Contacts of the helix formed by residues 22 - 35 (chain M) in PDB entry 5KGF
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 THR 22 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20M SER 4.4 2.2 - - - +
21M ASP* 1.3 73.9 - - - +
23M ILE* 1.3 59.2 + - - +
24M GLU* 3.3 18.5 + - - +
25M ASN* 2.8 46.0 + - - +
26M VAL* 2.8 17.2 + - - +
52M ASP 3.4 13.2 - - - +
53M GLY* 4.4 7.4 - - - +
54M ARG 3.3 6.3 - - - +
55M THR* 3.8 16.8 - - + -
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Residues in contact with ILE 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M THR* 1.3 70.7 - - - +
24M GLU* 1.3 63.0 + - - +
26M VAL* 4.2 9.0 - - + -
27M LYS* 3.0 56.7 + - + +
43M LEU* 5.7 1.8 - - + -
50M LEU* 3.7 46.4 - - + -
51M GLU 3.1 26.2 - - - +
52M ASP* 3.2 7.6 + - - +
54M ARG* 2.8 20.6 + - + +
55M THR 5.1 1.3 - - - +
56M LEU* 4.6 20.4 - - + -
59M TYR* 4.9 3.4 - - + -
61M ILE* 5.4 0.7 - - + -
67M LEU* 6.3 1.1 - - + -
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Residues in contact with GLU 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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22M THR* 3.3 18.2 + - - +
23M ILE* 1.3 78.2 - - - +
25M ASN* 1.3 63.7 + - - +
27M LYS* 4.6 1.5 - - - +
28M ALA* 3.3 21.5 + - + +
52M ASP* 3.4 37.5 + - + +
53M GLY* 5.5 1.4 - - - -
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Residues in contact with ASN 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 ASP* 3.8 26.2 + - + +
22M THR* 2.8 31.9 + - - +
24M GLU* 1.3 74.0 - - - +
26M VAL* 1.3 62.6 + - - +
28M ALA* 3.3 7.3 + - - +
29M LYS* 3.0 55.7 + - - +
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Residues in contact with VAL 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ILE* 6.0 2.5 - - + -
15M LEU* 5.1 13.9 - - + -
17M VAL* 4.7 18.2 - - + -
21M ASP* 4.6 9.0 - - + +
22M THR 2.8 24.5 + - - +
23M ILE* 3.1 12.9 + - + +
25M ASN* 1.3 72.2 - - + +
27M LYS* 1.3 66.9 + - + +
29M LYS* 2.8 22.4 + - + +
30M ILE* 2.9 17.4 + - + +
43M LEU* 3.8 24.7 - - + -
56M LEU* 4.4 21.8 - - + -
67M LEU* 6.2 2.0 - - + -
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Residues in contact with LYS 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ILE* 3.0 38.0 + - + +
24M GLU* 4.6 1.6 - - - +
26M VAL* 1.3 77.4 - - - +
28M ALA* 1.3 51.5 + - - +
30M ILE* 2.9 9.8 + - - +
31M GLN* 2.5 37.4 + - - +
38M PRO* 4.3 20.4 - - + -
41M GLN* 3.4 28.1 + - + +
42M ARG* 3.6 35.6 - - - +
43M LEU* 3.8 21.3 - - + +
50M LEU* 4.0 16.7 + - - -
52M ASP* 4.3 10.4 + - - +
72M ARG* 4.9 1.6 - - - +
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Residues in contact with ALA 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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24M GLU 3.3 20.0 + - - +
25M ASN* 3.3 8.3 + - - +
26M VAL 3.2 0.2 - - - -
27M LYS* 1.3 78.2 - - - +
29M LYS* 1.3 51.6 + - + +
31M GLN* 3.1 19.9 + - - +
32M ASP* 2.3 38.0 + - - +
38M PRO* 4.7 3.0 - - + +
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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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15M LEU* 5.9 6.3 - - + -
16M GLU 4.8 15.3 - - - +
17M VAL* 5.0 8.5 - - + -
21M ASP* 5.2 3.8 - - - -
25M ASN* 3.0 51.6 + - - +
26M VAL* 2.8 16.1 + - + +
28M ALA* 1.3 72.3 - - + +
30M ILE* 1.3 54.3 + - + +
32M ASP* 3.1 10.8 - - + +
33M LYS* 2.7 40.6 + - + +
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Residues in contact with ILE 30 (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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5M VAL* 5.0 6.1 - - + -
13M ILE* 3.8 23.8 - - + -
15M LEU* 4.5 10.1 - - + -
26M VAL* 2.9 16.9 + - + +
27M LYS* 2.9 10.1 + - - +
29M LYS* 1.3 74.2 - - - +
31M GLN* 1.3 58.4 + - - +
33M LYS* 4.0 5.2 - - + -
34M GLU* 2.7 51.8 + - + +
35M GLY 3.4 0.2 + - - -
36M ILE* 4.1 2.2 + - + -
41M GLN* 3.3 20.4 - - - +
43M LEU* 3.6 40.8 - - + -
69M LEU* 5.1 13.2 - - + -
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Residues in contact with GLN 31 (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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27M LYS 2.5 16.8 + - - +
28M ALA* 3.2 17.8 - - - +
30M ILE* 1.3 73.9 - - - +
32M ASP* 1.3 58.1 + - - +
35M GLY* 2.8 28.5 + - - +
36M ILE 3.2 25.1 - - - +
37M PRO* 3.7 15.1 - - + +
38M PRO* 3.1 30.9 - - + +
41M GLN* 3.7 1.0 - - - +
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Residues in contact with ASP 32 (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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28M ALA 2.3 28.4 + - - +
29M LYS* 3.0 13.8 + - - +
31M GLN* 1.3 74.2 - - - +
33M LYS* 1.3 65.0 + - - +
35M GLY* 4.0 2.1 + - - -
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Residues in contact with LYS 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LYS* 5.7 2.4 - - - +
13M ILE* 3.3 36.1 - - + +
14M THR* 3.5 24.9 + - - +
15M LEU* 5.1 3.1 - - + -
29M LYS* 2.7 23.8 + - + +
30M ILE* 4.0 4.3 - - - +
32M ASP* 1.3 78.9 - - - +
34M GLU* 1.3 91.6 + - + +
35M GLY 3.7 0.3 + - - -
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Residues in contact with GLU 34 (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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11M LYS* 4.3 24.5 + - - -
13M ILE* 4.3 11.7 - - + -
30M ILE* 2.7 26.6 + - + +
33M LYS* 1.3 110.1 - - + +
35M GLY* 1.3 54.3 + - - +
36M ILE* 2.9 32.3 + - + +
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Residues in contact with GLY 35 (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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30M ILE 3.4 0.2 + - - -
31M GLN* 2.8 22.9 + - - +
32M ASP 4.0 1.9 + - - -
33M LYS 3.4 3.2 + - - -
34M GLU* 1.3 75.4 - - - +
36M ILE* 1.3 58.8 + - - +
37M PRO* 3.3 13.3 - - - +
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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