Contacts of the helix formed by residues 23 - 38 (chain A) in PDB entry 1G8I
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 THR 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A THR* 3.9 5.2 - - - -
22A PHE* 1.3 76.5 - - - +
24A GLU* 1.3 60.1 + - - +
25A LYS* 3.4 9.0 + - - +
26A GLU* 2.9 39.9 + - - +
27A VAL* 2.9 27.5 + - - +
901A EDO 4.3 20.0 - - - -
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Residues in contact with GLU 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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13A VAL* 3.9 21.3 - - + +
14A GLU* 5.3 6.9 - - - +
17A THR* 3.4 30.9 + - + +
23A THR* 1.3 74.0 - - - +
25A LYS* 1.3 62.9 + - - +
27A VAL* 3.3 2.5 + - - +
28A GLN* 3.0 36.0 + - - +
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Residues in contact with LYS 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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23A THR* 3.2 7.5 + - - +
24A GLU* 1.3 80.2 - - - +
26A GLU* 1.3 58.0 + - + +
28A GLN* 3.4 11.4 + - - +
29A GLN* 2.9 59.8 + - + +
32A LYS* 4.8 0.2 + - - -
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Residues in contact with GLU 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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21A TYR 4.2 0.2 - - - +
22A PHE* 3.4 12.6 - - + -
23A THR* 2.9 38.3 + - - +
25A LYS* 1.3 75.1 - - + +
27A VAL* 1.3 66.5 + - - +
29A GLN* 3.3 17.4 + - - +
30A TRP* 2.9 30.3 + - - -
94A ARG* 2.8 39.4 + - - -
901A EDO 2.6 27.4 + - - -
954A P6G 4.1 12.0 - - - +
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Residues in contact with VAL 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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8A LEU* 3.6 23.1 - - + -
13A VAL* 4.9 5.4 - - + -
16A LEU* 4.1 15.3 - - + -
17A THR* 3.7 29.8 - - - +
20A THR* 4.1 4.7 - - - +
22A PHE* 3.8 17.3 - - + -
23A THR 2.9 17.9 + - - +
24A GLU 3.3 7.2 + - - +
26A GLU* 1.3 75.4 - - - +
28A GLN* 1.3 59.4 + - + +
30A TRP* 3.3 5.2 + - - -
31A TYR* 3.0 24.1 + - - +
82A PHE* 3.6 18.3 - - + -
86A ILE* 4.7 7.4 - - + -
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Residues in contact with GLN 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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6A SER 5.1 1.0 - - - +
7A LYS* 4.0 33.2 + - + +
8A LEU* 4.8 9.6 + - + +
13A VAL* 3.9 32.7 - - + +
24A GLU* 3.0 26.6 + - - +
25A LYS* 3.8 7.8 - - - +
27A VAL* 1.3 74.8 - - - +
29A GLN* 1.3 63.4 + - - +
31A TYR* 3.3 8.1 + - - +
32A LYS* 3.1 38.0 + - - +
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Residues in contact with GLN 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 LYS* 2.9 55.0 + - + +
26A GLU* 3.7 20.5 - - - +
28A GLN* 1.3 75.6 - - - +
30A TRP* 1.3 62.5 + - - +
32A LYS* 3.2 26.5 + - - +
33A GLY* 3.1 18.4 + - - -
954A P6G 3.9 29.6 + - - -
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Residues in contact with TRP 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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22A PHE* 3.7 14.1 - + - -
26A GLU 2.9 23.9 + - - +
27A VAL 3.7 3.1 - - - +
29A GLN* 1.3 72.5 - - - +
31A TYR* 1.3 60.7 + - - +
33A GLY* 3.3 4.9 + - - -
34A PHE* 2.8 33.0 + - - +
82A PHE* 3.8 5.8 - - + -
85A PHE* 3.8 22.9 - + - -
86A ILE* 3.7 31.4 - - + -
89A LEU* 3.8 19.3 - - + -
954A P6G 2.7 100.8 + - - -
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Residues in contact with TYR 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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5A ASN* 2.8 41.7 + - - -
6A SER* 3.6 18.8 - - - -
7A LYS 3.7 0.7 - - - -
8A LEU* 3.4 40.5 - - + +
27A VAL 3.0 16.1 + - - +
28A GLN* 3.7 5.4 - - - +
29A GLN 3.3 0.2 - - - -
30A TRP* 1.3 78.5 - - - +
32A LYS* 1.3 55.7 + - - +
34A PHE* 3.5 3.8 - + - +
35A ILE* 2.8 64.0 + - + +
41A GLY* 5.7 1.3 - - - -
82A PHE* 3.4 38.5 - + + -
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Residues in contact with LYS 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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6A SER* 3.7 32.1 + - - +
7A LYS* 5.2 10.5 - - + +
25A LYS 4.8 0.2 + - - -
28A GLN* 3.1 31.6 + - - +
29A GLN* 3.2 36.1 - - - +
31A TYR* 1.3 76.8 - - - +
33A GLY* 1.3 56.7 + - - +
35A ILE* 3.4 2.4 + - - +
36A LYS* 2.9 29.5 + - - +
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Residues in contact with GLY 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 GLN 3.1 11.2 + - - -
30A TRP* 3.8 7.9 - - - -
32A LYS* 1.3 75.3 - - - +
34A PHE* 1.3 65.0 + - - +
36A LYS* 3.3 6.5 + - - +
37A ASP* 3.1 33.7 + - - +
954A P6G 6.2 0.2 - - - -
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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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30A TRP* 2.8 23.3 + - - +
31A TYR* 3.5 6.3 - + - +
33A GLY* 1.3 71.7 - - - +
35A ILE* 1.3 63.6 + - + +
37A ASP* 3.7 3.4 - - - +
38A CYS* 2.7 40.8 + - + +
41A GLY* 3.5 30.1 - - - -
43A LEU* 4.3 17.7 - - + -
80A ILE 3.5 24.0 - - - -
82A PHE* 3.7 35.9 - + + -
85A PHE* 3.8 48.0 - + + -
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Residues in contact with ILE 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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4A SER 5.0 5.4 - - - +
5A ASN* 5.5 5.6 - - + +
6A SER* 4.2 23.8 - - - +
31A TYR* 2.8 60.3 + - + +
32A LYS 3.8 2.9 - - - +
34A PHE* 1.3 76.7 - - + +
36A LYS* 1.3 68.3 + - - +
38A CYS 3.9 13.9 - - - +
39A PRO* 3.3 31.6 - - + +
41A GLY* 4.1 16.8 - - - -
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Residues in contact with LYS 36 (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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32A LYS 2.9 18.1 + - - +
33A GLY* 3.3 7.6 + - - +
35A ILE* 1.3 79.6 - - - +
37A ASP* 1.3 71.6 + - - +
39A PRO* 3.8 10.2 - - - +
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Residues in contact with ASP 37 (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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33A GLY* 3.1 19.1 + - - +
34A PHE* 4.1 3.1 - - - +
36A LYS* 1.3 91.3 - - - +
38A CYS* 1.3 58.8 + - + +
39A PRO* 3.5 6.9 - - - +
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Residues in contact with CYS 38 (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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34A PHE* 2.7 32.0 + - + +
35A ILE* 3.4 8.6 + - - +
37A ASP* 1.3 76.2 - - + +
39A PRO* 1.3 55.7 - - - +
40A SER* 3.2 12.3 - - - -
41A GLY* 2.7 26.2 + - - +
42A GLN 3.1 42.0 - - - -
43A LEU* 3.6 16.2 - - + -
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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
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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