Contacts of the helix formed by residues 24 - 37 (chain D) in PDB entry 3G3B
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 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ASP* 3.7 9.4 - - - -
19D ASN* 3.9 4.3 - - - +
22D GLY 3.7 4.8 + - - -
23D TYR* 1.3 76.7 - - - +
25D LEU* 1.3 68.0 + - - +
26D GLY 3.2 0.4 - - - -
27D ASN* 3.0 35.6 + - - +
28D TRP* 3.6 2.1 - - - -
120D VAL* 4.0 6.1 - - - +
121D GLN* 3.6 27.6 + - - +
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Residues in contact with LEU 25 (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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9D ALA* 3.7 29.6 - - + +
12D MET* 3.8 15.0 - - + -
13D LYS* 3.7 48.5 - - + +
17D LEU* 4.8 2.5 - - + -
18D ASP* 3.1 27.8 + - + +
23D TYR 3.8 0.4 + - - -
24D SER* 1.3 73.5 - - - +
26D GLY* 1.3 56.4 + - - +
28D TRP* 2.8 30.6 + - + +
29D VAL* 3.3 11.4 + - + +
121D GLN* 3.7 3.9 + - - +
124D ILE* 3.8 30.1 - - + -
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Residues in contact with GLY 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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25D LEU* 1.3 76.1 - - - +
27D ASN* 1.3 56.8 + - - +
29D VAL* 3.9 1.0 - - - +
30D CYS* 2.8 33.5 + - - +
120D VAL* 3.2 28.9 - - - +
121D GLN* 2.9 15.0 + - - -
123D TRP* 4.1 2.8 - - - +
124D ILE* 3.5 16.2 - - - +
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Residues in contact with ASN 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 TYR* 4.2 12.0 - - + +
24D SER* 3.0 40.9 + - - +
26D GLY* 1.3 78.0 - - - +
28D TRP* 1.3 56.2 - - - +
30D CYS* 3.8 1.5 - - - +
31D ALA* 3.0 22.2 + - - +
105D MET* 3.5 14.0 - - - +
111D TRP* 3.0 50.9 + - - +
116D LYS* 5.0 1.7 - - - -
120D VAL* 3.5 25.4 - - - +
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Residues in contact with TRP 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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12D MET* 3.6 29.3 - - + +
17D LEU* 2.8 55.2 + - + -
20D TYR* 3.8 26.2 - + + -
23D TYR* 3.3 32.2 + + + +
24D SER 3.6 8.5 - - - -
25D LEU* 2.8 17.2 + - + +
27D ASN* 1.3 73.0 - - - +
29D VAL* 1.3 62.0 + - - +
31D ALA* 3.3 3.3 + - - +
32D ALA* 3.1 23.2 + - - +
56D LEU* 4.4 9.2 - - + +
95D ALA* 4.2 18.4 - - + -
99D VAL* 3.6 39.0 - - + -
105D MET* 3.8 23.1 - - + -
108D TRP* 4.4 3.1 - + - -
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Residues in contact with VAL 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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5D ARG* 4.1 17.9 - - + +
8D LEU* 4.6 4.3 - - + -
9D ALA* 3.8 21.8 - - - +
12D MET* 3.9 14.6 - - - -
25D LEU* 3.3 7.3 + - + +
26D GLY 3.9 4.7 - - - +
28D TRP* 1.3 73.0 - - - +
30D CYS* 1.3 64.6 + - - +
32D ALA 3.3 1.9 + - - -
33D LYS* 3.1 19.2 + - - +
38D PHE* 3.5 28.6 - - + -
123D TRP* 4.1 17.5 - - + +
124D ILE* 3.6 27.4 - - + -
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Residues in contact with CYS 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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26D GLY 2.8 23.0 + - - +
27D ASN* 3.8 2.9 - - - +
29D VAL* 1.3 72.6 - - - +
31D ALA* 1.3 60.5 + - - +
33D LYS* 3.4 8.5 - - - +
34D PHE* 3.2 31.6 - - - -
114D ARG 4.5 1.3 - - - -
115D CYS* 2.0 52.0 - - + -
120D VAL* 5.0 1.8 - - + -
123D TRP* 3.4 46.3 - - + +
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Residues in contact with ALA 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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27D ASN 3.0 19.2 + - - +
28D TRP 3.5 6.1 - - - +
29D VAL 3.2 0.4 - - - -
30D CYS* 1.3 76.1 - - - +
32D ALA* 1.3 62.0 + - - +
33D LYS 3.3 0.3 + - - -
34D PHE* 3.3 4.3 + - - +
35D GLU* 3.1 27.5 + - - +
56D LEU* 3.9 14.1 - - + -
105D MET* 3.7 19.5 - - + -
108D TRP* 5.2 6.3 - - + -
111D TRP* 3.8 21.7 + - + +
115D CYS* 3.9 0.6 - - - -
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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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8D LEU* 3.7 29.6 - - + -
12D MET* 4.2 7.4 - - + -
28D TRP 3.1 13.4 + - - +
29D VAL 3.3 1.3 + - - +
31D ALA* 1.3 74.1 - - - +
33D LYS* 1.3 64.5 + - - +
36D SER* 2.8 29.1 + - - -
37D ASN 3.2 2.6 + - - -
38D PHE* 3.6 4.9 + - + -
55D ILE* 3.4 25.6 - - + +
56D LEU* 3.7 6.4 - - + +
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D VAL 3.1 11.8 + - - +
30D CYS 3.4 11.2 - - - +
31D ALA 3.2 0.2 - - - -
32D ALA* 1.3 77.3 - - - +
34D PHE* 1.3 71.8 + - + +
37D ASN* 2.9 53.7 + - - +
38D PHE* 3.7 34.1 - - + -
123D TRP* 3.7 30.0 - - + -
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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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30D CYS* 3.2 40.8 + - - +
31D ALA* 3.3 5.4 + - - +
32D ALA 3.3 0.2 - - - -
33D LYS* 1.3 87.6 - - + +
35D GLU* 1.3 63.8 + - - +
110D ALA* 3.7 25.0 - - + +
111D TRP 5.4 0.2 - - - +
114D ARG* 3.2 66.4 - - + -
115D CYS* 3.8 8.3 - - - -
123D TRP* 4.1 19.3 - + - -
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Residues in contact with GLU 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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139C ASN* 5.9 0.7 + - - -
31D ALA* 3.1 19.3 + - - +
32D ALA 3.4 0.2 + - - -
33D LYS 3.3 0.2 - - - -
34D PHE* 1.3 82.3 - - - +
36D SER* 1.3 58.2 + - - +
42D ALA* 5.3 0.2 - - - +
55D ILE 3.5 15.9 - - - +
56D LEU* 4.0 13.2 - - + +
57D GLN* 3.3 32.9 + - + +
108D TRP* 3.5 38.8 - - + +
109D VAL 4.9 0.5 + - - -
110D ALA* 3.7 24.4 + - - +
111D TRP* 4.6 0.7 + - - +
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Residues in contact with SER 36 (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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32D ALA 2.8 7.4 + - - -
35D GLU* 1.3 77.4 - - - +
37D ASN* 1.3 70.0 + - - +
38D PHE 3.4 6.6 + - - -
39D ASN* 3.2 35.2 + - - +
42D ALA* 3.9 12.5 - - - +
54D GLY 3.6 10.8 - - - -
55D ILE* 2.7 32.0 + - - +
57D GLN* 4.7 0.2 - - - -
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Residues in contact with ASN 37 (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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2D VAL* 4.1 10.7 - - - +
32D ALA 3.2 1.0 + - - -
33D LYS* 2.9 54.3 + - - +
36D SER* 1.3 78.1 - - - +
38D PHE* 1.3 69.1 + - - +
39D ASN* 3.5 2.0 + - + +
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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