Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 2G3T
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 ASP 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG* 2.8 38.8 + - - -
9A ALA* 3.4 12.1 - - + -
10A THR* 2.7 38.7 + - - +
12A ALA* 1.3 79.1 - - - +
14A CYS* 1.3 63.8 + - - +
15A SER 3.2 3.4 - - - -
16A ASP* 3.0 14.6 + - + +
17A ILE* 2.9 25.8 + - + +
56A VAL* 4.6 9.2 - - + -
71A ILE* 4.2 11.4 - - - +
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Residues in contact with CYS 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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10A THR 4.5 0.2 - - - -
11A ALA* 3.1 11.5 + - - +
12A ALA 3.3 0.4 - - - -
13A ASP* 1.3 78.3 - - - +
15A SER* 1.3 61.2 + - - +
17A ILE* 4.3 9.6 - - - -
18A LEU* 3.0 25.5 + - - +
38A GLU* 4.0 15.7 - - + +
41A LEU* 3.6 28.1 - - + +
42A LEU* 3.6 25.8 - - + -
46A PHE* 3.5 33.2 - - - -
52A TYR* 4.0 2.2 - - - -
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Residues in contact with SER 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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12A ALA 3.8 9.3 + - - -
14A CYS* 1.3 78.4 - - - +
16A ASP* 1.3 74.0 + - - +
18A LEU* 3.5 4.6 + - - +
19A ARG* 3.0 24.2 + - - +
38A GLU* 3.5 30.6 + - - -
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Residues in contact with ASP 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 ALA 4.2 3.1 - - - +
13A ASP* 3.0 17.4 + - + +
15A SER* 1.3 91.1 + - - +
17A ILE* 1.3 56.6 + - + +
19A ARG* 2.9 32.3 + - - +
20A LEU* 2.9 35.5 + - - +
69A HIS* 4.3 11.1 - - - +
70A SER 4.9 0.3 + - - -
71A ILE* 3.2 47.6 - - + +
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Residues in contact with ILE 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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9A ALA* 3.8 18.4 - - + -
13A ASP 2.9 22.4 + - - +
14A CYS* 3.8 14.6 - - - +
15A SER 3.3 0.2 - - - -
16A ASP* 1.3 74.6 - - + +
18A LEU* 1.3 60.9 + - - +
20A LEU* 3.1 8.8 + - + +
21A ILE* 2.8 51.9 + - + +
41A LEU* 4.0 11.4 - - + -
46A PHE* 5.7 1.1 - - + -
52A TYR* 5.3 4.5 - - + +
54A CYS* 3.8 40.6 - - + -
56A VAL* 4.1 15.7 - - + -
74A PHE* 4.7 11.7 - - + -
76A MET* 5.0 0.2 - - + -
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Residues in contact with LEU 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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14A CYS 3.0 17.8 + - - +
15A SER* 3.9 5.4 - - - +
17A ILE* 1.3 77.3 - - - +
19A ARG* 1.3 57.6 + - - +
21A ILE* 3.2 7.4 + - + -
22A LYS* 2.9 61.1 + - + +
34A VAL* 4.1 11.0 - - + -
36A LEU* 3.6 22.4 - - + +
37A THR* 4.0 2.9 - - - -
38A GLU* 3.6 31.0 - - + +
41A LEU* 3.8 14.3 - - + +
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Residues in contact with ARG 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 SER 3.0 14.3 + - - +
16A ASP* 2.9 40.6 + - - +
17A ILE 3.2 0.2 - - - -
18A LEU* 1.3 77.1 - - - +
20A LEU* 1.3 75.0 + - - +
22A LYS* 3.4 9.2 + - - +
23A GLU* 3.0 32.2 + - - +
69A HIS* 3.4 48.4 + - - +
71A ILE 3.0 20.8 + - - -
97A MET* 3.9 19.0 - - - +
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Residues in contact with LEU 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 ASP 2.9 19.6 + - - +
17A ILE* 3.1 2.2 + - - +
19A ARG* 1.3 90.1 - - - +
21A ILE* 1.3 60.3 + - - +
23A GLU* 3.3 6.4 + - - +
24A LEU* 2.8 29.5 + - - +
71A ILE* 3.6 31.4 - - + +
72A VAL 4.3 3.8 - - - -
73A GLY 3.7 22.9 - - - +
74A PHE* 3.5 24.0 - - + -
95A PHE* 3.8 15.1 - - + -
97A MET* 3.6 32.5 - - + -
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Residues in contact with ILE 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 ILE* 2.8 40.9 + - + +
18A LEU* 3.2 11.2 + - + +
20A LEU* 1.3 72.7 - - - +
22A LYS* 1.3 58.9 + - - +
24A LEU* 3.1 12.0 + - + +
25A ALA* 2.8 27.8 + - + +
34A VAL* 4.2 25.8 - - + -
36A LEU* 4.5 11.0 - - + -
41A LEU* 4.4 11.9 - - + -
74A PHE* 3.8 19.5 - - + -
76A MET* 4.4 16.8 - - + -
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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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18A LEU* 2.9 49.1 + - + +
19A ARG* 3.7 7.6 - - - +
21A ILE* 1.3 77.4 - - - +
23A GLU* 1.3 62.1 + - - +
25A ALA* 3.5 9.1 + - - +
26A LYS* 3.2 22.0 + - - +
34A VAL* 3.7 31.4 + - + +
36A LEU 3.8 7.3 + - - -
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Residues in contact with GLU 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 ARG* 3.0 24.3 + - - +
20A LEU* 3.6 9.9 - - - +
21A ILE 3.1 0.2 - - - -
22A LYS* 1.3 75.3 - - - +
24A LEU* 1.3 61.0 + - - +
26A LYS* 3.4 14.8 + - + +
27A TYR* 3.1 24.1 + - - +
95A PHE* 3.7 15.9 - - + -
97A MET* 3.1 45.0 - - - +
98A SER* 4.7 3.7 + - - -
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Residues in contact with LEU 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 LEU 2.8 17.7 + - - +
21A ILE* 3.1 11.0 + - + +
23A GLU* 1.3 75.6 - - - +
25A ALA* 1.3 58.0 + - - +
27A TYR* 3.0 11.2 + - + +
28A GLU* 2.9 63.5 + - + +
74A PHE* 4.2 19.5 - - + -
93A ASP* 3.7 34.5 - - + +
94A PHE 5.0 2.9 - - - +
95A PHE* 3.8 34.3 - - + -
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Residues in contact with ALA 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 ILE* 2.8 17.2 + - + +
22A LYS 3.6 6.1 - - - +
23A GLU 3.3 0.2 - - - -
24A LEU* 1.3 77.2 - - - +
26A LYS* 1.3 61.3 + - - +
28A GLU* 3.7 21.8 - - - +
31A GLU* 4.1 16.4 - - - +
32A GLU 4.3 13.3 + - - +
34A VAL* 3.5 25.1 - - + -
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Residues in contact with LYS 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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22A LYS 3.2 11.7 + - - +
23A GLU* 3.5 17.1 - - + +
24A LEU 3.1 0.4 - - - -
25A ALA* 1.3 78.2 - - - +
27A TYR* 1.3 67.4 + - - +
28A GLU 3.1 8.3 - - - +
31A GLU* 5.4 2.0 - - - -
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Residues in contact with TYR 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 GLU 3.1 13.5 + - - +
24A LEU* 3.0 16.7 + - + +
26A LYS* 1.3 74.6 - - - +
28A GLU* 1.3 80.9 + - - +
29A TYR* 3.7 29.4 + + - -
95A PHE* 4.2 20.4 - + + -
101A ARG* 3.8 30.0 + - - -
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Residues in contact with GLU 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 LEU* 2.9 48.9 + - + +
25A ALA* 3.7 15.6 - - - +
26A LYS 3.1 10.6 - - - +
27A TYR* 1.3 93.3 - - - +
29A TYR* 1.3 63.5 + - - +
30A MET* 4.2 15.5 - - + +
31A GLU* 4.8 2.5 + - - +
93A ASP* 5.1 4.0 - - - +
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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