Contacts of the helix formed by residues 103 - 121 (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 LEU 103 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R ASP* 2.8 29.1 + - - +
49R ILE* 4.6 0.9 - - + -
56R MET* 3.6 37.2 - - + -
59R ALA* 4.2 12.8 - - + +
60R LEU* 3.8 17.7 - - + -
63R LEU* 3.7 40.6 - - + -
71R ARG* 5.0 1.3 - - - +
102R TYR* 1.3 86.9 - - + +
104R LEU* 1.3 64.2 + - - +
105R PRO 3.4 0.2 - - - -
106R TYR* 3.1 19.0 + - + +
107R ILE* 3.3 22.0 + - + +
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Residues in contact with LEU 104 (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 36.3 - - + +
382N ARG* 6.1 0.2 - - - +
383N VAL* 4.7 0.2 - - + -
385N LYS* 4.6 11.0 - - - +
5R PHE* 3.5 41.5 - - + +
9R ALA* 5.7 0.2 - - + -
46R ASP* 3.1 9.4 + - - +
101R PRO* 3.5 32.1 - - + +
103R LEU* 1.3 76.3 - - - +
105R PRO* 1.3 63.8 - - + +
107R ILE* 3.4 7.7 + - + +
108R LEU* 3.0 46.4 + - + +
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Residues in contact with PRO 105 (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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101R PRO 3.5 7.6 - - - +
102R TYR 3.3 17.3 - - - +
103R LEU 3.5 0.2 - - - -
104R LEU* 1.3 92.7 - - + +
106R TYR* 1.3 70.2 + - + +
108R LEU* 3.3 10.7 + - + +
109R GLU* 2.9 31.7 + - - +
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Residues in contact with TYR 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 6.1 0.9 - - - -
58R THR* 5.7 0.2 - - - +
59R ALA* 3.8 24.8 - - + +
62R ARG* 3.7 34.5 + - + +
63R LEU* 3.7 18.4 - - + -
64R PRO* 3.1 26.6 - - + +
102R TYR 3.5 24.2 - - - -
103R LEU* 3.1 12.5 + - + +
105R PRO* 1.3 81.9 - - + +
107R ILE* 1.3 57.6 + - - +
109R GLU* 3.5 18.6 + - - +
110R ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R PHE* 3.7 39.3 - - + -
49R ILE* 3.8 28.3 - - + -
55R ILE* 4.1 10.3 - - + -
56R MET* 4.1 14.8 - - + -
59R ALA* 4.1 15.5 - - + -
103R LEU* 3.4 19.5 - - + +
104R LEU* 3.4 14.1 - - - +
105R PRO 3.1 0.2 - - - -
106R TYR* 1.3 74.7 - - - +
108R LEU* 1.3 56.1 + - - +
110R ALA* 2.8 10.7 + - - +
111R GLU* 2.7 50.4 + - + +
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Residues in contact with LEU 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385N LYS* 4.0 21.5 - - - +
5R PHE* 3.9 8.1 - - + +
6R THR* 3.7 41.0 + - - +
9R ALA* 4.6 10.8 - - + -
104R LEU* 3.0 39.0 + - + +
105R PRO* 3.6 7.6 - - + +
107R ILE* 1.3 79.3 - - - +
109R GLU* 1.3 56.7 + - - +
111R GLU* 3.9 5.6 - - - +
112R ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 5.9 0.7 + - - -
115B LYS* 3.5 23.8 + - - +
117B HIS* 3.2 33.7 + - - -
62R ARG* 4.9 9.3 + - - +
105R PRO 2.9 15.9 + - - +
106R TYR* 3.6 20.9 - - - +
108R LEU* 1.3 76.6 - - - +
110R ALA* 1.3 59.4 + - - +
112R ALA* 3.3 7.7 + - + +
113R ALA* 3.0 29.2 + - + +
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Residues in contact with ALA 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ILE* 3.7 25.4 - - + +
58R THR* 3.9 26.5 - - + -
59R ALA 5.0 0.4 - - - +
62R ARG* 4.7 7.4 - - - +
106R TYR 2.9 18.2 + - - +
107R ILE* 2.8 5.5 + - - +
109R GLU* 1.3 74.8 - - - +
111R GLU* 1.3 64.2 + - - +
113R ALA* 3.5 6.4 + - - +
114R ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R SER* 3.7 13.9 - - - -
5R PHE* 3.1 20.3 + - - +
6R THR* 2.7 50.5 + - - +
55R ILE* 3.8 28.4 - - + +
107R ILE* 2.7 34.7 + - + +
108R LEU* 3.9 3.5 - - - +
110R ALA* 1.3 69.0 - - - +
112R ALA* 1.3 56.3 + - - +
114R ALA* 3.1 2.7 + - - +
115R LYS* 2.8 37.5 + - - +
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Residues in contact with ALA 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R THR* 4.9 2.4 + - - +
108R LEU 3.0 18.7 + - - +
109R GLU* 3.4 9.6 - - + +
110R ALA 3.3 0.2 - - - -
111R GLU* 1.3 78.0 - - - +
113R ALA* 1.3 62.9 + - - +
115R LYS* 3.3 7.2 + - - +
116R GLU* 3.1 23.6 + - - +
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Residues in contact with ALA 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 5.1 1.4 - - - +
62R ARG* 5.4 7.2 - - - +
109R GLU* 3.0 18.3 + - + +
110R ALA* 3.8 7.6 - - - +
111R GLU 3.3 0.2 - - - -
112R ALA* 1.3 75.9 - - - +
114R ALA* 1.3 61.6 - - - +
116R GLU* 3.5 12.2 + - - +
117R LYS* 3.1 22.7 + - - +
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Residues in contact with ALA 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ILE* 3.9 17.9 - - + -
110R ALA 3.0 17.7 + - - +
111R GLU* 3.1 4.2 + - - +
113R ALA* 1.3 74.7 - - - +
115R LYS* 1.3 65.2 + - - +
117R LYS* 3.2 7.7 + - - +
118R ASP* 3.1 22.3 + - - +
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Residues in contact with LYS 115 (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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6R THR* 5.3 11.5 - - - +
111R GLU 2.8 20.4 + - - +
112R ALA* 3.5 7.4 - - - +
114R ALA* 1.3 72.1 - - - +
116R GLU* 1.3 63.4 + - - +
118R ASP* 3.2 11.4 + - + +
119R GLU* 3.1 43.8 + - + +
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Residues in contact with GLU 116 (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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63B SER* 2.7 36.0 + - - -
65B LEU* 4.5 6.5 - - + +
66B LYS* 3.5 23.3 + - + +
112R ALA 3.1 13.0 + - - +
113R ALA* 3.6 13.3 - - - +
114R ALA 3.2 0.2 - - - -
115R LYS* 1.3 75.4 - - - +
117R LYS* 1.3 55.0 + - - +
119R GLU* 2.9 13.3 + - + +
120R LEU* 2.8 52.8 + - + +
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Residues in contact with LYS 117 (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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303A ASP* 3.1 30.7 + - - -
65B LEU* 3.8 29.1 - - + +
69B ARG* 4.5 8.8 - - - +
113R ALA 3.1 11.2 + - - +
114R ALA* 3.2 11.0 + - - +
116R GLU* 1.3 78.7 - - - +
118R ASP* 1.3 59.3 + - - +
120R LEU* 3.3 3.0 + - - +
121R ASP* 2.6 67.8 + - - +
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Residues in contact with ASP 118 (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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114R ALA 3.1 12.2 + - - +
115R LYS* 3.4 13.6 - - + +
116R GLU 3.2 0.2 - - - -
117R LYS* 1.3 77.1 - - - +
119R GLU* 1.3 63.6 + - + +
121R ASP* 3.3 13.4 + - - +
122R ASN* 3.2 36.1 + - - -
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Residues in contact with GLU 119 (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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115R LYS* 3.1 42.1 + - + +
116R GLU* 2.9 12.3 + - - +
118R ASP* 1.3 78.5 - - + +
120R LEU* 1.3 60.2 + - + +
122R ASN* 3.0 19.4 + - - +
123R ILE* 3.1 19.6 + - + +
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Residues in contact with LEU 120 (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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65B LEU* 3.9 17.5 - - + -
66B LYS* 3.7 48.0 - - + -
69B ARG* 3.6 34.6 + - + +
70B GLU 6.0 0.2 - - - +
116R GLU* 2.8 42.6 + - + +
117R LYS* 3.6 5.2 - - - +
119R GLU* 1.3 73.4 - - + +
121R ASP* 1.3 60.9 + - - +
122R ASN 3.3 0.8 + - - -
123R ILE* 3.8 33.9 - - + +
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Residues in contact with ASP 121 (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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300A LYS* 3.5 24.0 + - - +
303A ASP* 4.2 7.6 - - - +
360A THR* 6.1 0.7 - - - -
69B ARG* 2.7 31.6 + - - +
117R LYS* 2.6 48.0 + - - +
118R ASP* 3.5 10.6 - - - +
119R GLU 3.1 0.6 - - - -
120R LEU* 1.3 76.5 - - - +
122R ASN* 1.3 70.6 + - - +
123R ILE* 5.5 0.2 - - - -
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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
------------------------------------------------------------
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