Contacts of the helix formed by residues 20 - 36 (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 ALA 20 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ALA* 2.9 12.9 + - - +
18F HIS 4.4 2.9 - - - +
19F TYR* 1.3 76.7 - - - +
21F TYR* 1.3 65.3 + - - +
22F ARG 3.5 1.6 - - - -
23F ASP* 3.5 21.4 + - + +
24F ALA* 3.0 21.5 + - - +
73H TYR* 5.1 2.0 - - - +
116H PHE* 4.0 23.1 - - + -
119H SER* 6.1 0.7 - - - +
150H SER* 5.4 0.7 - - - +
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Residues in contact with TYR 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LEU* 4.1 24.4 + - + -
19F TYR* 3.2 52.4 + + + -
20F ALA* 1.3 72.9 - - - +
22F ARG* 1.3 58.7 + - + +
24F ALA* 2.9 2.5 + - - +
25F VAL* 2.6 40.2 + - - +
50F ARG* 3.5 40.5 + - + +
51F SER* 3.3 34.5 - - - +
49H TYR* 5.1 5.2 - + - -
50H ARG* 5.0 3.3 - - - -
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TYR* 1.3 78.2 - - - +
23F ASP* 1.3 61.9 + - - +
25F VAL* 4.0 4.6 - - - +
26F PHE* 3.1 25.6 + - - +
123H HIS* 5.6 8.3 + - - -
149H TRP* 6.4 0.2 - - - -
150H SER* 3.9 28.9 + - - -
153H GLU* 2.8 40.9 + - - +
154H SER* 4.9 6.1 - - - +
157H GLU* 4.5 12.5 + - - -
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Residues in contact with ASP 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA* 4.7 3.1 - - + -
20F ALA* 3.5 24.4 + - + +
21F TYR 3.2 0.4 - - - -
22F ARG* 1.3 79.1 - - - +
24F ALA* 1.3 64.9 + - - +
26F PHE* 3.5 3.8 + - - +
27F LEU* 3.1 28.7 + - - +
116H PHE* 5.2 0.2 - - - -
119H SER* 4.7 3.6 + - - -
148H LEU* 3.1 29.9 - - + +
149H TRP 2.7 15.8 + - - +
150H SER* 2.3 55.6 + - - +
151H PRO* 3.2 4.5 - - - +
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 3.7 10.1 - - - +
15F ALA* 3.7 20.9 - - + -
16F LEU* 3.7 29.4 - - + +
20F ALA 3.0 14.3 + - - +
21F TYR* 2.9 6.5 + - - +
23F ASP* 1.3 77.1 - - - +
25F VAL* 1.3 62.0 + - + +
27F LEU* 3.9 2.4 - - - -
28F ALA* 2.9 30.1 + - - +
47F CYS* 3.6 5.4 - - + -
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TYR* 2.6 23.4 + - + +
22F ARG* 4.0 4.7 - - - +
24F ALA* 1.3 75.1 - - - +
26F PHE* 1.3 54.2 + - - +
28F ALA* 2.9 2.6 + - - +
29F GLU* 2.7 40.1 + - - +
44F LEU* 3.9 1.8 - - + +
47F CYS* 3.6 27.1 - - + -
48F TYR* 3.6 36.3 - - + +
51F SER* 3.6 23.1 - - - +
532H ARG* 6.2 0.9 - - - +
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Residues in contact with PHE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ARG 3.1 18.5 + - - +
23F ASP 4.0 2.0 - - - +
25F VAL* 1.3 79.3 - - - +
27F LEU* 1.3 69.1 + - + +
29F GLU* 3.3 10.7 + - - +
30F ARG* 3.1 43.3 + - + +
149H TRP* 3.3 57.9 - + + -
466H LEU* 3.8 18.2 - - + -
469H MET* 3.5 25.1 - - - -
500H TRP* 3.6 47.1 - + - -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 3.7 28.3 - - + +
11F ALA* 4.5 11.7 - - + +
12F ILE* 3.9 22.2 - - + +
15F ALA* 5.8 0.4 - - + -
23F ASP 3.1 18.3 + - - +
24F ALA* 4.0 1.1 - - - +
26F PHE* 1.3 83.7 - - + +
28F ALA* 1.3 62.5 + - - +
30F ARG* 3.5 5.6 + - + +
31F LEU* 3.2 19.2 + - - +
147H PHE* 2.9 48.0 - - + +
148H LEU* 4.8 6.1 - - + -
149H TRP 6.1 0.2 - - - +
462H LEU* 4.0 13.5 - - + -
466H LEU* 5.7 4.5 - - + -
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 3.5 18.1 - - + +
24F ALA 2.9 18.7 + - - +
25F VAL 2.9 4.9 + - - +
27F LEU* 1.3 76.5 - - - +
29F GLU* 1.3 59.5 + - - +
31F LEU* 3.3 3.6 + - - +
32F TYR* 2.9 27.9 + - - +
40F ALA 4.8 1.6 - - - +
43F LEU* 4.2 4.3 - - + -
44F LEU* 3.9 22.1 - - + +
47F CYS* 3.7 19.5 - - - -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 2.7 20.3 + - - +
26F PHE* 3.4 15.0 - - - +
28F ALA* 1.3 76.5 - - - +
30F ARG* 1.3 73.6 + - - +
32F TYR* 3.4 4.6 + - + +
33F ALA* 3.0 27.5 + - - +
44F LEU* 3.7 19.4 - - + +
48F TYR* 4.0 19.6 + - - +
498H THR* 4.3 5.5 - - + +
500H TRP* 3.3 32.1 + - - +
529H GLU* 3.3 22.5 - - - +
532H ARG* 4.0 11.5 + - - -
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F PHE* 3.1 46.4 + - + +
27F LEU* 3.6 8.5 - - - +
29F GLU* 1.3 102.6 + - - +
31F LEU* 1.3 60.5 + - - +
33F ALA* 3.1 4.3 + - - +
34F GLU* 2.9 28.8 + - - +
462H LEU* 3.8 25.4 - - + -
465H LEU* 4.5 4.3 - - + -
466H LEU* 5.6 4.0 - - + -
469H MET* 3.7 31.0 - - - +
495H HIS* 3.5 28.0 + - - -
498H THR* 2.9 36.7 + - - +
500H TRP* 3.5 12.2 - - - +
501H VAL* 4.2 0.9 - - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLU* 6.1 4.5 - - + -
8F VAL* 3.8 27.4 - - + -
9F GLN* 4.5 14.6 - - + +
12F ILE* 4.2 7.2 - - + -
27F LEU 3.2 10.7 + - - +
28F ALA* 3.5 9.0 - - - +
30F ARG* 1.3 79.4 - - - +
32F TYR* 1.3 64.2 + - - +
34F GLU* 4.2 11.4 - - - +
35F VAL* 2.9 44.5 + - + +
40F ALA* 4.0 21.0 - - + +
43F LEU* 4.1 26.0 - - + -
462H LEU* 4.7 2.9 - - + +
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Residues in contact with TYR 32 (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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28F ALA 2.9 13.3 + - - +
29F GLU* 3.6 8.1 - - + +
30F ARG 3.2 0.2 - - - -
31F LEU* 1.3 78.2 - - - +
33F ALA* 1.3 58.3 + - - +
36F HIS* 2.7 64.8 + + - +
37F SER 4.0 9.6 - - - -
40F ALA* 3.9 7.2 - - - +
41F LEU* 3.5 41.9 - - + +
44F LEU* 3.8 26.7 - - + -
60F LEU* 4.4 7.4 - - + -
64F HIS* 3.0 47.4 + + - +
498H THR* 6.3 2.5 - - + -
531H TYR* 5.5 2.2 - - - -
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Residues in contact with ALA 33 (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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29F GLU 3.0 8.9 + - - +
30F ARG* 3.3 9.9 - - - +
32F TYR* 1.3 81.7 - - - +
34F GLU* 1.3 61.8 + - - +
36F HIS* 4.2 10.7 + - - +
494H HIS* 3.8 24.8 - - - +
495H HIS* 3.7 17.0 - - - +
498H THR* 3.4 32.8 - - + -
68X PRO* 4.0 6.8 - - - +
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Residues in contact with GLU 34 (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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8F VAL* 5.9 1.7 - - - +
30F ARG 2.9 18.4 + - - +
31F LEU* 3.9 12.3 - - - +
33F ALA* 1.3 72.8 - - - +
35F VAL* 1.3 78.0 + - - +
458H ALA 4.8 6.0 - - - +
461H GLY* 4.3 4.3 - - - -
462H LEU* 3.7 37.2 + - + +
494H HIS* 3.9 14.7 + - - +
495H HIS* 3.8 15.5 - - + +
68X PRO* 3.2 24.3 - - - +
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Residues in contact with VAL 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 2.9 24.8 + - + +
34F GLU* 1.3 101.0 - - - +
36F HIS* 1.3 68.0 + - - +
37F SER* 3.1 28.1 + - - +
40F ALA* 4.5 7.2 - - + -
66X ASN 3.6 4.2 - - - +
67X ASN* 5.0 0.2 - - - -
68X PRO* 3.6 13.5 - - - +
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Residues in contact with HIS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU 3.9 0.2 + - - -
32F TYR* 2.7 65.3 + + - +
33F ALA* 4.4 11.7 - - - +
35F VAL* 1.3 73.5 - - - +
37F SER* 1.3 62.4 + - - +
38F GLU 4.0 0.2 + - - -
40F ALA* 4.7 0.2 - - - +
64F HIS* 4.6 11.7 + + - -
65X ASN* 3.3 29.7 + - + +
66X ASN* 3.5 37.0 + - - +
68X PRO* 4.4 1.6 - - + -
268Y ARG* 5.5 2.4 + - - -
269Y ASP* 5.5 2.2 - - - -
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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
------------------------------------------------------------
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