Contacts of the helix formed by residues 9 - 30 (chain A) in PDB entry 1KNY
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 ARG 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 1.3 72.2 - - - +
10A GLU* 1.3 68.3 + - + +
12A ARG* 3.4 5.1 - - - +
13A MET* 2.7 53.7 + - + +
40A LEU* 4.5 4.7 - - + -
43A GLN* 3.1 50.0 + - - +
44A THR* 4.1 1.8 - - - +
45A ASP* 2.3 61.3 + - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 2.7 29.4 - - - +
9A ARG* 1.3 90.5 + - + +
11A GLU* 1.3 55.6 + - - +
13A MET* 3.5 6.6 + - - +
14A LYS* 2.8 39.6 + - - +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.4 1.4 - - - +
6A ILE 3.9 3.1 - - - +
7A MET* 3.0 42.8 - - + +
8A THR* 2.7 40.6 + - - +
10A GLU* 1.3 69.7 - - - +
12A ARG* 1.3 67.5 + - - +
14A LYS* 3.2 34.9 + - + +
15A ILE* 2.9 18.3 + - + +
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE 5.3 0.4 + - - -
7A MET* 3.7 38.1 + - + +
8A THR 2.6 16.0 + - - +
9A ARG 3.4 8.7 - - - +
11A GLU* 1.3 75.0 - - - +
13A MET* 1.3 63.1 + - - +
15A ILE* 3.1 13.8 + - - +
16A VAL* 3.0 24.5 + - - +
40A LEU* 3.9 17.9 - - + -
45A ASP* 2.9 36.5 + - - +
46A GLY 2.3 36.7 + - - -
47A PRO 3.2 16.4 + - - -
49A SER* 3.4 25.6 + - - -
50A ASP 4.6 2.5 - - - -
51A ILE* 3.9 18.3 - - + +
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Residues in contact with MET 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.7 38.8 + - + +
10A GLU* 3.8 7.0 - - - +
11A GLU 3.2 0.2 - - - -
12A ARG* 1.3 76.1 - - - +
14A LYS* 1.3 56.3 + - - +
16A VAL* 2.9 12.3 - - + +
17A HIS* 2.9 43.3 + - + +
36A VAL* 4.9 0.9 - - + -
40A LEU* 3.6 31.6 - - + +
43A GLN* 6.3 1.1 - - - -
107A LEU* 4.5 19.7 - - + -
109A ILE* 3.9 27.8 - - + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 4.8 0.2 + - - -
10A GLU* 2.8 26.2 + - - +
11A GLU* 3.2 39.5 - - + +
13A MET* 1.3 69.6 - - - +
15A ILE* 1.3 54.7 + - + +
17A HIS* 3.2 7.9 + - - +
18A GLU* 2.7 44.8 + - - +
250B ARG* 5.7 2.7 - - - +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET* 3.4 28.0 - - + -
11A GLU* 2.9 22.9 + - + +
12A ARG* 3.1 9.1 + - - +
14A LYS* 1.3 77.2 - - + +
16A VAL* 1.3 57.4 + - - +
18A GLU* 2.7 29.4 + - + +
19A ILE* 2.8 37.6 + - + +
51A ILE* 3.5 20.9 - - + -
73A TRP* 4.1 32.3 - - + +
250B ARG* 3.9 20.4 - - - +
251B ILE* 6.2 0.4 - - + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG 3.0 15.1 + - - +
13A MET* 2.9 18.6 - - + +
15A ILE* 1.3 73.3 - - - +
17A HIS* 1.3 58.4 + - - +
19A ILE* 3.5 2.4 + - - +
20A LYS* 2.8 29.3 + - - +
36A VAL* 3.5 9.4 - - + -
40A LEU* 3.5 28.0 - - + -
51A ILE* 4.1 14.1 - - + -
53A MET* 4.2 16.9 - - + +
109A ILE* 3.0 39.5 - - + -
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Residues in contact with HIS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 2.9 34.9 + - + +
14A LYS* 3.7 9.6 - - - +
16A VAL* 1.3 75.3 - - - +
18A GLU* 1.3 66.6 + - - +
20A LYS* 3.4 35.9 + - + +
21A GLU* 3.1 34.1 + - - +
109A ILE* 4.1 26.6 + - + +
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 2.7 24.6 + - - +
15A ILE* 2.7 14.8 + - - +
17A HIS* 1.3 74.0 - - - +
19A ILE* 1.3 60.2 - - - +
21A GLU* 3.4 12.7 + - - +
22A ARG* 3.2 19.9 + - - +
73A TRP* 5.8 0.7 - - - -
250B ARG* 2.8 47.3 + - - +
251B ILE* 3.9 21.3 - - + +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 2.8 39.7 + - + +
16A VAL* 3.8 3.8 - - - +
18A GLU* 1.3 71.7 - - - +
20A LYS* 1.3 68.9 + - - +
22A ARG* 3.1 4.1 + - - +
23A ILE* 2.9 38.4 + - + +
51A ILE* 5.1 0.4 - - + -
53A MET* 4.1 13.7 - - - -
68A TRP* 4.3 6.3 - - + -
75A VAL* 3.6 26.9 - - + -
77A VAL* 4.1 16.8 - - + -
251B ILE* 3.9 24.5 - - + -
253B PHE* 4.1 14.8 - - + -
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL 2.8 19.7 + - - +
17A HIS* 3.4 33.5 + - + +
18A GLU 3.3 0.2 - - - -
19A ILE* 1.3 77.6 - - - +
21A GLU* 1.3 80.1 + - - +
23A ILE* 3.0 24.0 + - - +
24A LEU* 3.2 25.9 + - + +
34A ILE* 3.9 18.4 - - + -
53A MET* 4.9 0.7 - - - -
109A ILE* 3.8 36.9 + - + +
110A TYR* 4.7 4.9 - - + -
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 3.1 20.9 + - - +
18A GLU* 3.4 15.3 - - - +
20A LYS* 1.3 89.4 + - - +
22A ARG* 1.3 59.2 + - - +
24A LEU* 3.5 5.9 + - - +
25A ASP* 3.0 39.6 + - - +
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU 3.2 8.8 + - - +
19A ILE* 3.1 11.6 + - - +
20A LYS 3.1 0.6 - - - -
21A GLU* 1.3 78.3 - - - +
23A ILE* 1.3 65.8 + - - +
25A ASP* 3.4 33.5 + - - +
26A LYS* 3.1 42.6 + - - +
251B ILE* 4.1 20.4 - - + -
253B PHE* 2.4 56.3 + - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 2.9 41.3 + - + +
20A LYS* 3.0 10.9 + - - +
22A ARG* 1.3 75.1 - - - +
24A LEU* 1.3 57.8 + - - +
27A TYR* 2.9 42.7 + - + +
31A VAL* 3.6 22.7 - - + -
34A ILE* 4.1 17.9 - - + -
53A MET* 4.3 10.3 - - + -
55A CYS* 4.0 15.9 - - + -
77A VAL* 4.6 12.1 - - + -
79A PHE* 4.1 16.8 - - + -
253B PHE* 4.1 12.6 - - + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.2 36.8 + - + +
21A GLU* 4.0 5.2 - - - +
22A ARG 3.2 0.2 - - - -
23A ILE* 1.3 75.6 - - - +
25A ASP* 1.3 68.0 + - - +
28A GLY* 2.9 44.8 + - - +
31A VAL* 3.9 17.7 - - + -
34A ILE* 4.4 4.9 - - + -
110A TYR* 4.0 36.3 - - + +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.0 27.3 + - - +
22A ARG* 3.6 22.7 + - - +
24A LEU* 1.3 78.6 - - - +
26A LYS* 1.4 62.4 + - - +
27A TYR 4.8 0.3 - - - -
28A GLY* 4.4 1.7 + - - -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.1 31.3 + - - +
23A ILE 3.8 2.0 - - - +
25A ASP* 1.4 81.5 - - - +
27A TYR* 1.3 103.8 + - + +
66A HIS* 4.0 6.1 + - - -
253B PHE* 3.1 47.8 + - + +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 2.9 37.6 + - + -
25A ASP 4.8 0.4 - - - -
26A LYS* 1.3 119.9 + - + +
28A GLY* 1.3 64.4 + - - +
29A ASP 3.2 3.8 + - - -
30A ASP* 3.3 30.4 + - + +
31A VAL* 3.5 16.8 - - + -
57A MET* 4.1 13.9 - - + -
64A PHE* 3.7 29.6 - + - -
66A HIS* 3.8 5.0 + - - -
79A PHE* 3.9 20.6 - + - -
253B PHE* 4.9 2.9 - + - -
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE 3.9 0.8 + - - -
24A LEU* 2.9 34.5 + - - +
25A ASP 4.4 1.1 + - - -
27A TYR* 1.3 72.9 - - - +
29A ASP* 1.3 59.9 + - - -
30A ASP 3.0 8.8 + - - -
31A VAL* 3.2 22.2 + - - +
110A TYR* 4.9 1.2 + - - -
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR 3.2 3.4 + - - -
28A GLY* 1.3 71.4 - - - -
30A ASP* 1.3 64.4 + - - +
31A VAL 3.3 6.7 + - - +
32A LYS* 5.9 0.2 - - - +
58A SER* 4.0 9.4 + - - -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.3 27.5 + - + +
28A GLY 3.0 1.8 - - - -
29A ASP* 1.3 82.8 - - - +
31A VAL* 1.4 57.5 + - - +
57A MET* 3.2 10.4 - - - -
58A SER* 2.4 44.0 + - - -
59A THR* 4.4 21.8 + - - -
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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
------------------------------------------------------------
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