Contacts of the helix formed by residues 19 - 30 (chain A) in PDB entry 1GO1
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 GLY 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL 3.8 0.6 + - - +
18A MET* 1.4 73.9 - - - +
20A ALA* 1.4 63.4 + - - -
21A ARG 3.6 2.0 - - - -
22A LYS* 4.1 9.9 - - - -
23A SER* 2.9 22.0 + - - -
80A VAL* 4.4 5.5 - - - +
81A SER 5.9 0.7 - - - -
82A ALA 2.9 22.5 + - - +
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Residues in contact with ALA 20 (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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19A GLY* 1.4 72.8 - - - +
21A ARG* 1.4 63.7 + - - +
23A SER 3.6 3.8 + - - -
24A ILE* 3.5 21.2 - - - +
45A ILE* 3.6 34.5 - - + -
49A ILE* 3.7 8.1 - - - +
81A SER* 4.1 17.1 - - - +
82A ALA* 4.0 9.0 + - - +
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Residues in contact with ARG 21 (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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19A GLY 3.6 0.2 - - - -
20A ALA* 1.4 78.1 - - - +
22A LYS* 1.4 65.4 + - + +
24A ILE* 3.4 23.0 + - + +
25A GLN* 3.4 12.0 + - - +
45A ILE* 6.2 0.4 - - - -
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Residues in contact with LYS 22 (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 VAL* 3.9 29.9 - - + +
18A MET 4.2 12.7 + - - +
19A GLY* 4.0 11.5 + - - +
20A ALA 3.5 0.6 - - - -
21A ARG* 1.4 75.1 - - + +
23A SER* 1.4 63.9 + - - +
25A GLN* 3.4 12.7 + - - +
26A TYR* 3.2 33.6 + - + -
84A ALA* 5.6 0.2 - - - -
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Residues in contact with SER 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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17A VAL 4.3 1.1 + - - -
19A GLY 2.9 22.4 + - - -
20A ALA 3.8 0.7 - - - -
21A ARG 3.4 0.4 - - - -
22A LYS* 1.4 76.1 - - - +
24A ILE* 1.4 61.9 + - - +
26A TYR* 3.8 2.1 + - - +
27A ALA* 3.3 22.5 + - - +
35A ILE* 4.3 8.7 - - - +
49A ILE* 3.7 33.4 - - - +
82A ALA* 3.5 17.9 + - - -
83A LEU* 3.5 14.0 + - - -
84A ALA* 3.6 11.0 + - - +
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Residues in contact with ILE 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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20A ALA 3.5 14.4 - - - +
21A ARG* 3.7 16.4 - - + +
22A LYS 3.3 0.6 - - - -
23A SER* 1.4 74.2 - - - +
25A GLN* 1.4 59.7 + - - +
27A ALA* 3.2 6.0 + - - +
28A LYS* 2.9 51.5 + - + +
45A ILE* 4.9 15.9 - - + +
48A ASP* 3.2 37.9 - - + +
49A ILE* 3.4 25.4 - - + +
52A TYR* 4.7 4.9 - - + -
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Residues in contact with GLN 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 ARG 3.4 8.9 + - - +
22A LYS* 3.4 16.7 + - - +
24A ILE* 1.4 78.3 - - - +
26A TYR* 1.4 73.5 + - + +
28A LYS* 3.4 21.2 + - + +
29A MET* 3.5 36.5 + - + +
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Residues in contact with TYR 26 (chain A).
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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15A LYS* 5.7 2.6 - - - +
17A VAL* 3.8 29.6 - - + +
22A LYS* 3.2 28.2 + - + +
23A SER 4.2 3.8 - - - +
24A ILE 3.4 0.2 - - - -
25A GLN* 1.4 89.6 - - + +
27A ALA* 1.4 57.9 + - - +
29A MET* 4.4 11.4 - - + -
30A GLY* 3.0 23.6 + - - -
31A GLY* 3.2 34.0 + - - -
32A ALA* 4.5 6.5 - - + -
35A ILE* 5.6 0.4 - - + -
58A ILE* 4.0 4.1 - - - +
84A ALA* 4.3 15.0 - - + -
86A VAL* 3.6 27.9 - - + +
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Residues in contact with ALA 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 SER 3.3 17.2 + - - +
24A ILE* 3.2 8.6 + - - +
26A TYR* 1.4 75.2 - - - +
28A LYS* 1.4 62.3 + - - +
30A GLY 3.9 1.0 + - - -
35A ILE* 4.0 15.0 - - + +
49A ILE* 4.3 4.7 - - + +
52A TYR* 3.5 13.0 - - + +
53A ALA* 3.9 23.1 - - + +
55A LEU* 5.9 0.2 - - - +
56A SER* 3.2 26.3 + - - -
58A ILE* 4.0 10.5 - - - +
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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 ILE* 2.9 30.1 + - - +
25A GLN* 3.6 18.2 - - + +
26A TYR 3.4 0.2 - - - -
27A ALA* 1.4 77.5 - - - +
29A MET* 1.4 61.7 + - + +
52A TYR* 3.4 40.4 - - + -
55A LEU* 5.9 1.9 - - - +
56A SER* 4.9 4.2 - - - -
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Residues in contact with MET 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 GLN* 3.5 38.8 + - + +
26A TYR* 4.0 15.0 - - + +
28A LYS* 1.4 79.2 - - - +
30A GLY* 1.4 63.6 + - - +
31A GLY* 4.2 9.4 - - - +
56A SER* 5.5 1.3 - - - -
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Residues in contact with GLY 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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26A TYR 3.0 10.4 + - - -
27A ALA 3.9 3.1 + - - -
28A LYS 3.6 1.8 - - - -
29A MET* 1.4 80.0 - - - +
31A GLY* 1.4 58.1 + - - +
32A ALA 3.7 3.3 + - - -
56A SER* 4.7 7.9 - - - -
58A ILE* 3.9 16.6 - - - -
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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