Contacts of the helix formed by residues 23 - 38 (chain A) in PDB entry 1MK0
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 ASP 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 28.2 - - + -
2A LYS* 3.1 26.9 + - - +
21A ALA* 3.8 2.9 - - - -
22A LYS* 1.3 82.2 - - + +
24A PHE* 1.3 65.9 + - - +
25A GLU* 3.6 8.6 + - - +
26A LYS* 3.0 46.9 + - + +
27A ARG* 3.0 22.7 + - - +
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 2.9 43.3 + - + -
3A SER 3.3 18.2 - - - -
4A GLY* 3.4 42.6 - - - -
5A ILE 3.6 9.9 - - - -
6A TYR* 3.7 28.0 - + + -
21A ALA* 4.0 6.7 - - + +
23A ASP* 1.3 72.1 + - - +
25A GLU* 1.3 65.9 + - - +
27A ARG* 3.1 2.6 + - - +
28A TRP* 2.9 47.0 + + + +
60A ILE* 3.5 42.0 - - + -
62A GLU 3.9 0.2 - - - -
63A GLU* 4.5 3.8 - - + -
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Residues in contact with GLU 25 (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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2A LYS* 5.2 6.9 - - + +
23A ASP* 3.5 10.7 + - - +
24A PHE* 1.3 77.5 - - - +
26A LYS* 1.3 64.4 + - + +
28A TRP* 3.5 27.9 + - - +
29A LYS* 3.1 45.6 + - - +
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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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1A MET* 4.3 21.7 - - + +
23A ASP* 3.0 29.8 + - + +
25A GLU* 1.3 74.3 - - + +
27A ARG* 1.3 66.6 + - - +
29A LYS* 3.3 12.6 + - + +
30A ARG* 3.0 23.4 + - - +
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Residues in contact with ARG 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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6A TYR* 3.6 20.2 - - + +
17A TYR* 5.0 0.4 + - - -
20A SER 4.4 5.1 + - - -
21A ALA* 3.5 20.2 - - + +
23A ASP 3.0 19.0 + - - +
24A PHE 3.1 3.3 + - - +
26A LYS* 1.3 76.9 - - - +
28A TRP* 1.3 63.7 + - - +
30A ARG* 3.2 56.7 + - - +
31A HIS* 3.0 54.2 + - + +
34A ASP* 5.2 2.6 + - - -
40A HIS* 5.3 0.4 + - - -
41A SER* 5.5 2.6 + - - -
300A CIT 3.1 39.8 + - - -
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Residues in contact with TRP 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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6A TYR* 3.3 55.6 - + + -
8A ILE* 4.5 1.3 - - + -
24A PHE* 2.9 45.4 + + + +
25A GLU* 3.8 31.4 - - - +
27A ARG* 1.3 76.6 - - + +
29A LYS* 1.3 65.2 + - + +
31A HIS* 3.2 15.9 + + - +
32A PHE* 3.1 25.8 + - + -
58A CYS* 3.5 54.1 - - + +
59A SER* 4.0 9.6 - - - -
60A ILE* 4.1 14.6 - - + -
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Residues in contact with LYS 29 (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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25A GLU* 3.1 37.1 + - + +
26A LYS* 3.6 15.7 - - + +
28A TRP* 1.3 75.0 - - + +
30A ARG* 1.3 63.2 + - - +
32A PHE* 3.4 8.0 + - - +
33A LYS* 3.1 38.5 + - - +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LYS 3.0 13.4 + - - +
27A ARG* 3.2 56.0 + - - +
29A LYS* 1.3 75.3 - - - +
31A HIS* 1.3 64.3 + - - +
33A LYS* 3.3 9.4 + - + +
34A ASP* 2.9 41.3 + - - +
300A CIT 4.6 6.9 + - - -
401A BME 5.6 3.1 - - - -
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Residues in contact with HIS 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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6A TYR* 2.7 27.3 + + - -
8A ILE* 3.6 25.7 - - + +
17A TYR* 3.6 15.5 - + - -
27A ARG* 3.0 57.1 + - + +
28A TRP* 3.2 10.1 + - - +
30A ARG* 1.3 75.9 - - - +
32A PHE* 1.3 61.9 + - + +
34A ASP* 3.3 4.9 + - - +
35A LEU* 2.9 37.7 + - + +
40A HIS* 2.8 32.3 + + + +
45A LEU* 4.8 0.6 - - + +
300A CIT 3.3 11.2 - - - -
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Residues in contact with PHE 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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8A ILE* 4.4 9.2 - - + -
28A TRP* 3.1 26.9 + - + -
29A LYS* 4.0 6.3 - - - +
30A ARG 3.3 0.4 - - - -
31A HIS* 1.3 76.2 - - + +
33A LYS* 1.3 65.7 + - - +
35A LEU* 3.8 21.3 - - + +
36A GLU* 3.0 38.7 + - - +
45A LEU* 6.3 0.2 - - + -
49A PHE* 4.3 9.0 - + + -
54A ASN* 3.5 44.4 - - + +
56A PHE* 4.1 21.8 - + + -
58A CYS* 3.9 29.4 - - - -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.1 33.0 + - + +
30A ARG* 3.7 8.7 - - + +
32A PHE* 1.3 75.7 - - - +
34A ASP* 1.3 66.7 + - - +
36A GLU* 3.4 10.4 + - - +
37A LYS* 3.1 34.0 + - - +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 5.2 2.8 + - - -
30A ARG* 2.9 40.3 + - - +
31A HIS* 3.5 5.6 - - - +
33A LYS* 1.3 76.7 - - - +
35A LEU* 1.3 64.7 + - - +
37A LYS* 3.1 8.9 + - - +
38A GLY 3.0 17.3 + - - -
39A CYS 3.3 10.7 + - - -
40A HIS* 4.1 20.4 - - + -
41A SER 5.7 0.3 + - - -
401A BME 2.7 47.5 - - - +
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Residues in contact with LEU 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 HIS* 2.9 23.2 + - + +
32A PHE* 3.8 23.3 - - + +
33A LYS 3.4 0.2 - - - -
34A ASP* 1.3 75.5 - - - +
36A GLU* 1.3 61.9 + - - +
38A GLY* 3.1 4.5 + - - -
40A HIS* 3.5 28.0 - - + -
45A LEU* 3.9 24.9 - - + +
46A GLN* 2.9 51.0 + - - +
49A PHE* 3.6 44.1 - - + -
50A ASN* 4.6 0.7 - - - +
56A PHE* 5.3 0.9 - - + -
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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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32A PHE* 3.0 30.9 + - - +
33A LYS* 3.7 8.9 - - - +
34A ASP 3.2 0.2 - - - -
35A LEU* 1.3 76.7 - - - +
37A LYS* 1.3 60.9 + - + +
38A GLY* 3.1 1.3 + - - -
49A PHE* 3.7 23.3 - - + -
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Residues in contact with LYS 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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33A LYS* 3.1 25.9 + - + +
34A ASP* 3.1 15.3 + - - +
36A GLU* 1.3 76.8 - - + +
38A GLY* 1.3 62.0 + - - +
39A CYS* 3.4 17.0 + - - +
401A BME 3.3 26.4 + - - +
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Residues in contact with GLY 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 ASP 3.0 3.6 + - - -
35A LEU 3.1 9.5 + - - -
36A GLU 3.1 1.6 - - - -
37A LYS* 1.3 79.4 - - - +
39A CYS* 1.3 58.1 + - - +
40A HIS 4.0 0.2 + - - -
46A GLN* 3.2 29.9 - - - +
50A ASN* 5.4 0.7 - - - -
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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