Contacts of the helix formed by residues 22 - 35 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LYS* 6.0 3.9 - - - +
20D LYS 3.9 1.8 + - - +
21D ILE* 1.3 78.0 - - - +
23D LYS* 1.3 65.6 + - - +
24D ASP* 3.4 4.3 - - + +
25D GLU* 3.5 20.9 + - + +
26D LEU* 3.0 23.4 + - - +
47D ARG* 3.4 17.3 - - - +
13S G 3.6 30.2 + - - +
14S C 3.1 29.4 + - - +
110S U 5.7 4.0 - - + +
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE 3.9 0.8 + - - -
22D LYS* 1.3 74.1 - - - +
24D ASP* 1.3 65.8 + - + +
26D LEU* 3.9 1.8 - - - +
27D LYS* 3.0 57.4 + - - +
43D ILE 5.4 0.2 - - - -
45D VAL* 3.3 49.4 + - + +
46D SER* 5.3 2.2 - - - -
47D ARG* 4.0 16.5 - - + +
110S U 5.7 4.7 - - - +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 3.4 2.7 - - + +
23D LYS* 1.3 83.1 - - + +
25D GLU* 1.3 59.7 + - - +
27D LYS* 3.4 13.7 + - - +
28D LYS* 2.9 62.0 + - - +
110S U 4.9 18.4 - - - +
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS* 3.5 58.6 + - + +
31C HIS* 6.1 0.2 - - - +
21D ILE* 4.2 14.3 - - + +
22D LYS* 3.5 29.0 + - + +
24D ASP* 1.3 77.3 - - - +
26D LEU* 1.3 50.0 + - - +
28D LYS* 3.4 6.2 + - - +
29D SER* 2.7 43.1 + - - +
78D TYR* 3.2 30.0 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 4.3 27.8 - - + -
18D ASN 5.0 7.4 - - - +
21D ILE* 3.6 20.7 - - + +
22D LYS 3.0 17.8 + - - +
23D LYS 3.9 2.7 - - - +
25D GLU* 1.3 75.1 - - - +
27D LYS* 1.3 57.8 + - - +
29D SER* 3.7 4.1 - - - -
30D LEU* 2.9 48.6 + - + +
45D VAL* 3.8 27.6 - - + -
47D ARG* 6.2 2.5 - - - -
53D GLY* 6.0 2.5 - - - +
54D GLN 5.0 3.4 - - - +
77D PHE* 3.8 28.5 - - + -
78D TYR* 4.3 9.0 - - + -
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LYS* 3.0 41.3 + - - +
24D ASP* 3.6 15.7 + - - +
25D GLU 3.3 0.2 - - - -
26D LEU* 1.3 78.2 - - - +
28D LYS* 1.3 60.9 + - + +
30D LEU* 4.1 0.5 - - - +
31D HIS* 3.5 6.1 + - - +
42D ASP* 4.5 10.0 + - - -
43D ILE* 3.3 68.9 + - + +
45D VAL* 4.4 9.8 - - + +
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS* 6.3 0.8 - - - +
25C GLU* 3.4 42.0 + - + +
28C LYS* 6.2 1.8 - - - +
29C SER* 4.6 1.8 - - - -
78C TYR* 3.9 6.6 + - - -
24D ASP* 2.9 53.0 + - - +
25D GLU* 4.0 4.5 - - - +
27D LYS* 1.3 78.1 - - + +
29D SER* 1.3 63.5 + - - +
31D HIS* 3.4 7.8 + - + +
32D ALA* 3.1 20.6 + - - +
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C SER* 3.9 24.0 + - - -
32C ALA* 4.4 3.6 - - - -
25D GLU* 2.7 26.5 + - - +
26D LEU 3.7 2.7 - - - -
28D LYS* 1.3 75.2 - - - +
30D LEU* 1.3 63.8 + - - +
32D ALA* 3.2 17.7 - - - +
33D ILE* 3.6 11.8 + - - +
77D PHE* 3.6 22.0 - - - -
78D TYR* 2.7 25.3 + - - -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 4.5 3.8 - - + -
17D LEU* 4.4 5.6 - - + -
26D LEU* 2.9 34.8 + - + +
27D LYS 4.1 3.8 - - - +
29D SER* 1.3 73.8 - - - +
31D HIS* 1.3 64.2 + - - +
33D ILE* 3.5 2.4 + - + +
34D PHE* 3.1 43.7 + - + +
40D ILE* 4.8 0.2 - - - +
43D ILE* 4.1 19.7 - - + -
45D VAL* 4.7 1.1 - - + -
55D ALA* 3.6 30.1 - - + -
57D VAL* 4.8 3.8 - - + -
77D PHE* 3.6 26.5 - - + -
82D MET* 3.8 24.5 - - + -
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Residues in contact with HIS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR* 5.5 7.3 - - + -
27D LYS 3.5 7.0 + - - +
28D LYS* 3.4 12.0 + - + +
29D SER 3.2 0.4 - - - -
30D LEU* 1.3 76.3 - - - +
32D ALA* 1.3 65.5 + - - +
33D ILE 3.2 0.9 + - - -
35D SER* 3.2 39.9 + - - -
40D ILE* 3.5 41.4 + - + +
43D ILE* 3.6 23.3 - - + +
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C SER* 4.2 3.8 - - - +
77C PHE* 3.7 20.4 - - + -
78C TYR* 2.7 71.4 + - + +
79C ASP 4.5 0.2 + - - -
28D LYS 3.1 8.0 + - - +
29D SER* 3.2 13.9 + - - +
31D HIS* 1.3 76.6 - - - +
33D ILE* 1.3 61.5 + - + +
35D SER* 3.5 2.1 + - - -
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 4.5 11.4 - - + -
75C PHE* 3.9 17.3 - - + -
76C PRO 4.3 7.8 - - - +
77C PHE* 5.2 0.4 - - + -
79C ASP 5.8 0.2 + - - -
29D SER 3.9 8.1 - - - +
30D LEU* 3.5 5.3 + - + +
31D HIS 3.2 0.2 - - - -
32D ALA* 1.3 80.4 - - + +
34D PHE* 1.3 73.2 + - + +
35D SER* 3.1 9.9 + - - -
36D ARG* 3.4 22.0 + - - +
37D PHE* 4.7 0.9 - - + -
72D MET* 3.4 40.2 - - + -
75D PHE* 4.3 16.6 - - + -
77D PHE* 3.6 38.6 - - + -
82D MET* 5.0 2.7 - - - -
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Residues in contact with PHE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 3.8 9.2 - - + -
14D ILE* 3.7 16.2 - - + -
30D LEU* 3.1 34.6 + - + +
33D ILE* 1.3 84.4 - - + +
35D SER* 1.3 63.9 + - - +
36D ARG 3.1 3.1 - - - -
37D PHE* 3.1 28.1 + + - +
38D GLY 3.8 0.3 + - - -
40D ILE* 3.6 15.1 - - + +
57D VAL* 4.5 10.1 - - + -
59D PHE* 3.7 20.3 - + + -
68D ALA* 3.7 31.6 - - + -
72D MET* 3.6 27.1 - - + -
82D MET* 3.6 32.8 - - + -
84D ILE* 4.2 2.2 - - + -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR* 3.7 3.3 - - - -
79C ASP* 3.0 47.8 + - - +
31D HIS* 3.2 34.9 + - - -
32D ALA 3.5 7.8 + - - -
33D ILE 4.1 0.2 + - - -
34D PHE* 1.3 76.3 - - - +
36D ARG* 1.3 60.4 + - - +
38D GLY* 2.9 21.0 + - - +
40D ILE* 3.6 9.1 - - - +
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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