Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 3G8T
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 LYS 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS 3.9 1.4 + - - +
21A ILE* 1.3 73.5 - - - +
23A LYS* 1.3 67.4 + - - +
24A ASP* 3.3 2.9 - - + +
25A GLU* 3.0 39.2 + - + +
26A LEU* 3.1 10.3 + - - +
47A ARG* 3.4 17.8 - - - +
28B LYS* 5.0 11.7 - - - +
13P G 4.1 32.3 - - - +
14P C 3.9 22.4 - - - +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE 3.7 0.6 + - - -
22A LYS* 1.3 71.7 - - - +
24A ASP* 1.3 65.0 + - + +
26A LEU* 3.5 3.5 + - - +
27A LYS* 3.0 56.9 + - + +
45A VAL* 3.3 46.5 + - + +
46A SER* 5.1 3.7 - - - +
47A ARG* 3.7 18.2 - - + +
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.0 2.4 + - + +
23A LYS* 1.3 84.2 - - + +
25A GLU* 1.3 65.5 + - - +
27A LYS* 3.3 11.6 + - - +
28A LYS* 3.1 49.4 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.0 13.3 - - + +
22A LYS* 3.0 35.6 + - + +
24A ASP* 1.3 77.0 - - - +
26A LEU* 1.3 57.8 + - - +
28A LYS* 3.3 9.5 + - - +
29A SER* 2.8 34.5 + - - +
78A TYR* 2.9 32.2 + - - +
28B LYS* 3.9 48.6 - - + +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.5 24.9 - - + -
18A ASN 4.7 10.1 - - - +
21A ILE* 3.6 25.7 - - + +
22A LYS 3.1 7.5 + - - +
23A LYS* 3.7 7.4 - - - +
25A GLU* 1.3 75.6 - - - +
27A LYS* 1.3 57.3 + - - +
29A SER* 4.0 3.9 - - - -
30A LEU* 2.9 42.9 + - + +
45A VAL* 3.8 29.8 - - + -
47A ARG* 6.4 0.9 - - - -
53A GLY* 6.0 2.2 - - - +
54A GLN 4.7 2.5 - - - +
77A PHE* 3.7 28.0 - - + -
78A TYR* 3.9 14.4 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.0 43.3 + - + +
24A ASP* 3.6 14.6 - - - +
25A GLU 3.3 0.2 - - - -
26A LEU* 1.3 77.2 - - - +
28A LYS* 1.3 60.8 + - + +
30A LEU* 4.2 0.9 - - - -
31A HIS* 3.7 5.2 + - - +
42A ASP* 4.0 11.6 + - - -
43A ILE* 3.1 66.0 + - + +
44A LEU* 5.5 0.4 - - - +
45A VAL* 4.8 6.9 - - + +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 3.1 40.6 + - - +
25A GLU* 3.9 6.7 - - - +
27A LYS* 1.3 78.6 - - + +
29A SER* 1.3 64.2 + - - +
30A LEU 3.2 1.3 - - - -
31A HIS* 3.2 8.4 + - + +
32A ALA* 3.1 21.5 + - - +
22B LYS* 5.6 8.5 - - - +
25B GLU* 3.5 49.1 + - + +
28B LYS* 5.7 6.6 - - - +
29B SER* 4.5 2.0 - - - -
78B TYR* 4.0 4.7 + - - -
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU* 2.8 18.6 + - - +
26A LEU 4.0 1.3 - - - -
28A LYS* 1.3 74.0 - - - +
30A LEU* 1.3 64.5 + - - +
32A ALA* 3.6 13.8 - - - +
33A ILE* 3.9 6.4 - - - +
77A PHE* 3.6 26.9 - - - -
78A TYR* 2.8 27.6 + - - -
28B LYS* 4.1 1.0 + - - +
29B SER* 3.6 29.6 + - - -
32B ALA* 4.2 5.6 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.0 17.0 - - + -
17A LEU* 4.8 3.6 - - + -
26A LEU* 2.9 34.8 + - + +
29A SER* 1.3 76.0 - - - +
31A HIS* 1.3 65.3 + - - +
32A ALA 3.1 1.2 + - - -
33A ILE* 3.1 12.0 + - - -
34A PHE* 3.2 42.3 + - + -
43A ILE* 3.8 28.7 - - + -
45A VAL* 4.2 1.6 - - + -
55A ALA* 3.7 26.9 - - + -
57A VAL* 4.4 2.7 - - + -
77A PHE* 3.9 22.7 - - + -
82A MET* 4.0 5.4 - - + -
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS 3.7 13.1 + - - +
28A LYS* 3.2 11.3 + - - +
30A LEU* 1.3 78.1 - - - +
32A ALA* 1.3 61.6 + - - +
34A PHE 4.1 0.2 - - - -
35A SER* 3.1 34.4 + - - -
40A ILE* 3.9 39.9 + - + +
43A ILE* 3.6 16.4 - - + +
78B TYR* 4.9 8.4 - - + -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 3.1 6.0 + - - +
29A SER 3.6 13.5 - - - +
30A LEU 3.1 0.2 + - - -
31A HIS* 1.3 78.3 - - - +
33A ILE* 1.3 59.3 + - + +
35A SER* 3.0 8.1 + - - -
36A ARG* 5.9 0.2 - - - +
29B SER* 4.4 3.4 - - - +
76B PRO 4.4 0.3 - - - +
77B PHE* 3.8 19.4 - - + -
78B TYR* 2.8 69.6 + - + +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER 3.9 7.6 - - - +
30A LEU* 3.1 5.1 + - - +
32A ALA* 1.3 80.8 - - + +
34A PHE* 1.3 67.1 + - + +
35A SER 3.3 4.7 - - - -
36A ARG* 3.4 25.3 - - - +
37A PHE* 3.7 4.2 - - - -
72A MET* 3.5 33.4 - - + -
75A PHE* 3.8 21.1 - - + -
77A PHE* 3.7 31.2 - - + -
82A MET* 6.0 0.4 - - - -
33B ILE* 4.2 17.0 - - + -
75B PHE* 3.5 26.2 - - + -
76B PRO 4.6 4.8 - - - +
77B PHE* 4.8 0.9 - - + -
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.6 22.2 - - + -
14A ILE* 3.7 7.9 - - + -
30A LEU* 3.2 32.2 + - + +
33A ILE* 1.3 85.6 - - + +
35A SER* 1.3 62.1 + - - +
36A ARG 3.2 3.2 + - - -
37A PHE* 3.5 13.2 + + - +
38A GLY 3.5 1.2 - - - +
40A ILE* 3.7 18.7 - - + +
57A VAL* 4.2 7.6 - - + -
59A PHE* 3.2 32.6 - + + -
68A ALA* 3.7 23.3 - - + -
72A MET* 3.9 28.7 - - + -
77A PHE* 6.3 0.2 - + - -
82A MET* 3.5 34.5 - - + -
84A ILE* 4.2 2.5 - - + -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A HIS* 3.1 30.2 + - - -
32A ALA 3.0 20.3 + - - -
34A PHE* 1.3 78.0 - - - +
36A ARG* 1.3 61.4 + - - +
38A GLY* 3.2 20.6 + - - +
39A GLN* 5.2 0.2 - - - -
40A ILE* 4.2 4.3 - - - -
78B TYR* 3.6 3.9 - - - -
79B ASP* 3.1 41.3 + - - +
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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