Contacts of the helix formed by residues 5 - 13 (chain J) in PDB entry 3AOI
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 5 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925I GLU* 2.8 13.9 + - - -
929I ARG* 5.4 3.4 - - - +
3J GLU 3.3 0.2 + - - -
4J PRO* 1.3 70.0 - - - +
6J ILE* 1.3 64.2 + - - -
7J ASP 3.0 2.7 - - - -
8J LYS* 3.0 29.4 + - - +
9J LEU* 2.9 23.1 + - - +
69J LEU* 5.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I ILE* 4.4 17.7 - - + -
767I HIS* 3.7 39.5 - - + +
924I MET* 4.8 5.8 - - + -
925I GLU* 2.5 34.5 + - + +
3J GLU* 4.3 6.3 - - + -
4J PRO 2.8 5.3 + - - -
5J GLY* 1.3 72.8 - - - -
7J ASP* 1.3 54.9 + - - +
9J LEU* 2.9 29.1 - - + +
10J PHE* 2.7 57.3 + - + +
19J LEU* 3.8 14.8 - - + -
65J MET* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 7 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922I LEU 4.4 2.1 - - - +
923I GLY* 3.2 15.3 - - - -
924I MET* 2.7 35.8 + - - +
925I GLU* 2.5 27.3 + - - +
926I LYS* 4.7 1.4 + - - +
1211I MET* 4.2 18.4 - - - +
5J GLY 4.8 0.4 - - - -
6J ILE* 1.3 75.0 - - - +
8J LYS* 1.3 71.8 + - + +
10J PHE* 3.3 8.8 + - - +
11J GLY* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926I LYS* 5.8 4.0 - - - +
5J GLY* 3.0 24.5 + - - +
7J ASP* 1.3 82.0 - - + +
9J LEU* 1.3 67.6 + - + +
11J GLY* 3.0 11.3 + - - +
12J MET* 3.2 21.6 + - + +
69J LEU* 5.7 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I ILE* 5.5 0.2 - - + -
4J PRO 3.8 10.8 - - - +
5J GLY 2.9 11.0 + - - +
6J ILE* 2.9 40.8 - - + +
8J LYS* 1.3 75.1 - - + +
10J PHE* 1.3 53.0 + - - +
12J MET* 2.7 39.7 + - - +
13J VAL* 3.6 6.4 + - - +
19J LEU* 3.3 32.2 - - + +
65J MET* 4.2 44.6 - - + +
68J LEU* 4.3 14.4 - - + -
69J LEU* 4.7 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 10 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I ILE* 4.6 15.9 - - + -
767I HIS* 6.2 0.9 - + + -
924I MET* 4.0 26.2 - - + -
1209I LEU* 5.5 0.2 - - + -
1211I MET* 4.2 26.7 - - + -
1213I ARG* 2.5 33.7 + - - +
6J ILE* 2.7 35.1 + - + +
7J ASP* 3.6 12.1 - - - +
9J LEU* 1.3 72.3 - - - +
11J GLY* 1.3 54.7 + - - +
12J MET 3.1 0.6 + - - -
13J VAL* 3.1 21.9 + - + +
16J LYS* 3.7 53.4 - - + -
19J LEU* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 11 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213I ARG* 3.7 6.2 - - - +
7J ASP 3.0 13.8 + - - -
8J LYS* 3.0 6.7 + - - -
9J LEU 3.0 0.2 + - - -
10J PHE* 1.3 77.3 - - - +
12J MET* 1.3 60.3 + - - +
13J VAL 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 12 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LYS* 3.2 18.6 - - + +
9J LEU* 2.7 25.3 + - - +
11J GLY* 1.3 73.3 - - - -
13J VAL* 1.3 61.9 + - + +
19J LEU* 6.5 0.4 - - + -
68J LEU* 3.3 30.7 - - - +
69J LEU* 4.1 16.4 - - - +
70J THR 4.7 7.2 - - - +
71J GLY* 5.1 4.0 - - - +
75J PHE* 3.8 33.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213I ARG* 3.6 7.6 + - - +
9J LEU 4.2 4.5 - - - +
10J PHE* 3.1 29.5 - - + +
11J GLY 4.4 2.8 - - - +
12J MET* 1.3 87.4 - - + +
14J ASP* 1.3 62.5 + - - +
15J SER 3.0 25.8 - - - +
16J LYS* 4.6 1.1 - - - +
18J ARG* 3.8 21.5 - - + -
19J LEU* 3.9 30.7 - - + -
22J VAL* 5.5 2.9 - - + -
75J PHE* 4.7 14.4 - - + -
----------------------------------------------------------
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