Contacts of the helix formed by residues 16 - 29 (chain M) in PDB entry 6K4Y
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 ASN 16 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M ILE* 3.7 7.2 - - - -
15M LEU* 1.3 77.7 - - - +
17M GLU* 1.3 69.2 + - - +
18M LYS* 3.1 33.5 - - - +
19M THR* 3.2 23.9 + - - +
20M ALA* 3.0 26.7 + - - +
52M ASN* 3.9 6.2 + - - +
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Residues in contact with GLU 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 4.2 18.3 - - + +
8M ILE* 3.7 19.8 - - + +
16M ASN* 1.3 80.4 - - - +
18M LYS* 1.3 62.2 + - + +
20M ALA* 3.4 8.1 - - - +
21M THR* 3.0 32.1 + - - +
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Residues in contact with LYS 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M ASN* 3.1 32.8 - - - +
17M GLU* 1.3 79.1 + - + +
19M THR* 1.3 58.0 + - - +
21M THR* 3.3 5.7 + - - +
22M ILE* 2.9 35.3 + - - +
44M LEU* 3.7 35.9 - - + -
48M VAL* 3.9 14.6 - - + -
52M ASN* 3.4 20.2 - - - +
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Residues in contact with THR 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 3.7 30.0 - - + +
16M ASN* 3.2 22.6 + - - +
18M LYS* 1.3 75.5 - - - +
20M ALA* 1.3 61.7 + - - +
22M ILE* 4.0 8.1 - - - -
23M LEU* 2.9 29.7 + - - +
52M ASN* 3.6 24.0 + - - +
55M VAL* 5.0 6.7 - - + +
56M LEU* 3.3 30.3 - - - +
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Residues in contact with ALA 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 3.7 24.0 - - + -
7M ILE* 4.0 19.9 - - + +
8M ILE* 4.0 7.0 - - + -
15M LEU* 5.0 2.0 - - - -
16M ASN 3.0 19.6 + - - +
17M GLU* 3.4 9.9 - - - +
18M LYS 3.1 0.2 - - - -
19M THR* 1.3 77.0 - - - +
21M THR* 1.3 58.8 + - - +
23M LEU* 3.1 7.3 + - - +
24M ILE* 2.9 32.0 + - - +
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Residues in contact with THR 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 4.4 8.5 - - - +
17M GLU 3.0 13.2 + - - +
18M LYS* 3.3 13.7 - - - +
20M ALA* 1.3 73.9 - - - +
22M ILE* 1.3 63.0 + - - +
24M ILE* 3.3 13.3 + - - +
25M THR* 2.9 30.5 + - - -
41M HIS* 3.4 24.6 + - + +
43M ASP* 6.1 0.4 - - - +
44M LEU* 5.4 0.9 - - + -
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Residues in contact with ILE 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LYS 2.9 17.3 + - - +
19M THR* 4.0 6.5 - - - -
21M THR* 1.3 76.4 - - - +
23M LEU* 1.3 57.1 + - - +
25M THR* 3.0 2.6 + - - -
26M ILE* 2.8 44.2 + - + +
37M VAL* 3.8 16.8 - - + -
41M HIS* 3.4 27.1 - - + +
44M LEU* 3.8 12.3 - - + -
49M VAL* 4.1 17.7 - - + -
52M ASN* 3.4 36.1 - - + +
53M ILE* 4.4 11.9 - - + -
56M LEU* 4.8 4.3 - - + -
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M ILE* 4.2 15.9 - - + -
15M LEU* 3.9 25.6 - - + -
19M THR 2.9 21.0 + - - +
20M ALA 3.1 5.4 + - - +
22M ILE* 1.3 74.5 - - - +
24M ILE* 1.3 59.7 + - - +
26M ILE* 4.4 2.7 - - + +
27M ALA* 2.9 30.7 + - - +
56M LEU* 3.8 27.1 - - + -
61M LEU* 5.5 2.7 - - + -
62M VAL* 3.9 4.9 - - + -
71M ILE* 3.8 25.6 - - + -
75M ALA* 5.0 13.0 - - + +
78M ILE* 5.6 6.7 - - + -
79M ILE* 4.4 18.2 - - + -
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Residues in contact with ILE 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610F PHE* 3.9 39.0 - - + +
611F LEU* 5.4 0.2 - - - +
3M LYS 6.3 0.2 - - - -
4M VAL* 5.1 5.4 - - + -
7M ILE* 3.7 33.0 - - + -
20M ALA 2.9 19.6 + - - +
21M THR* 3.4 15.7 - - - +
22M ILE 3.3 0.2 - - - -
23M LEU* 1.3 74.9 - - - +
25M THR* 1.3 51.3 + - - +
27M ALA* 3.8 2.4 - - + -
28M LYS* 2.6 46.7 + - + +
79M ILE* 4.5 11.9 - - + -
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Residues in contact with THR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M THR* 2.9 15.6 + - - -
22M ILE 3.0 8.5 + - - -
24M ILE* 1.3 79.6 - - - +
26M ILE* 1.3 60.9 + - - +
28M LYS* 3.1 33.3 + - - +
29M LYS* 3.3 14.0 + - - +
32M ILE* 4.6 12.9 - - + +
36M GLU 5.2 0.2 - - - +
37M VAL* 4.2 20.6 - - + -
40M VAL* 3.8 21.5 - - + +
41M HIS* 3.1 16.7 + - + -
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Residues in contact with ILE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ILE* 2.8 37.4 + - + +
23M LEU* 4.0 3.8 - - - +
25M THR* 1.3 76.2 - - - +
27M ALA* 1.3 59.4 + - - +
29M LYS 2.9 24.9 - - - +
30M ASP* 4.5 3.5 - - - +
32M ILE* 4.8 5.2 - - + -
37M VAL* 4.8 13.0 - - + -
53M ILE* 4.7 11.2 - - + -
56M LEU* 4.0 9.9 - - + -
62M VAL* 3.7 47.3 - - + -
69M LEU* 3.7 28.6 - - + +
70M ILE* 3.8 10.6 - - - +
71M ILE* 4.0 4.0 - - + -
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Residues in contact with ALA 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593F LYS* 4.8 5.9 + - - +
611F LEU* 4.0 9.8 - - + +
23M LEU* 2.9 17.9 + - + +
24M ILE* 3.8 3.8 - - + +
26M ILE* 1.3 77.1 - - - +
28M LYS* 1.3 60.4 + - - +
29M LYS 4.9 0.7 - - - -
30M ASP* 4.5 9.2 - - - +
70M ILE* 5.8 1.1 - - - -
71M ILE* 4.0 31.6 - - + +
76M GLN* 5.6 2.0 - - - +
79M ILE* 4.6 18.6 - - + -
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Residues in contact with LYS 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610F PHE 4.7 2.9 - - - +
611F LEU* 3.7 46.0 - - + +
24M ILE* 2.6 25.7 + - + +
25M THR* 3.3 39.7 + - - +
26M ILE 3.1 0.6 - - - -
27M ALA* 1.3 82.0 - - - +
29M LYS* 1.3 61.6 + - + +
30M ASP* 5.3 0.8 - - - +
32M ILE* 5.9 1.6 - - - +
40M VAL* 5.2 5.7 - - - +
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Residues in contact with LYS 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M THR 3.3 3.7 + - - +
26M ILE 2.9 17.1 - - - +
28M LYS* 1.3 84.8 - - + +
30M ASP* 1.3 74.7 + - - +
31M PHE 3.5 1.7 + - - -
32M ILE* 3.8 45.8 + - + +
69M LEU 4.6 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
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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