Contacts of the helix formed by residues 20 - 36 (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 ALA 20 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F TYR* 5.1 2.5 - - - +
77F LYS* 5.4 0.4 - - - +
116F PHE* 4.5 15.9 - - + -
150F SER* 5.4 0.7 - - - +
15H ALA 2.9 11.6 + - - +
18H HIS 4.4 4.0 - - - +
19H TYR* 1.3 76.5 - - - +
21H TYR* 1.3 63.5 + - - +
22H ARG 3.5 1.3 - - - -
23H ASP* 2.8 38.1 - - - +
24H ALA* 3.0 10.8 + - - +
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Residues in contact with TYR 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F TYR* 5.0 4.6 - + - -
50F ARG* 5.1 2.9 + - - -
77F LYS* 6.1 0.2 - - - -
16H LEU* 4.1 25.2 + - + -
19H TYR* 3.2 52.7 + + + -
20H ALA* 1.3 70.9 - - - +
22H ARG* 1.3 60.0 + - + +
24H ALA* 2.9 2.7 + - - -
25H VAL* 2.6 39.9 + - - +
50H ARG* 3.5 41.0 + - + +
51H SER* 3.3 33.2 - - - +
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F SER* 4.9 10.3 - - - -
153F GLU* 4.3 25.3 + - - +
473F TYR* 6.0 0.2 + - - -
500F TRP* 5.7 4.0 - - - +
532F ARG* 5.7 1.2 - - - +
534F GLU* 4.2 32.8 + - - +
20H ALA 3.5 0.2 - - - -
21H TYR* 1.3 78.4 - - + +
23H ASP* 1.3 63.1 + - - +
25H VAL* 3.5 4.6 + - - +
26H PHE* 3.1 25.1 + - - +
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Residues in contact with ASP 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 4.8 0.3 - - - -
119F SER* 5.1 1.2 + - - -
148F LEU* 4.1 18.6 - - + +
149F TRP* 3.9 10.9 - - - +
150F SER* 2.6 46.1 + - - +
151F PRO* 4.1 5.5 - - - +
15H ALA* 3.6 12.2 - - - +
20H ALA* 2.8 38.7 - - - +
21H TYR 3.2 0.2 - - - -
22H ARG* 1.3 79.6 - - - +
24H ALA* 1.3 66.4 + - - +
26H PHE* 3.5 5.1 + - - +
27H LEU* 3.1 30.0 + - + +
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ILE* 3.7 10.1 - - - +
15H ALA* 3.7 21.1 - - + -
16H LEU* 3.7 29.2 - - + +
20H ALA 3.0 17.2 + - - +
21H TYR* 2.9 6.8 + - - +
23H ASP* 1.3 73.9 + - - +
25H VAL* 1.3 61.3 + - - +
27H LEU* 3.7 3.0 + - - +
28H ALA* 3.0 30.3 + - - +
47H CYS* 3.5 5.8 - - - -
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532F ARG* 6.2 1.3 - - - +
21H TYR* 2.6 23.3 + - - +
22H ARG* 3.9 4.9 - - - +
24H ALA* 1.3 73.8 - - - +
26H PHE* 1.3 55.6 + - - +
28H ALA* 2.9 2.9 + - - +
29H GLU* 2.7 39.4 + - - +
44H LEU* 3.9 2.7 - - + +
47H CYS* 3.6 26.5 - - + -
48H TYR* 3.5 37.2 - - + +
51H SER* 3.6 22.7 - - - +
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Residues in contact with PHE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TRP* 3.2 57.7 - + + -
466F LEU* 4.2 9.6 - - + -
469F MET* 3.6 24.5 - - - -
500F TRP* 3.4 52.3 - + + +
22H ARG 3.1 18.1 + - - +
23H ASP* 4.0 2.0 - - - +
25H VAL* 1.3 78.1 - - - +
27H LEU* 1.3 68.2 + - + +
29H GLU* 3.3 11.9 + - - +
30H ARG* 3.0 49.1 + - + +
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 3.2 35.7 - - + +
148F LEU* 5.1 6.3 - - + -
149F TRP* 5.7 1.6 - - + +
462F LEU* 4.1 13.0 - - + -
466F LEU* 5.6 6.3 - - + -
8H VAL* 3.7 28.0 - - + +
11H ALA* 4.5 16.8 - - + +
12H ILE* 3.8 21.5 - - + +
23H ASP* 3.1 19.9 + - + +
24H ALA* 4.0 1.1 - - - +
26H PHE* 1.3 84.8 - - + +
28H ALA* 1.3 63.6 + - - +
30H ARG* 3.5 6.7 + - + +
31H LEU* 3.2 19.4 + - - +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ILE* 3.5 17.9 - - + +
24H ALA 3.0 18.9 + - - +
25H VAL 2.9 5.3 + - - +
27H LEU* 1.3 76.5 - - - +
29H GLU* 1.3 60.2 + - - +
31H LEU* 3.3 3.2 + - + +
32H TYR* 2.9 28.1 + - - +
40H ALA 4.8 1.7 - - - +
43H LEU* 4.2 4.3 - - + -
44H LEU* 3.9 21.4 - - + +
47H CYS* 3.7 20.0 - - - -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498F THR* 4.6 3.5 - - + +
500F TRP* 3.6 25.2 + - - +
529F GLU* 3.1 25.6 - - - +
531F TYR* 5.8 0.2 - - - +
532F ARG* 3.6 20.0 + - - -
25H VAL* 2.7 17.5 + - - +
26H PHE* 3.4 15.4 - - - +
28H ALA* 1.3 76.1 - - - +
30H ARG* 1.3 74.3 + - - +
32H TYR* 3.4 4.5 + - - +
33H ALA* 3.0 27.9 + - - +
44H LEU* 3.7 18.5 - - + +
48H TYR* 4.0 17.6 + - - +
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F LEU* 4.3 19.7 - - + -
465F LEU* 4.9 2.2 - - + -
466F LEU* 5.8 4.5 - - + -
469F MET* 3.8 17.5 - - - -
495F HIS* 3.8 28.7 + - - +
498F THR* 2.7 46.2 + - - +
500F TRP* 3.3 21.8 - - - +
501F VAL* 4.0 8.4 - - - +
26H PHE* 3.0 49.2 + - + +
27H LEU* 3.6 8.5 - - + +
29H GLU* 1.3 91.2 - - - +
31H LEU* 1.3 60.0 + - - +
33H ALA* 3.1 4.5 + - - +
34H GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 31 (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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462F LEU* 5.0 3.3 - - + +
6H GLU* 6.5 1.3 - - + -
8H VAL* 3.8 28.0 - - + -
9H GLN* 4.6 14.1 - - + +
12H ILE* 4.2 7.6 - - + -
27H LEU 3.2 11.5 + - - +
28H ALA* 3.3 9.2 + - - +
30H ARG* 1.3 78.3 - - - +
32H TYR* 1.3 64.6 + - - +
34H GLU* 4.2 11.2 - - - +
35H VAL* 2.9 44.7 + - + +
40H ALA* 4.0 21.3 - - + +
43H LEU* 4.1 25.1 - - + -
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Residues in contact with TYR 32 (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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498F THR* 6.6 0.2 - - + -
531F TYR* 5.8 1.3 - - - -
28H ALA 2.9 14.3 + - - +
29H GLU 3.6 8.1 - - - +
30H ARG 3.2 0.2 - - - -
31H LEU* 1.3 76.9 - - - +
33H ALA* 1.3 57.6 + - - +
36H HIS* 2.7 65.5 + + - +
37H SER 4.0 9.4 - - - -
40H ALA* 3.9 8.0 - - - +
41H LEU* 3.5 44.6 - - + +
44H LEU* 3.8 27.6 - - + -
60H LEU* 4.3 7.4 - - + -
64H HIS* 3.0 47.3 + + - +
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Residues in contact with ALA 33 (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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494F HIS* 3.1 45.8 + - - +
495F HIS* 4.0 12.1 - - - +
498F THR* 3.3 33.2 - - + -
29H GLU 3.0 9.2 + - - +
30H ARG* 3.3 9.9 - - - +
32H TYR* 1.3 82.6 - - - +
34H GLU* 1.3 61.6 + - - +
35H VAL 3.5 0.2 + - - -
36H HIS* 4.2 2.0 + - - -
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F GLY* 4.3 3.3 - - - -
462F LEU* 3.6 38.3 + - + +
494F HIS* 5.1 5.7 + - - +
495F HIS* 3.6 23.8 - - + +
8H VAL* 6.0 0.9 - - - +
30H ARG 2.9 19.3 + - - +
31H LEU* 3.9 11.4 - - - +
33H ALA* 1.3 75.1 - - - +
35H VAL* 1.3 79.3 + - - +
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Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F HIS* 6.1 0.2 - - - -
31H LEU* 2.9 27.0 + - + +
34H GLU* 1.3 101.7 - - - +
36H HIS* 1.3 68.8 + - - +
37H SER* 3.2 28.1 + - - +
40H ALA* 4.6 5.2 - - + -
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Residues in contact with HIS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F HIS* 3.6 31.6 + + + -
31H LEU 3.9 0.4 + - - -
32H TYR* 2.7 66.1 + + - +
33H ALA* 4.4 4.9 - - - +
35H VAL* 1.3 74.8 - - - +
37H SER* 1.3 62.4 + - - +
38H GLU 4.0 0.3 + - - -
64H HIS* 4.5 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
------------------------------------------------------------
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