Contacts of the helix formed by residues 37 - 51 (chain F) in PDB entry 5G04
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 37 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F TYR* 4.0 0.6 - - - -
35F VAL* 3.1 26.0 + - - +
36F HIS* 1.3 81.6 - - - +
38F GLU* 1.3 60.7 + - - +
39F GLU* 3.2 19.9 + - - +
40F ALA* 3.2 7.8 + - - +
41F LEU* 3.0 25.9 + - - +
66X ASN 5.6 0.2 - - - -
268Y ARG* 5.5 2.7 - - - +
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F HIS 4.0 0.4 + - - -
37F SER* 1.3 73.4 + - - +
39F GLU* 1.3 52.4 + - - +
41F LEU* 3.2 19.1 + - + +
42F PHE* 2.8 35.4 + - - +
65F SER 3.3 17.7 - - - +
66F CYS* 3.9 4.7 - - + -
67F THR* 3.3 21.2 + - - +
68F THR* 3.2 45.9 + - + +
71F CYS* 4.3 2.4 - - - -
268Y ARG* 3.1 44.7 + - - +
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLU* 5.1 5.6 - - - +
9F GLN* 3.7 30.7 + - - +
37F SER* 3.2 11.5 + - - +
38F GLU* 1.3 74.8 - - - +
40F ALA* 1.3 63.6 + - - +
42F PHE* 3.5 11.8 + - + +
43F LEU* 3.1 24.1 + - - +
68F THR* 5.7 1.9 - - - +
70F GLN* 5.8 3.4 - - - +
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLN* 5.4 1.1 + - - -
28F ALA* 4.8 2.3 - - - +
31F LEU* 4.0 31.0 - - + +
32F TYR* 3.9 26.3 - - + +
35F VAL* 4.5 6.3 - - + -
37F SER* 3.2 21.1 + - - +
39F GLU* 1.3 77.4 - - - +
41F LEU* 1.3 57.5 + - - +
43F LEU* 3.3 4.0 + - - +
44F LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 3.5 28.0 - - + +
37F SER 3.0 8.9 + - - +
38F GLU* 3.3 26.5 - - + +
40F ALA* 1.3 73.8 - - - +
42F PHE* 1.3 56.3 + - - +
44F LEU* 3.2 3.3 + - - +
45F ALA* 2.8 31.7 + - - +
60F LEU* 3.7 37.0 - - + +
61F LEU* 4.1 21.1 - - + -
64F HIS* 3.7 33.0 - - + +
65F SER 4.6 4.7 - - - +
66F CYS* 4.8 3.1 - - + -
71F CYS* 4.7 0.9 - - - -
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Residues in contact with PHE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F TRP* 4.5 20.0 - + - -
38F GLU 2.8 16.8 + - - +
39F GLU* 3.7 12.6 - - + +
41F LEU* 1.3 73.2 - - - +
43F LEU* 1.3 62.5 + - + +
45F ALA* 3.2 4.8 + - - +
46F THR* 2.9 45.0 + - + -
61F LEU* 5.6 0.4 - - + -
68F THR* 5.4 0.7 - - - +
70F GLN* 3.6 49.4 - - + -
71F CYS* 3.4 31.2 - - - -
73F TYR* 6.5 0.2 - + - -
74F LEU* 3.7 24.0 - - + -
19H TYR* 5.6 3.1 - + - -
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLN* 3.7 37.2 - - + +
12F ILE* 3.2 49.8 - - + -
13F TRP* 4.1 22.2 - - + +
16F LEU* 5.3 4.3 - - + -
28F ALA* 4.2 1.6 - - + -
31F LEU* 4.1 10.5 - - + -
39F GLU 3.1 13.9 + - - +
40F ALA 3.5 5.2 - - - +
42F PHE* 1.3 84.5 - - + +
44F LEU* 1.3 63.0 + - - +
46F THR* 3.3 8.9 + - - -
47F CYS* 3.1 23.7 + - - -
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 3.9 9.0 - - + +
28F ALA* 3.9 17.9 - - + +
29F GLU* 3.7 34.3 - - + +
32F TYR* 3.8 31.6 - - + -
40F ALA 2.9 16.4 + - - +
41F LEU 3.7 4.5 - - - +
43F LEU* 1.3 78.1 - - - +
45F ALA* 1.3 62.2 + - - +
47F CYS* 3.0 14.5 + - + +
48F TYR* 3.2 35.3 + - + +
60F LEU* 3.5 24.5 - - + -
531H TYR* 4.8 3.1 - - - +
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU 2.8 19.9 + - - +
42F PHE 3.7 4.3 - - - +
44F LEU* 1.3 71.7 - - - +
46F THR* 1.3 57.8 - - - +
48F TYR* 3.2 2.3 + - - -
49F TYR* 2.9 24.3 + - - +
57F ALA* 3.2 20.6 - - + +
60F LEU* 3.7 15.8 - - + +
61F LEU* 3.4 38.6 - - + -
74F LEU* 4.2 4.0 - - + -
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TRP* 4.5 9.6 - - + -
16F LEU* 3.6 25.1 - - + -
42F PHE* 2.9 36.6 + - + -
43F LEU* 3.3 11.7 - - - -
44F LEU 3.1 0.2 - - - -
45F ALA* 1.3 78.4 - - - +
47F CYS* 1.3 53.3 + - - +
49F TYR* 3.1 3.0 + - - +
50F ARG* 2.8 47.1 + - + +
74F LEU* 3.4 19.7 - - - +
19H TYR* 3.1 21.5 - - - +
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Residues in contact with CYS 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 3.8 11.2 - - - -
16F LEU* 3.7 28.3 - - + -
21F TYR* 4.6 1.2 - - - -
24F ALA 3.6 22.4 - - - -
25F VAL* 3.6 20.6 - - + -
28F ALA* 3.7 10.5 - - + -
43F LEU* 3.1 15.9 + - - -
44F LEU* 3.0 11.5 + - + +
46F THR* 1.3 79.5 - - - +
48F TYR* 1.3 55.7 + - - +
50F ARG* 3.4 2.4 + - - +
51F SER* 2.6 34.5 + - - -
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Residues in contact with TYR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 3.6 24.7 - - + -
29F GLU* 4.0 21.8 + - - +
44F LEU* 3.2 37.1 + - + +
45F ALA* 3.6 5.8 - - - +
47F CYS* 1.3 75.3 - - - +
49F TYR* 1.3 67.6 + - - +
51F SER* 3.2 10.7 + - - -
53F LYS* 3.0 42.1 + - + +
56F LYS* 3.4 36.5 - - + +
57F ALA 3.8 6.7 - - - +
60F LEU* 3.6 23.1 - - + -
529H GLU* 4.4 2.6 + - - -
531H TYR* 3.6 26.3 - + - -
532H ARG* 4.6 4.8 + - - -
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Residues in contact with TYR 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA 2.9 14.0 + - - +
46F THR* 3.1 9.4 + - - +
48F TYR* 1.3 77.2 - - - +
50F ARG* 1.3 56.2 + - - +
52F GLY* 3.1 19.8 + - - -
53F LYS 4.2 2.9 - - - -
54F ALA* 4.2 9.6 - - + +
57F ALA* 3.8 5.8 - - + +
74F LEU* 4.1 10.8 - - + -
77F LYS* 3.3 37.2 + - + +
78F CYS* 3.5 33.7 - - - -
81F ASP* 3.8 25.9 + - - -
19H TYR* 3.3 48.8 - + + +
21H TYR* 5.0 5.0 - + - -
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Residues in contact with ARG 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TRP* 3.7 25.9 - - - -
16F LEU* 3.4 39.1 + - + +
17F ASN* 4.4 2.6 + - - -
21F TYR* 3.5 40.0 + - + +
46F THR* 2.8 28.0 + - + +
47F CYS 3.9 2.9 - - - +
49F TYR* 1.3 68.6 - - - +
51F SER* 1.3 57.6 + - - +
52F GLY* 3.0 9.8 + - - -
17H ASN* 4.0 22.6 + - - +
19H TYR* 3.1 39.0 + - + -
21H TYR* 5.1 2.7 - - - -
50H ARG* 4.2 36.1 - - - +
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Residues in contact with SER 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TYR* 3.3 36.1 - - - +
25F VAL* 3.6 11.6 - - - +
47F CYS 2.6 22.8 + - - -
48F TYR* 3.4 11.0 - - - -
49F TYR 3.2 0.4 - - - -
50F ARG* 1.3 74.4 - - - +
52F GLY* 1.3 55.9 + - - +
53F LYS* 3.1 24.0 + - - +
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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
------------------------------------------------------------
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