Contacts of the helix formed by residues 13 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ARG* 2.8 38.1 + - - -
9B ALA* 3.4 12.4 - - + -
10B THR* 2.8 38.7 + - - +
12B ALA* 1.3 80.5 - - - +
14B CYS* 1.3 64.3 + - - +
15B SER 3.3 2.0 - - - -
16B ASP* 3.0 14.5 + - + +
17B ILE* 2.9 23.1 + - + +
56B VAL* 4.5 12.3 - - + -
71B ILE* 4.3 10.6 - - + +
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Residues in contact with CYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR 3.9 0.2 + - - -
11B ALA 3.1 13.3 + - - +
12B ALA 3.3 0.2 - - - -
13B ASP* 1.3 77.4 - - - +
15B SER* 1.3 63.3 + - - +
17B ILE* 3.1 10.4 + - - +
18B LEU* 2.9 25.5 + - - +
38B GLU* 4.1 11.0 - - + +
41B LEU* 3.7 15.6 - - + +
42B LEU* 3.5 46.4 - - + -
46B PHE* 3.6 27.1 - - - -
52B TYR* 4.1 2.2 - - - -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 4.0 8.2 + - - -
14B CYS* 1.3 76.7 - - - +
16B ASP* 1.3 68.9 + - - +
18B LEU* 3.5 6.4 + - - +
19B ARG* 3.0 27.1 + - - +
38B GLU* 3.6 31.8 + - - -
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 4.1 9.0 - - - +
13B ASP* 3.0 13.0 + - + +
15B SER* 1.3 84.4 + - - +
17B ILE* 1.3 60.5 + - + +
19B ARG* 3.0 37.3 + - - +
20B LEU* 2.9 34.0 + - - +
69B HIS* 3.9 14.2 - - - +
71B ILE* 3.9 35.5 - - + +
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.8 2.7 - - + -
13B ASP* 2.9 24.0 + - + +
14B CYS* 3.1 10.3 + - - +
16B ASP* 1.3 76.8 - - - +
18B LEU* 1.3 56.6 + - - +
20B LEU* 3.2 8.2 + - + +
21B ILE* 2.8 52.7 + - + +
41B LEU* 4.1 13.2 - - + -
52B TYR* 5.7 2.0 - - + +
54B CYS* 4.3 29.2 - - + -
56B VAL* 3.4 33.2 - - + -
71B ILE* 5.2 0.9 - - + -
74B PHE* 3.8 22.7 - - + -
76B MET* 5.0 0.2 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B CYS 2.9 15.9 + - - +
15B SER* 3.8 5.6 - - - +
17B ILE* 1.3 76.9 - - - +
19B ARG* 1.3 58.2 + - - +
21B ILE* 3.6 8.1 - - + +
22B LYS* 2.9 62.6 + - + +
34B VAL* 3.9 12.1 - - + -
36B LEU* 3.7 16.6 - - + +
37B THR* 3.8 3.6 - - - -
38B GLU* 3.5 33.4 - - + +
41B LEU* 3.7 17.4 - - + +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B SER 3.0 14.3 + - - +
16B ASP* 3.0 41.0 + - - +
17B ILE 3.2 0.2 - - - -
18B LEU* 1.3 78.1 - - - +
20B LEU* 1.3 64.3 + - + +
22B LYS* 3.5 7.4 + - - +
23B GLU* 2.9 32.6 + - - +
26B LYS* 5.1 0.5 + - - -
65B THR* 4.8 0.2 - - - +
69B HIS* 3.4 47.4 + - - +
71B ILE* 2.8 22.8 + - - +
97B MET* 3.6 33.3 - - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP 2.9 18.8 + - - +
17B ILE* 3.7 1.8 - - - +
19B ARG* 1.3 92.8 - - - +
21B ILE* 1.3 56.0 + - - +
23B GLU* 3.2 7.1 - - + +
24B LEU* 2.7 33.1 + - - +
71B ILE* 3.5 20.0 - - + +
73B GLY* 3.4 39.3 - - - +
74B PHE* 3.5 23.5 - - + -
95B PHE* 3.8 12.6 - - + -
97B MET* 3.5 33.0 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 2.8 36.1 + - + +
18B LEU* 3.6 8.5 - - + +
20B LEU* 1.3 72.2 - - - +
22B LYS* 1.3 54.9 + - - +
23B GLU 3.0 1.3 - - - -
24B LEU* 2.9 13.7 + - + +
25B ALA* 2.6 33.8 + - + +
34B VAL* 3.8 27.6 - - + -
36B LEU* 5.2 9.0 - - + -
41B LEU* 4.4 14.6 - - + -
74B PHE* 3.8 18.4 - - + -
76B MET* 4.4 17.9 - - + -
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 2.9 53.4 + - + +
19B ARG* 3.8 6.1 - - - +
21B ILE* 1.3 77.1 - - - +
23B GLU* 1.3 57.0 + - - +
25B ALA* 3.5 3.7 + - - +
26B LYS* 2.7 40.8 + - - +
33B GLN* 5.6 0.2 + - - -
34B VAL* 3.6 36.1 + - + +
36B LEU 3.7 5.7 + - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 2.9 21.6 + - - +
20B LEU* 3.2 15.7 - - + +
22B LYS* 1.3 79.5 - - - +
24B LEU* 1.3 60.9 + - - +
26B LYS* 3.3 34.8 + - - +
27B TYR* 3.3 12.1 + - - +
95B PHE* 3.3 26.0 - - + -
97B MET* 3.9 25.9 - - + +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU 2.7 14.8 + - - +
21B ILE* 3.2 13.7 - - + +
23B GLU* 1.3 72.9 - - - +
25B ALA* 1.3 56.9 + - - +
26B LYS 3.0 5.2 - - - -
27B TYR* 2.8 29.4 + - + +
28B GLU* 3.0 34.3 + - + +
74B PHE* 4.2 19.7 - - + -
93B ASP* 3.7 35.7 - - + +
94B PHE 5.1 1.6 - - - +
95B PHE* 3.7 33.0 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 2.6 18.7 + - + +
22B LYS* 3.7 7.6 - - - +
23B GLU 3.3 0.2 - - - -
24B LEU* 1.3 72.6 - - - +
26B LYS* 1.3 58.9 + - - +
28B GLU* 3.8 21.6 - - - +
31B GLU* 5.5 4.3 - - - -
32B GLU* 4.4 8.8 + - - +
33B GLN* 3.7 27.3 - - - +
34B VAL* 3.7 24.2 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG 5.1 0.6 + - - -
22B LYS* 2.7 38.5 + - - +
23B GLU* 3.3 28.6 + - - +
24B LEU 3.0 0.8 - - - -
25B ALA* 1.3 78.0 - - - +
27B TYR* 1.3 58.4 + - - +
28B GLU 3.1 11.9 + - - +
33B GLN* 4.9 11.4 - - - +
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 3.3 9.4 + - - +
24B LEU* 2.8 14.4 + - + +
26B LYS* 1.3 78.2 - - - +
28B GLU* 1.3 65.9 + - - +
29B TYR* 3.9 23.1 - + - -
95B PHE* 4.2 18.4 - + + -
98B SER* 5.8 0.4 - - - -
101B ARG* 3.5 44.1 + - - -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.0 37.2 + - + +
25B ALA* 3.8 15.7 - - - +
26B LYS 3.1 10.1 - - - +
27B TYR* 1.3 87.4 - - - +
29B TYR* 1.3 66.3 + - - +
30B MET* 4.5 13.2 - - + +
31B GLU* 5.0 2.6 + - - +
32B GLU* 4.9 10.3 - - - +
93B ASP* 4.8 9.2 - - - +
132B TRP* 5.8 3.6 - - - -
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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