Contacts of the helix formed by residues 4 - 18 (chain R) in PDB entry 1KYO
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 SER 4 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R GLN* 1.3 83.8 - - - +
5R PHE* 1.3 59.4 + - - +
6R THR* 3.9 8.2 - - - +
7R SER* 3.1 24.0 + - - -
8R ILE* 3.0 21.8 + - - +
111R GLU* 3.7 21.3 - - - -
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Residues in contact with PHE 5 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312N VAL* 3.2 42.0 - - + -
379N TYR* 6.1 1.3 - + - -
3R GLN 5.0 0.2 - - - -
4R SER* 1.3 71.0 - - - +
6R THR* 1.3 61.2 + - - +
7R SER 3.1 0.7 - - - -
8R ILE* 3.7 18.3 - - + +
9R ALA* 2.8 34.3 + - - +
45R PHE* 5.0 6.3 - + - -
46R ASP* 5.4 1.1 - - - -
49R ILE* 3.4 43.7 - - + -
56R MET* 5.6 2.5 - - + -
104R LEU* 3.5 29.3 - - + +
107R ILE* 3.7 29.8 - - + -
108R LEU* 3.9 5.1 - - + +
111R GLU* 3.1 15.2 + - - +
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Residues in contact with THR 6 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R SER* 4.0 8.7 - - - +
5R PHE* 1.3 77.4 - - - +
7R SER* 1.3 57.6 + - - +
9R ALA* 4.0 1.7 - - - +
10R ARG* 3.1 29.5 + - + +
108R LEU* 3.7 18.6 + - - +
111R GLU* 2.7 32.5 + - - +
112R ALA* 4.9 2.3 + - - -
115R LYS* 5.3 11.4 - - - +
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Residues in contact with SER 7 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R GLN* 3.3 19.1 + - - +
4R SER* 3.1 22.7 + - - -
6R THR* 1.3 80.5 - - - +
8R ILE* 1.3 64.8 + - - +
10R ARG* 3.2 10.4 + - - +
11R ILE* 3.0 33.3 + - - +
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Residues in contact with ILE 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312N VAL* 4.5 15.3 - - + -
375N ASN* 3.4 45.1 - - + +
376N VAL* 4.4 5.8 - - + +
379N TYR* 3.6 33.4 - - + -
3R GLN* 3.5 20.6 - - + +
4R SER 3.0 19.8 + - - +
5R PHE* 3.1 24.0 + - + +
7R SER* 1.3 75.1 - - - +
9R ALA* 1.3 51.9 + - - +
11R ILE* 3.2 6.1 + - - +
12R GLY* 2.7 32.4 + - - -
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Residues in contact with ALA 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379N TYR* 3.6 34.1 - - + +
385N LYS* 5.2 1.6 - - - +
5R PHE 2.8 18.9 + - - +
6R THR 4.2 2.5 - - - +
8R ILE* 1.3 71.1 - - - +
10R ARG* 1.3 66.9 + - - +
13R ASP* 2.9 35.9 + - - +
104R LEU* 5.6 0.9 - - + -
108R LEU* 4.6 19.3 - - + -
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Residues in contact with ARG 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R THR* 3.1 23.0 + - + +
7R SER* 3.4 11.4 - - - +
8R ILE 3.2 0.2 - - - -
9R ALA* 1.3 78.9 - - - +
11R ILE* 1.3 62.1 + - + +
13R ASP* 4.4 1.8 - - - +
14R TYR* 3.5 20.3 + - - +
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Residues in contact with ILE 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372N THR* 5.1 6.7 - - + -
376N VAL* 4.0 27.1 - - + -
3R GLN* 4.3 11.7 - - - +
7R SER* 3.0 26.2 + - - +
8R ILE 3.7 3.1 - - - +
10R ARG* 1.3 79.3 - - + +
12R GLY* 1.3 64.9 + - - +
14R TYR* 3.6 9.6 + - + +
15R ILE* 3.3 30.1 + - + +
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Residues in contact with GLY 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376N VAL* 4.5 4.9 - - - +
379N TYR* 3.6 21.8 - - - -
380N ILE* 3.7 13.0 - - - +
8R ILE 2.7 21.0 + - - -
11R ILE* 1.3 72.8 - - - +
13R ASP* 1.3 64.6 + - - +
15R ILE* 3.0 6.3 + - - +
16R LEU* 2.9 25.5 + - - +
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Residues in contact with ASP 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379N TYR* 2.7 27.4 + - - -
383N VAL* 4.4 3.8 - - - +
385N LYS* 4.5 15.1 + - - +
9R ALA* 2.9 28.4 + - - +
10R ARG* 4.4 2.2 - - - +
12R GLY* 1.3 70.5 - - - -
14R TYR* 1.3 54.5 + - - +
16R LEU* 3.0 12.3 + - - +
17R LYS* 2.7 65.3 + - - +
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Residues in contact with TYR 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R ARG 3.5 17.9 + - - +
11R ILE* 3.7 11.0 - - + +
12R GLY 3.2 0.2 - - - -
13R ASP* 1.3 79.8 - - - +
15R ILE* 1.3 67.9 + - + +
17R LYS* 4.2 7.6 - - + +
18R SER* 3.5 28.4 + - - -
21R LEU* 5.3 13.1 - - + +
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Residues in contact with ILE 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376N VAL* 4.0 23.1 - - + -
380N ILE* 4.4 12.1 - - + -
11R ILE* 3.3 21.3 + - + +
12R GLY 3.0 7.8 + - - +
14R TYR* 1.3 84.1 - - + +
16R LEU* 1.3 65.1 + - + +
18R SER 3.2 18.0 + - - +
21R LEU* 3.8 26.8 - - + +
22R SER* 3.3 8.6 + - - -
25R CYS* 3.9 35.7 - - + -
26R VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379N TYR* 4.2 6.3 - - + -
380N ILE* 3.7 37.0 - - + +
383N VAL* 3.7 26.5 - - + +
385N LYS 5.9 0.4 - - - +
12R GLY 2.9 21.4 + - - +
13R ASP* 3.4 19.1 - - - +
15R ILE* 1.3 80.6 - - + +
17R LYS* 1.3 63.3 + - + +
18R SER 3.3 1.6 + - - +
19R PRO* 5.4 0.2 - - - +
22R SER* 3.7 18.0 + - - +
26R VAL* 3.9 23.6 - - + -
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Residues in contact with LYS 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ASP* 2.7 47.7 + - - +
14R TYR* 4.3 8.1 - - + +
16R LEU* 1.3 73.4 - - + +
18R SER* 1.3 59.0 + - - +
19R PRO* 3.6 7.8 - - - +
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Residues in contact with SER 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R TYR* 3.5 22.9 + - - -
15R ILE 3.2 3.6 + - - +
16R LEU 3.2 1.9 - - - -
17R LYS* 1.3 78.4 - - - +
19R PRO* 1.3 63.5 - - - +
20R VAL* 3.5 14.0 + - - +
21R LEU* 3.7 23.1 + - - +
22R SER* 2.9 31.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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