Contacts of the helix formed by residues 37 - 51 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 4.0 0.6 - - - -
35H VAL* 3.1 25.9 + - - +
36H HIS* 1.3 81.3 - - - +
38H GLU* 1.3 61.1 + - - +
39H GLU* 3.2 19.6 + - - +
40H ALA* 3.2 7.7 + - - +
41H LEU* 3.0 26.7 + - - +
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Residues in contact with GLU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H HIS 4.0 0.4 + - - -
37H SER* 1.3 73.6 + - - +
39H GLU* 1.3 52.9 + - - +
41H LEU* 3.2 18.9 + - + +
42H PHE* 2.8 35.5 + - - +
65H SER 3.3 21.6 - - - +
66H CYS* 3.9 6.3 - - + -
67H THR* 3.3 26.0 + - - +
68H THR* 3.3 44.1 + - + +
71H CYS* 4.5 1.8 - - - -
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Residues in contact with GLU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 4.5 10.0 - - - +
9H GLN* 3.7 32.6 + - - +
37H SER* 3.2 11.9 + - - +
38H GLU* 1.3 74.8 - - - +
40H ALA* 1.3 63.7 + - - +
42H PHE* 3.5 10.6 + - + +
43H LEU* 3.1 24.3 + - - +
68H THR* 5.8 1.7 - - - +
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLN* 5.4 0.9 + - - -
28H ALA* 4.8 2.3 - - - +
31H LEU* 4.0 30.8 - - + +
32H TYR* 3.9 26.4 - - + +
35H VAL* 4.6 6.1 - - + -
37H SER* 3.2 19.8 + - - +
39H GLU* 1.3 76.5 - - - +
41H LEU* 1.3 57.8 + - - +
43H LEU* 3.3 4.8 + - - +
44H LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H TYR* 3.5 26.6 - - + +
37H SER 3.0 8.5 + - - +
38H GLU* 3.2 28.5 + - + +
40H ALA* 1.3 73.4 - - - +
42H PHE* 1.3 57.9 + - - +
44H LEU* 3.2 3.1 + - - +
45H ALA* 2.8 31.4 + - - +
60H LEU* 3.7 33.7 - - + +
61H LEU* 3.7 17.3 - - + -
64H HIS* 3.8 33.7 - - + +
65H SER 4.5 5.6 - - - +
66H CYS* 4.8 8.5 - - + -
71H CYS* 4.8 2.0 - - - -
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Residues in contact with PHE 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 5.5 1.8 - + - -
13H TRP* 4.4 22.0 - + - -
38H GLU 2.8 17.2 + - - +
39H GLU* 3.7 11.4 - - + +
41H LEU* 1.3 73.4 - - - +
43H LEU* 1.3 63.4 + - + +
45H ALA* 3.2 4.6 + - - +
46H THR* 2.9 50.5 + - + -
68H THR* 5.3 1.6 - - - +
70H GLN* 3.4 58.8 - - + -
71H CYS* 3.4 31.2 - - - -
74H LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLN* 3.7 37.0 - - + +
12H ILE* 3.2 50.7 - - + -
13H TRP* 4.2 19.3 - - + +
16H LEU* 5.4 3.8 - - + -
28H ALA* 4.2 1.8 - - + -
31H LEU* 4.1 10.3 - - + -
39H GLU 3.1 14.5 + - - +
40H ALA 3.5 5.4 - - - +
42H PHE* 1.3 85.2 - - + +
44H LEU* 1.3 63.7 + - - +
46H THR* 3.3 9.8 + - - -
47H CYS* 3.1 23.4 + - - -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F TYR* 5.0 3.1 - - - +
25H VAL* 3.9 8.3 - - + +
28H ALA* 3.9 18.8 - - + +
29H GLU* 3.7 34.1 - - + +
32H TYR* 3.8 32.3 - - + -
40H ALA 2.8 16.7 + - - +
41H LEU 3.2 4.9 + - - +
43H LEU* 1.3 77.2 - - - +
45H ALA* 1.3 62.5 + - - +
47H CYS* 3.0 14.8 + - + +
48H TYR* 3.2 35.7 + - + +
60H LEU* 3.5 23.1 - - + -
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LEU 2.8 13.9 + - - +
42H PHE* 3.7 4.7 - - - +
44H LEU* 1.3 72.6 - - - +
46H THR* 1.3 57.1 + - - +
48H TYR* 3.2 2.5 + - - -
49H TYR* 2.9 24.4 + - - +
57H ALA* 3.2 19.0 - - + +
60H LEU* 3.7 11.8 - - + +
61H LEU* 3.3 48.0 - - + -
74H LEU* 4.1 4.0 - - + -
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Residues in contact with THR 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.4 18.4 - - - +
13H TRP* 4.6 9.6 - - + -
16H LEU* 3.6 24.9 - - + -
42H PHE* 2.9 36.0 + - + -
43H LEU* 3.3 12.1 - - - -
45H ALA* 1.3 77.7 - - - +
47H CYS* 1.3 53.8 + - - +
49H TYR* 3.1 4.0 + - - +
50H ARG* 2.8 46.7 + - + +
74H LEU* 3.4 20.4 - - - +
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Residues in contact with CYS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 3.8 11.7 - - - -
16H LEU* 3.7 29.2 - - + -
21H TYR* 4.6 1.2 - - - -
24H ALA 3.5 22.4 - - - -
25H VAL* 3.6 20.2 - - + -
28H ALA* 3.7 10.8 - - + -
43H LEU* 3.1 15.5 + - - -
44H LEU* 3.0 11.3 + - + +
46H THR* 1.3 79.9 - - - +
48H TYR* 1.3 57.0 + - - +
50H ARG* 3.4 2.1 + - - +
51H SER* 2.6 34.1 + - - -
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Residues in contact with TYR 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529F GLU* 4.6 1.6 + - - -
531F TYR* 3.6 23.3 + + - -
532F ARG* 4.9 3.9 + - - -
25H VAL* 3.5 26.8 - - + +
29H GLU* 4.0 21.1 + - - +
44H LEU* 3.2 38.4 + - + +
45H ALA* 3.2 5.8 + - - +
47H CYS* 1.3 76.5 - - - +
49H TYR* 1.3 66.4 + - - +
51H SER* 3.2 10.1 + - - -
53H LYS* 3.0 42.5 + - + +
56H LYS* 3.4 40.4 - - + +
57H ALA 3.8 6.3 - - - +
60H LEU* 3.7 23.3 - - + -
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.6 49.0 - + + +
21F TYR* 5.1 5.1 - + - -
45H ALA 2.9 14.0 + - - +
46H THR* 3.1 8.9 + - - +
48H TYR* 1.3 77.1 - - - +
50H ARG* 1.3 58.9 + - - +
52H GLY* 3.0 19.2 + - - -
53H LYS 4.2 3.4 - - - -
54H ALA* 4.3 9.0 + - + +
57H ALA* 3.8 4.4 - - + +
74H LEU* 4.0 13.2 - - + -
77H LYS* 3.3 34.1 + - + +
78H CYS* 3.5 37.7 - - - -
81H ASP* 3.8 23.5 + - - -
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Residues in contact with ARG 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ASN* 4.0 21.4 + - - +
19F TYR* 3.1 37.2 + - + -
21F TYR* 5.0 4.3 - - - -
50F ARG* 4.2 34.2 - - - +
13H TRP* 3.7 25.3 - - - -
16H LEU* 3.4 38.8 + - + +
17H ASN* 4.5 3.6 + - - -
21H TYR* 3.5 38.8 + - + -
46H THR* 2.8 30.2 + - + +
47H CYS 3.9 2.7 - - - +
49H TYR* 1.3 69.0 - - - +
51H SER* 1.3 57.6 + - - +
52H GLY* 3.0 9.8 + - - -
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Residues in contact with SER 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TYR* 3.3 34.8 - - - +
25H VAL* 3.6 11.7 - - - +
47H CYS 2.6 21.8 + - - -
48H TYR* 3.4 11.4 - - - -
49H TYR 3.2 0.4 - - - -
50H ARG* 1.3 75.5 - - - +
52H GLY* 1.3 55.2 + - - +
53H LYS* 3.1 27.3 + - - +
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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