Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 1K9K
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 2.6 33.2 + - - -
28A THR 3.9 0.6 + - - -
29A LEU* 1.3 75.7 - - - +
31A LYS* 1.3 60.3 + - - +
32A LYS* 3.4 2.8 + - - -
33A GLU* 2.8 28.6 + - - +
34A LEU* 2.9 26.7 + - - +
57A MET* 3.9 2.0 - - - -
66A GLN 4.4 6.3 - - - -
67A GLU* 4.5 14.3 + - - -
300A CA 4.5 0.2 - - - -
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Residues in contact with LYS 31 (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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30A SER* 1.3 74.4 - - - +
32A LYS* 1.3 62.1 + - + +
34A LEU* 3.4 2.6 + - - +
35A LYS* 3.0 29.5 + - + +
50A ASP* 3.1 38.0 + - - -
53A ILE* 4.5 11.7 - - + +
54A ALA* 4.5 23.5 - - + +
57A MET* 3.6 27.1 - - + +
66A GLN 4.3 4.3 + - - +
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Residues in contact with LYS 32 (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 GLU* 2.7 42.4 + - - +
30A SER* 3.2 3.0 + - - -
31A LYS* 1.3 80.5 - - + +
33A GLU* 1.3 63.9 + - - +
35A LYS* 3.5 8.3 + - - +
36A GLU* 3.1 23.2 + - - +
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Residues in contact with GLU 33 (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 TYR* 3.1 25.1 - - - +
20A SER 2.8 7.2 - - - +
22A ARG* 2.9 18.5 + - + -
23A GLU* 2.8 30.7 + - + +
28A THR 3.0 4.2 - - - +
29A LEU* 3.3 8.2 - - + -
30A SER* 2.8 38.2 + - - +
32A LYS* 1.3 73.9 - - + +
34A LEU* 1.3 66.3 + - - +
36A GLU* 3.3 8.0 + - - +
37A LEU* 2.9 24.4 + - - +
300A CA 2.4 31.2 - - - -
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Residues in contact with LEU 34 (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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29A LEU* 4.2 25.7 - - + +
30A SER 2.9 18.4 + - - +
31A LYS* 3.6 4.0 - - - +
33A GLU* 1.3 77.2 - - - +
35A LYS* 1.3 57.9 + - - +
37A LEU* 3.3 8.0 + - + +
38A ILE* 2.9 54.4 + - + +
53A ILE* 4.3 17.5 - - + +
56A LEU* 4.4 12.3 - - + -
57A MET* 4.0 40.2 - - + +
60A LEU* 4.9 7.4 - - + -
68A VAL* 4.3 11.2 - - + -
73A TYR* 6.1 1.8 - - + -
76A PHE* 5.8 2.7 - - + -
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Residues in contact with LYS 35 (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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31A LYS* 3.0 21.5 + - + +
32A LYS* 3.7 8.3 - - - +
33A GLU 3.2 0.2 - - - -
34A LEU* 1.3 77.6 - - - +
36A GLU* 1.3 58.1 + - - +
38A ILE* 3.3 4.1 + - - +
39A GLN* 2.9 65.0 + - + +
48A LEU 5.7 2.0 - - - -
50A ASP* 2.8 43.6 + - - +
53A ILE* 4.1 25.1 - - + -
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Residues in contact with GLU 36 (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 TYR* 3.5 18.3 - - + -
22A ARG* 2.8 46.2 + - - +
32A LYS 3.1 17.2 + - - +
33A GLU* 3.8 6.1 - - - +
35A LYS* 1.3 75.6 - - - +
37A LEU* 1.3 63.2 + - - +
39A GLN* 4.3 9.6 - - - -
40A LYS* 2.8 58.0 + - + +
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Residues in contact with LEU 37 (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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15A ILE* 3.8 20.6 - - + +
16A PHE* 4.4 2.5 - - - -
19A TYR* 3.7 34.3 - - + -
29A LEU* 3.8 28.3 - - + -
33A GLU 2.9 17.4 + - - +
34A LEU* 3.5 6.7 - - + +
35A LYS 3.3 0.2 - - - -
36A GLU* 1.3 76.9 - - - +
38A ILE* 1.3 74.8 + - + +
41A GLU* 2.9 36.0 + - + +
42A LEU* 6.1 0.2 - - + -
73A TYR* 4.1 15.3 - - + -
76A PHE* 5.4 1.1 - - + -
5B LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 38 (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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34A LEU* 2.9 36.4 + - + +
35A LYS 3.7 3.4 - - - +
37A LEU* 1.3 85.8 - - + +
39A GLN* 1.3 63.6 + - + +
42A LEU* 3.0 40.2 + - + +
45A GLY* 3.3 13.1 - - - +
48A LEU* 3.7 29.6 - - + -
53A ILE* 4.0 12.6 - - + -
56A LEU* 4.0 14.4 - - + -
76A PHE* 3.8 35.7 - - + -
5B LEU* 6.1 0.4 - - + -
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Residues in contact with GLN 39 (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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35A LYS* 2.9 62.8 + - + +
36A GLU* 3.9 7.5 - - - +
38A ILE* 1.3 74.4 - - + +
40A LYS* 1.3 62.7 + - + +
42A LEU 4.4 3.8 - - - +
45A GLY 3.7 23.0 + - - +
46A SER* 3.8 26.8 + - - +
48A LEU 4.9 7.4 + - - +
53A ILE* 5.8 2.7 - - + +
200B BME 4.4 7.8 - - - +
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Residues in contact with LYS 40 (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 LYS* 6.0 0.9 - - - +
19A TYR* 3.5 23.3 - - - +
22A ARG* 4.5 4.0 - - - +
36A GLU* 2.8 50.6 + - + +
39A GLN* 1.3 83.1 - - + +
41A GLU* 1.3 64.7 + - - +
42A LEU 3.8 0.4 - - - -
3B CYS* 4.8 0.2 - - - +
4B PRO* 4.8 1.6 - - - +
200B BME 3.6 25.2 - - - +
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Residues in contact with GLU 41 (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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15A ILE* 3.6 25.8 - - + +
18A LYS* 4.6 7.8 + - - +
19A TYR* 2.6 41.1 + - + +
37A LEU 2.9 19.7 + - - +
40A LYS* 1.3 83.5 - - - +
42A LEU* 1.3 60.9 + - - +
3B CYS* 3.1 20.3 - - - +
4B PRO* 3.5 27.3 - - - +
5B LEU* 3.1 33.4 + - + +
6B ASP* 3.8 0.2 - - - +
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Residues in contact with LEU 42 (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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38A ILE* 3.0 38.6 + - + +
39A GLN 4.4 3.5 - - - +
41A GLU* 1.3 79.3 - - - +
43A THR* 1.3 68.2 + - - +
44A ILE* 3.3 26.2 - - + -
45A GLY* 2.8 15.5 + - - +
46A SER 4.4 1.4 + - - -
48A LEU* 4.7 4.0 - - + -
56A LEU* 6.3 0.2 - - + -
76A PHE* 4.4 17.0 - - + -
80A LEU* 3.9 32.8 - - + -
3B CYS* 3.8 5.4 - - - -
5B LEU* 4.1 11.4 - - + -
6B ASP* 3.2 26.5 - - - +
200B BME 5.4 0.5 - - - +
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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
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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