7 2.0 + - - -
53H ASN* 3.7 47.8 - - + +
54H THR* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G CYS* 4.0 13.9 - - - +
7G VAL* 1.3 72.3 - - - +
9G LYS* 1.3 69.3 + - - +
15G GLN* 3.2 20.1 - - - +
16G GLY* 2.9 32.4 + - - +
18G ILE* 3.6 31.9 - - + -
35G ILE* 4.9 9.4 - - + -
45G PHE* 5.8 0.7 - - + -
117G LEU* 3.4 24.7 - - + +
118G VAL* 4.8 1.1 - - - +
119G VAL* 5.0 9.9 - - + +
145G ALA* 4.1 15.0 - - + +
146G CYS* 3.4 29.2 - - - +
147G GLY 3.7 2.0 - - - +
----------------------------------------------------------
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