Contacts of the strand formed by residues 5 - 15 (chain A) in PDB entry 1DKT
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 1.3 68.4 + - + +
7A TYR* 3.3 34.0 + - - -
23A MET* 4.0 3.5 - - - +
24A LEU 5.0 0.2 - - - -
25A PRO* 3.8 41.2 - - + +
27A ASP* 4.2 9.5 + - - -
9B SER* 6.0 2.0 - - - -
10B ASP* 6.0 2.2 - - - +
21B HIS* 6.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 1.3 80.1 + - + +
7A TYR* 1.3 66.2 + - - +
8A TYR* 3.9 16.7 - - + +
22A VAL* 3.5 27.8 - - + -
23A MET 3.6 6.5 - - - +
24A LEU* 4.3 11.0 - - + -
25A PRO* 4.0 19.3 - - + -
28A ILE* 6.5 0.2 - - + -
46A LEU 4.1 11.7 - - - +
47A GLY* 3.5 33.2 - - - +
48A VAL* 4.2 2.5 - - + +
9B SER* 3.8 1.2 - - - -
10B ASP* 3.6 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.3 44.9 + - - -
6A ILE* 1.3 73.2 - - - +
8A TYR* 1.3 63.0 + - - +
22A VAL* 3.5 3.0 - - - +
23A MET* 2.7 52.9 + - + +
7B TYR* 3.8 31.7 - + + -
8B TYR 3.5 4.0 - - - -
9B SER* 3.7 24.0 - - - -
21B HIS* 2.7 40.9 + + - -
23B MET* 3.9 34.0 - - + +
66B ILE* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 19.5 - - + +
7A TYR* 1.3 74.3 - - - +
9A SER* 1.3 63.9 + - - +
20A ARG* 3.3 35.0 - - - +
21A HIS 3.9 4.5 - - - +
22A VAL* 3.7 26.0 - - + -
48A VAL* 3.8 14.3 - - + -
49A GLN 3.1 37.7 + - - -
50A GLN* 4.4 1.8 - - - -
7B TYR* 3.3 3.8 - - - -
8B TYR* 2.7 54.9 + - + +
9B SER 4.0 4.3 - - - -
10B ASP* 3.1 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 1.3 77.2 - - - +
10A ASP* 1.3 75.3 + - - +
11A LYS* 4.9 1.7 + - - +
12A TYR* 3.9 0.9 - - - -
20A ARG* 3.6 15.8 + - - +
21A HIS* 3.1 62.6 + - - -
5B GLN* 4.4 5.4 - - - -
6B ILE 3.9 10.3 - - - -
7B TYR* 3.8 8.4 - - - -
8B TYR* 4.0 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 1.3 90.8 + - - +
11A LYS* 1.3 67.2 + - - +
12A TYR* 3.2 15.7 - - + -
20A ARG* 4.2 1.8 - - - -
5B GLN* 5.2 6.2 + - + +
6B ILE* 3.6 25.4 + - - +
8B TYR* 2.7 36.2 + - - -
47B GLY 4.2 5.2 - - - +
49B GLN* 2.9 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER 5.2 1.4 + - - -
10A ASP* 1.3 82.1 + - - +
12A TYR* 1.3 65.2 + - - +
13A ASP* 5.8 0.9 - - - +
18A GLU* 3.8 22.9 - - + +
19A TYR 3.2 11.9 - - - +
20A ARG* 3.5 34.0 - - + +
54A TRP* 4.3 0.9 - - + -
71A ARG* 3.9 10.3 - - - +
100A V7O 2.9 50.7 + - - -
49B GLN* 4.6 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.9 9.2 - - - -
10A ASP* 3.2 23.8 - - + -
11A LYS* 1.3 75.0 - - - +
13A ASP* 1.3 61.5 + - - +
19A TYR* 2.9 59.3 + + + +
20A ARG* 4.0 3.1 + - - -
21A HIS* 2.9 36.7 + + - +
68A LEU* 5.7 1.9 - - - +
5B GLN* 5.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.8 1.0 - - - +
12A TYR* 1.3 75.6 + - - +
14A ASP* 1.3 61.0 + - - +
17A PHE 2.8 21.3 - - - +
18A GLU* 3.4 26.3 - - + +
19A TYR* 4.3 1.1 - - - -
73A LEU* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 1.3 75.7 - - - +
15A GLU* 1.3 74.9 + - - +
16A GLU* 2.7 12.8 + - - +
17A PHE* 2.8 30.1 + - - +
19A TYR* 2.9 29.7 + - + -
73A LEU* 3.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 1.3 87.4 - - - +
16A GLU* 1.3 72.3 + - - +
73A LEU* 5.3 0.4 - - - -
----------------------------------------------------------
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