Contacts of the helix formed by residues 11 - 25 (chain A) in PDB entry 1GXH
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 1.3 71.2 - - - +
12A GLU* 1.3 58.9 + - - +
13A THR* 3.8 3.7 + - - -
14A GLU* 2.7 43.6 + - - +
15A PHE* 2.9 30.5 + - - +
82A PHE* 3.4 8.3 - - - -
83A LYS* 3.5 38.4 - - + -
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Residues in contact with GLU 12 (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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11A THR* 1.3 73.6 - - - +
13A THR* 1.3 60.3 + - - +
15A PHE* 3.9 2.8 + - - +
16A LYS* 3.2 22.2 + - - +
67A ILE* 3.7 19.3 - - + +
71A LYS* 2.7 39.7 + - - +
82A PHE* 3.3 39.0 - - + +
83A LYS* 4.8 8.4 - - - +
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Residues in contact with THR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.2 4.4 + - - -
12A GLU* 1.3 80.2 - - - +
14A GLU* 1.3 58.4 + - - +
15A PHE 3.2 0.9 - - - -
16A LYS* 3.1 21.9 - - + +
17A LYS* 2.9 24.4 + - - +
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Residues in contact with GLU 14 (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 LYS* 3.6 25.2 - - + +
9A ASP 4.2 1.2 - - - +
10A TYR* 3.8 23.8 - - + -
11A THR* 2.7 47.4 + - - +
13A THR* 1.3 72.2 - - - +
15A PHE* 1.3 65.6 + - - +
17A LYS* 2.9 18.9 + - - +
18A ILE* 3.3 8.3 + - - +
83A LYS* 5.1 0.2 - - - -
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Residues in contact with PHE 15 (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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7A ILE* 3.9 9.6 - - + -
10A TYR* 3.5 22.3 - + + -
11A THR 2.9 17.6 + - - +
12A GLU 3.9 3.1 - - - +
14A GLU* 1.3 73.2 - - - +
16A LYS* 1.3 65.1 + - - +
18A ILE* 3.1 23.8 + - + +
19A ILE* 3.0 48.9 + - + +
39A PHE* 3.7 14.1 - + - -
42A VAL* 3.5 23.3 - - + -
43A THR* 3.5 22.4 - - - -
67A ILE* 4.1 7.0 - - + -
70A ILE* 3.7 24.7 - - + -
82A PHE* 3.4 29.2 - + + -
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Residues in contact with LYS 16 (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 GLU* 3.2 13.5 + - - +
13A THR* 3.1 27.9 + - + +
15A PHE* 1.3 74.3 - - - +
17A LYS* 1.3 57.1 + - - +
19A ILE* 2.9 5.7 + - - -
20A GLU* 2.7 78.8 + - + +
63A PRO* 5.1 2.9 - - + -
64A GLU* 2.7 46.6 + - - +
67A ILE* 4.1 21.6 - - + +
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Residues in contact with LYS 17 (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 THR 2.9 15.6 + - - +
14A GLU* 2.9 14.1 + - - +
16A LYS* 1.3 68.9 - - - +
18A ILE* 1.3 57.9 + - - +
20A GLU* 4.8 4.3 - - + -
21A ASP* 2.8 50.1 + - - +
26A GLU* 2.7 42.5 + - - +
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Residues in contact with ILE 18 (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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3A LEU* 4.4 11.7 - - + -
10A TYR* 3.9 9.0 - - + +
14A GLU 3.3 7.4 + - - +
15A PHE* 3.1 33.7 + - + +
16A LYS 3.1 1.2 - - - -
17A LYS* 1.3 79.1 - - - +
19A ILE* 1.3 74.7 + - + +
21A ASP* 3.3 5.6 - - - +
22A ILE* 3.3 19.8 + - - +
31A LYS* 4.7 10.1 - - - +
34A ASP* 5.4 0.7 - - - +
35A ASN* 3.2 48.3 - - + +
38A HIS* 3.5 31.2 - - + -
39A PHE* 5.2 1.6 - - + +
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Residues in contact with ILE 19 (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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15A PHE* 3.2 35.0 - - + +
16A LYS* 2.9 3.9 + - - +
18A ILE* 1.3 82.4 - - + +
20A GLU* 1.3 58.6 + - - +
22A ILE* 2.9 30.6 - - + +
23A ILE* 3.4 18.4 + - + +
35A ASN* 4.3 0.2 - - - +
39A PHE* 3.2 45.5 - - + -
52A ILE* 4.8 0.9 - - + -
63A PRO* 3.9 21.1 - - + +
66A VAL* 4.2 9.4 - - + -
67A ILE* 3.7 21.8 - - + -
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Residues in contact with GLU 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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16A LYS* 2.7 62.1 + - + +
17A LYS* 4.6 3.2 - - - +
19A ILE* 1.3 70.3 - - - +
21A ASP* 1.3 61.2 + - - +
22A ILE 3.3 0.2 - - - -
23A ILE* 3.3 4.8 + - + +
24A ASN* 2.7 45.9 + - - +
63A PRO* 3.4 28.5 - - + +
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Residues in contact with ASP 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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17A LYS* 2.8 46.2 + - - +
18A ILE* 3.3 8.8 - - - +
20A GLU* 1.3 73.0 - - - +
22A ILE* 1.3 65.7 + - - +
24A ASN* 4.7 1.3 - - - +
25A CYS 2.9 8.5 + - - -
26A GLU* 2.8 47.1 + - - +
31A LYS* 2.8 50.0 + - - +
32A GLN* 4.9 1.4 - - - +
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Residues in contact with ILE 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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18A ILE 3.4 3.1 - - - +
19A ILE* 2.9 37.5 - - + +
21A ASP* 1.3 79.3 - - - +
23A ILE* 1.3 67.9 + - + +
25A CYS* 3.1 13.3 + - - -
32A GLN* 3.2 42.9 + - + +
35A ASN* 3.1 55.2 - - + +
36A LEU* 5.1 3.1 - - + -
52A ILE* 3.4 31.0 - - + -
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Residues in contact with ILE 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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19A ILE* 3.4 24.2 - - + +
20A GLU* 3.3 7.2 + - + +
22A ILE* 1.3 87.0 - - + +
24A ASN* 1.3 62.4 + - - +
25A CYS* 4.1 5.2 - - - -
52A ILE* 5.3 14.6 - - + -
62A SER 5.4 0.2 - - - -
63A PRO* 3.7 37.9 - - + -
66A VAL* 4.8 8.7 - - + -
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Residues in contact with ASN 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 GLU* 2.7 42.4 + - - +
21A ASP* 3.7 4.6 - - - +
23A ILE* 1.3 76.8 - - - +
25A CYS* 1.3 71.6 + - - +
26A GLU* 4.3 6.7 + - + +
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Residues in contact with CYS 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 ASP 2.9 7.4 + - - -
22A ILE 3.1 9.9 + - - -
23A ILE 4.1 5.2 - - - -
24A ASN* 1.3 88.4 - - - +
26A GLU* 1.3 50.8 + - - +
27A GLY* 2.8 21.0 + - - +
32A GLN* 3.2 30.7 - - - +
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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