Contacts of the helix formed by residues 52 - 65 (chain M) in PDB entry 4FAO
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 52 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50M THR 3.2 1.1 + - - +
51M PRO* 1.3 77.1 - - - +
53M LYS* 1.3 65.6 + - - +
54M HIS* 3.3 6.4 + - - +
55M ALA* 2.9 26.2 + - - +
56M ILE* 3.1 22.0 + - - +
109M CYS 4.0 0.2 + - - -
110M ARG* 3.4 37.8 + - - +
79N LEU* 3.8 25.8 - - + +
101N GLY* 5.7 0.7 - - - -
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Residues in contact with LYS 53 (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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52M THR* 1.3 71.5 - - - +
54M HIS* 1.3 65.1 + - - +
56M ILE* 2.9 22.6 + - + +
57M VAL* 2.9 17.6 + - + +
22N TRP* 6.0 2.9 - - + -
99N TYR* 3.8 28.9 - - + +
100N GLU 3.6 17.3 - - - +
101N GLY* 3.2 14.8 + - - +
102N MET* 4.0 18.2 - - - -
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Residues in contact with HIS 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M THR* 3.1 7.1 - - - +
53M LYS* 1.3 75.0 - - - +
55M ALA* 1.3 64.1 + - - +
57M VAL* 2.9 8.6 + - + +
58M GLN* 2.8 57.6 + - + +
110M ARG 4.2 9.0 + - - +
13N LEU* 5.2 1.1 - - + +
32N TYR* 5.2 0.4 - - - -
34N ALA* 4.0 10.4 - - + +
35N TYR 2.9 25.5 + - - -
36N GLU* 5.1 0.4 - - - -
37N CYS 5.8 0.2 - - - -
76N PRO* 4.4 7.0 - - + +
79N LEU* 4.2 15.0 - - + -
101N GLY 2.8 18.8 + - - +
102N MET* 3.5 26.2 - - - +
103N SER* 4.2 1.1 - - - -
104N VAL* 3.4 20.9 - - + +
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Residues in contact with ALA 55 (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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45M LEU* 4.4 8.1 - - + -
51M PRO* 4.6 2.9 - - + -
52M THR* 2.9 25.4 + - - +
54M HIS* 1.3 77.7 + - - +
56M ILE* 1.3 64.7 + - - +
58M GLN* 3.9 3.0 - - - +
59M THR* 2.8 27.8 + - - -
72M ALA* 4.3 10.3 - - + +
109M CYS 3.8 22.9 - - - +
110M ARG* 3.9 17.4 + - - +
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Residues in contact with ILE 56 (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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43M PHE* 4.5 19.1 - - + -
45M LEU* 4.1 20.1 - - + +
51M PRO* 4.1 24.0 - - + +
52M THR 3.1 15.3 + - - +
53M LYS* 2.9 18.2 + - + +
55M ALA* 1.3 74.1 - - - +
57M VAL* 1.3 68.5 + - + +
59M THR* 3.1 3.8 + - - -
60M LEU* 3.0 30.6 + - + +
22N TRP* 4.8 12.6 - - + -
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Residues in contact with VAL 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M LYS* 2.9 14.6 + - + +
54M HIS* 2.9 10.5 + - + +
56M ILE* 1.3 77.7 - - + +
58M GLN* 1.3 65.1 + - - +
60M LEU* 2.9 18.7 + - - +
61M VAL* 2.9 13.5 + - + +
15N VAL* 4.0 32.3 - - + -
17N PHE* 5.8 0.2 - - + -
20N ILE* 4.2 7.2 - - + -
22N TRP* 3.9 30.7 - - + -
32N TYR* 3.9 16.2 - - + +
34N ALA* 5.4 2.0 - - + -
102N MET* 4.2 20.2 - - + -
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Residues in contact with GLN 58 (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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54M HIS* 2.8 48.4 + - + +
55M ALA* 3.9 4.3 - - - +
57M VAL* 1.3 74.3 - - - +
59M THR* 1.3 67.0 + - - +
61M VAL* 3.0 9.2 + - - +
62M HIS* 2.8 22.1 + - - +
69M VAL* 4.0 8.7 - - + -
70M GLY* 3.0 27.4 + - - +
71M LYS 3.7 13.4 + - - -
72M ALA* 4.7 5.6 - - + +
110M ARG* 5.0 4.7 + - - +
13N LEU* 4.8 8.7 - - + +
35N TYR 4.4 3.5 - - - +
36N GLU* 4.3 25.6 + - - +
37N CYS 5.0 4.1 + - - +
76N PRO* 5.4 1.7 - - - +
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Residues in contact with THR 59 (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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41M CYS 4.2 10.8 + - - +
43M PHE* 3.4 44.9 - - + +
45M LEU* 4.1 13.3 - - + +
55M ALA 2.8 22.6 + - - -
56M ILE* 3.3 4.9 - - - +
58M GLN* 1.3 73.9 - - - +
60M LEU* 1.3 58.6 + - - +
62M HIS* 3.3 10.9 + - - +
63M LEU* 2.9 30.5 + - + +
71M LYS* 5.0 1.7 - - - +
72M ALA* 4.1 19.5 + - - +
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Residues in contact with LEU 60 (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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43M PHE* 3.6 37.0 - - + -
56M ILE* 3.0 19.1 + - + +
57M VAL* 2.9 12.6 + - - +
59M THR* 1.3 67.7 - - - +
61M VAL* 1.3 67.2 + - - +
63M LEU* 2.8 32.6 + - + +
64M LYS* 3.1 10.6 + - - +
20N ILE* 3.7 28.0 - - + +
22N TRP* 4.0 35.2 - - + +
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Residues in contact with VAL 61 (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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57M VAL* 2.9 18.9 + - + +
58M GLN* 3.4 8.3 - - - +
60M LEU* 1.3 75.2 - - - +
62M HIS* 1.3 51.6 + - - +
64M LYS* 2.9 5.5 + - - +
65M PHE* 2.8 49.5 + - + +
69M VAL* 3.8 26.5 - - + -
13N LEU* 4.8 9.4 - - + -
15N VAL* 4.0 31.9 - - + -
19N ASP* 6.3 1.8 - - + -
20N ILE* 3.8 19.5 - - + -
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Residues in contact with HIS 62 (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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58M GLN 2.8 14.7 + - - +
59M THR* 3.3 14.0 + - - +
61M VAL* 1.3 70.6 - - - +
63M LEU* 1.3 80.2 + - + +
65M PHE 4.1 0.7 - - - +
66M PRO* 3.0 47.0 + - + +
69M VAL* 2.8 42.0 - - + +
70M GLY* 3.7 7.6 - - - +
71M LYS* 3.4 54.4 + - + +
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Residues in contact with LEU 63 (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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43M PHE* 4.2 26.7 - - + -
59M THR* 2.9 20.1 + - + +
60M LEU* 2.8 37.9 + - + +
62M HIS* 1.3 83.7 + - + +
64M LYS* 1.3 56.0 + - - +
66M PRO* 3.7 11.4 - - - +
71M LYS* 6.2 0.2 - - - +
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Residues in contact with LYS 64 (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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60M LEU 3.1 7.3 + - - +
61M VAL* 2.9 7.0 + - - +
63M LEU* 1.3 75.7 - - - +
65M PHE* 1.3 92.8 + - + +
66M PRO* 3.3 11.0 - - - +
18N GLU 4.9 1.4 + - - -
19N ASP* 3.4 47.1 + - + +
20N ILE* 5.8 0.9 - - + -
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Residues in contact with PHE 65 (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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61M VAL* 2.8 34.9 + - + +
62M HIS 3.1 3.3 + - - -
64M LYS* 1.3 112.1 - - + +
66M PRO* 1.3 54.5 - - - +
67M THR* 2.7 18.1 + - - +
68M LYS* 2.9 27.3 + - + -
69M VAL* 3.0 18.8 + - + +
19N ASP* 4.0 25.6 - - + -
20N ILE* 6.5 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