Contacts of the helix formed by residues 9 - 30 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B THR* 1.3 75.2 - - - +
10B GLU* 1.3 59.9 + - - +
12B ARG* 3.4 3.0 - - - +
13B MET* 2.5 47.9 + - + +
40B LEU* 3.7 8.5 - - + -
43B GLN* 2.5 54.7 + - - +
44B THR* 4.2 2.2 - - - +
45B ASP* 3.0 53.5 + - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 2.6 34.5 + - - +
9B ARG* 1.3 81.7 + - - +
11B GLU* 1.3 69.9 + - + +
13B MET* 3.6 5.5 - - - +
14B LYS* 2.8 25.3 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE 4.4 3.5 - - - +
7B MET* 4.1 28.1 - - + +
8B THR* 2.8 49.5 + - - +
10B GLU* 1.3 78.4 - - + +
12B ARG* 1.3 65.5 + - - +
14B LYS* 2.8 34.8 + - + +
15B ILE* 3.3 13.4 + - + +
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE 5.4 0.2 + - - -
7B MET* 3.7 34.9 + - + +
8B THR* 3.0 15.5 + - - +
9B ARG 3.4 4.3 - - - +
11B GLU* 1.3 72.3 - - - +
13B MET* 1.3 65.5 + - - +
14B LYS 2.9 1.4 + - - -
15B ILE* 2.9 23.1 + - - +
16B VAL* 3.0 16.5 + - - +
40B LEU* 3.9 21.5 - - + -
45B ASP* 2.7 31.5 + - - +
46B GLY* 2.3 41.6 + - - +
47B PRO 3.2 13.9 + - - -
49B SER* 3.0 32.2 + - - -
50B ASP 4.8 2.5 - - - -
51B ILE* 4.4 17.9 - - + +
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 2.5 39.4 + - + +
10B GLU* 3.7 5.6 - - - +
12B ARG* 1.3 73.7 - - - +
14B LYS* 1.3 60.4 + - - +
15B ILE 3.3 0.2 - - - -
16B VAL* 3.3 14.8 - - + +
17B HIS* 2.8 63.7 + - + +
36B VAL* 5.8 0.7 - - - -
40B LEU* 4.4 23.8 - - + -
43B GLN* 4.5 13.9 - - - +
107B LEU* 5.1 7.6 - - + -
109B ILE* 4.9 7.0 - - + -
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ARG* 4.4 19.8 - - - +
10B GLU 2.8 12.8 + - - +
11B GLU* 2.8 25.6 + - + +
13B MET* 1.3 78.6 - - - +
15B ILE* 1.3 57.9 + - - +
17B HIS* 3.5 6.5 + - - +
18B GLU* 3.1 45.7 + - - +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ARG* 3.8 21.1 - - - +
251A ILE* 5.8 1.1 - - + -
7B MET* 3.7 30.5 - - + -
11B GLU* 3.7 12.8 - - + +
12B ARG 2.9 4.2 + - - +
14B LYS* 1.3 78.3 - - + +
16B VAL* 1.3 60.5 + - - +
17B HIS 3.1 1.1 - - - -
18B GLU* 3.6 9.0 - - + +
19B ILE* 2.7 61.8 + - + +
51B ILE* 4.1 21.1 - - + -
73B TRP* 4.1 31.2 - - + +
75B VAL* 4.2 0.2 - - + -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG 3.0 22.7 - - - +
13B MET* 3.3 21.1 - - + +
15B ILE* 1.3 78.0 - - - +
17B HIS* 1.3 53.9 + - + +
19B ILE* 3.1 2.8 + - - +
20B LYS* 2.6 35.5 + - - +
36B VAL* 3.7 8.7 - - + -
40B LEU* 3.9 20.6 - - + -
51B ILE* 4.6 14.1 - - + -
53B MET* 4.1 15.3 - - + +
109B ILE* 3.4 34.8 - - + -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 2.8 46.4 + - + +
14B LYS* 3.5 7.6 + - - +
15B ILE 3.1 0.4 - - - -
16B VAL* 1.3 81.6 - - + +
18B GLU* 1.3 64.8 + - - +
20B LYS* 3.1 29.6 - - + +
21B GLU* 2.9 24.6 + - - +
109B ILE* 4.6 17.1 + - + +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ARG* 2.2 37.0 + - - -
251A ILE* 4.1 13.2 - - + +
14B LYS* 3.1 41.4 + - - +
15B ILE* 3.1 9.2 + - + +
17B HIS* 1.3 76.5 - - - +
19B ILE* 1.4 56.2 - - + +
21B GLU* 3.2 18.4 + - - +
22B ARG* 3.2 10.9 + - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 3.6 21.8 - - + -
253A PHE* 4.6 4.9 - - + -
15B ILE* 2.7 43.9 + - + +
16B VAL 3.2 4.3 - - - +
18B GLU* 1.4 66.7 - - - +
20B LYS* 1.3 67.4 + - - +
21B GLU 3.0 1.3 - - - -
22B ARG* 3.2 2.4 + - - +
23B ILE* 3.0 43.5 + - + +
51B ILE* 5.0 0.9 - - + -
53B MET* 3.6 23.8 - - - -
68B TRP* 3.5 13.5 - - + -
75B VAL* 3.2 34.5 - - + -
77B VAL* 4.3 9.6 - - + -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL 2.6 17.4 + - - +
17B HIS* 3.1 35.9 - - + +
19B ILE* 1.3 76.4 - - - +
21B GLU* 1.3 87.3 + - + +
23B ILE* 3.9 3.9 - - - +
24B LEU* 3.2 39.7 + - + +
34B ILE* 4.2 20.5 - - + +
53B MET* 4.8 0.9 - - + +
109B ILE* 4.0 33.0 - - + -
110B TYR* 5.0 7.9 - - + -
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS 2.9 13.6 + - - +
18B GLU* 3.2 9.4 + - - +
19B ILE 3.0 0.6 - - - -
20B LYS* 1.3 107.2 + - + +
22B ARG* 1.3 55.1 + - - +
24B LEU* 3.0 14.4 + - - +
25B ASP* 2.7 63.4 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 3.9 17.0 - - + -
253A PHE* 3.2 51.9 + - + +
18B GLU 3.2 12.8 + - - +
19B ILE 3.2 5.8 + - - +
21B GLU* 1.3 74.4 - - - +
23B ILE* 1.3 53.9 + - - +
25B ASP* 3.9 31.1 + - - +
26B LYS* 2.5 71.0 + - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 3.9 18.2 - - + -
19B ILE* 3.0 25.5 + - + +
20B LYS 3.9 3.4 - - - +
22B ARG* 1.3 78.0 - - - +
24B LEU* 1.3 55.1 + - - +
26B LYS* 4.4 0.2 - - - -
27B TYR* 2.6 41.1 + - + +
28B GLY 3.5 0.5 + - - -
31B VAL* 3.4 24.8 - - + +
34B ILE* 3.8 29.4 - - + -
53B MET* 4.6 0.4 - - + -
55B CYS* 4.3 4.0 - - + -
77B VAL* 4.0 26.9 - - + -
79B PHE* 4.2 20.6 - - + -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.2 32.5 + - - +
21B GLU* 3.0 14.3 + - - +
23B ILE* 1.3 77.9 - - - +
25B ASP* 1.3 61.2 + - - +
28B GLY* 2.9 51.7 + - - +
31B VAL* 3.5 23.6 - - + -
34B ILE* 4.2 6.5 - - + -
110B TYR* 3.6 42.4 - - + +
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU* 2.7 41.7 + - - +
22B ARG* 3.9 20.7 + - - +
24B LEU* 1.3 75.8 - - - +
26B LYS* 1.3 61.4 + - - +
28B GLY* 4.4 1.6 + - - -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 2.7 43.5 + - + +
22B ARG* 2.5 59.1 + - + +
25B ASP* 1.3 76.6 - - - +
27B TYR* 1.3 100.2 + - + +
66B HIS* 5.0 1.4 + - - -
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 4.3 5.8 - + - -
23B ILE* 2.6 30.2 + - + +
25B ASP 5.0 0.2 - - - -
26B LYS* 1.3 115.7 + - + +
28B GLY* 1.3 62.9 + - - +
29B ASP* 3.3 4.2 + - - +
30B ASP* 3.0 27.5 + - + +
31B VAL* 3.7 13.5 - - + -
57B MET* 3.3 28.0 - - + -
64B PHE* 3.5 28.5 - + - -
66B HIS* 4.3 6.9 + - - -
79B PHE* 4.0 16.6 - + - -
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE 3.5 2.2 + - - -
24B LEU* 2.9 32.7 + - - +
25B ASP 4.4 1.5 + - - -
26B LYS 3.6 1.0 - - - -
27B TYR* 1.3 75.2 - - - +
29B ASP* 1.4 57.8 + - - -
30B ASP 3.1 0.2 - - - -
31B VAL* 3.0 29.5 + - - +
110B TYR* 5.5 0.3 + - - -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR 4.3 3.5 - - - +
28B GLY* 1.4 66.5 - - - -
30B ASP* 1.3 69.3 + - - +
31B VAL* 3.1 7.9 + - - +
32B LYS* 5.6 0.7 - - - +
58B SER* 3.7 8.0 + - - -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.0 25.5 + - + +
29B ASP* 1.3 88.3 + - - +
31B VAL* 1.4 57.7 + - - +
57B MET* 3.1 16.7 - - + +
58B SER* 3.0 42.0 + - - +
59B THR* 4.2 20.5 + - - +
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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