Contacts of the helix formed by residues 8 - 20 (chain A) in PDB entry 2G9W
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG 3.6 2.2 + - - -
7A LEU* 1.3 76.6 - - - +
9A ASP* 1.3 60.9 + - - -
10A LEU 3.3 2.9 - - - -
11A GLU* 2.9 19.4 + - - -
12A ARG* 2.9 26.5 + - - +
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Residues in contact with ASP 9 (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 LEU 4.8 2.8 - - - +
8A GLY* 1.3 73.9 - - - -
10A LEU* 1.3 58.2 + - - +
12A ARG* 3.5 6.5 + - - +
13A ALA* 3.0 26.3 + - - +
38A ARG* 4.0 19.5 + - - +
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Residues in contact with LEU 10 (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 GLY 3.3 0.4 - - - -
9A ASP* 1.3 75.6 - - - +
11A GLU* 1.3 67.6 + - - +
12A ARG 3.2 0.2 - - - -
13A ALA* 3.2 3.4 + - + -
14A VAL* 3.0 29.3 + - + +
34A LEU* 3.7 17.3 - - + -
38A ARG* 4.1 18.8 - - - +
40A LEU* 3.7 40.2 - - + -
44A THR* 4.2 18.8 - - + -
45A VAL* 6.0 1.6 - - + -
48A VAL* 4.3 19.7 - - + -
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Residues in contact with GLU 11 (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 ARG 4.9 0.3 - - - +
7A LEU* 3.5 17.7 - - + +
8A GLY* 2.9 29.6 + - - +
10A LEU* 1.3 79.4 - - + +
12A ARG* 1.3 56.3 + - - +
14A VAL* 3.5 2.6 + - - +
15A MSE 3.0 33.4 + - - +
48A VAL* 4.1 18.7 - - + +
51A ARG* 5.1 5.9 - - + +
52A LEU* 3.8 25.1 - - + +
55A LYS* 2.8 37.7 + - - +
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Residues in contact with ARG 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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4A LEU 5.2 3.1 + - - -
5A THR* 6.1 0.2 - - - +
7A LEU* 4.0 23.1 - - + +
8A GLY 2.9 17.8 + - - +
9A ASP* 3.8 8.1 - - - +
11A GLU* 1.3 74.8 - - - +
13A ALA* 1.3 56.3 + - - +
15A MSE 3.0 0.9 + - - -
16A ASP* 2.7 61.9 + - - +
19A TRP* 3.9 14.6 - - - -
75A ARG* 4.2 14.1 - - - +
78A LEU* 3.5 36.8 - - - +
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Residues in contact with ALA 13 (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 ASP 3.0 18.7 + - - +
10A LEU* 3.2 8.5 + - + +
12A ARG* 1.3 75.0 - - - +
14A VAL* 1.3 63.0 + - - +
16A ASP* 3.5 12.2 + - - +
17A HIS* 3.2 16.6 + - - +
34A LEU* 3.5 30.5 - - + +
38A ARG* 3.7 19.7 - - - +
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Residues in contact with VAL 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 LEU* 3.0 16.3 + - + +
11A GLU 3.6 6.7 - - - +
13A ALA* 1.3 76.7 - - - +
15A MSE 1.3 63.4 + - - +
17A HIS* 2.9 15.6 + - - +
18A LEU* 3.1 19.1 + - + +
30A VAL* 4.0 18.2 - - + -
34A LEU* 3.8 20.9 - - + -
45A VAL* 5.1 4.9 - - + -
48A VAL* 4.1 17.7 - - + -
49A LEU* 3.7 24.2 - - + -
52A LEU* 3.6 21.5 - - + -
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Residues in contact with MSE 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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4A LEU* 4.8 6.1 - - + -
7A LEU* 3.7 20.4 - - + -
11A GLU 3.0 23.5 + - - +
12A ARG* 3.0 4.0 + - - +
14A VAL* 1.3 74.8 - - - +
16A ASP* 1.3 57.6 + - - +
18A LEU* 3.3 6.7 + - + +
19A TRP* 2.9 79.0 + - + +
52A LEU* 4.1 12.8 - - + -
57A LEU* 3.8 17.9 - - - +
58A VAL* 3.7 25.4 - - - -
71A PRO* 3.7 20.2 - - + -
73A HIS* 4.2 2.9 - - + +
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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 ARG* 2.7 57.9 + - - +
13A ALA* 3.5 10.4 - - - +
15A MSE 1.3 77.7 - - - +
17A HIS* 1.3 62.5 - - - +
19A TRP* 3.6 15.7 + - - +
20A SER* 3.1 22.5 + - - -
75A ARG* 5.1 2.9 + - - -
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Residues in contact with HIS 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 ALA 3.2 8.7 + - - +
14A VAL* 2.9 11.4 + - - +
16A ASP* 1.3 79.5 - - - +
18A LEU* 1.3 65.8 + - - +
20A SER* 2.4 29.3 + - - -
21A ARG* 3.5 36.8 - - + +
25A GLN* 2.7 38.7 + - + -
29A GLN* 3.8 8.7 + - + -
30A VAL* 3.9 27.6 - - + -
33A ALA* 3.3 30.8 - - + +
34A LEU* 5.5 2.7 - - + -
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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 VAL* 3.1 27.2 + - + +
15A MSE 3.7 12.3 - - - +
17A HIS* 1.3 81.3 - - - +
19A TRP* 1.3 56.8 + - - +
20A SER 3.3 0.3 + - - -
21A ARG* 3.0 26.0 + - - +
23A GLU 5.4 0.3 - - - +
25A GLN* 3.7 26.2 - - + +
30A VAL* 4.0 13.2 - - + -
49A LEU* 4.3 5.2 - - + -
58A VAL* 3.6 32.1 - - + -
69A TYR* 3.6 26.0 - - + +
71A PRO* 3.9 30.5 - - + +
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Residues in contact with TRP 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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4A LEU* 4.0 28.3 - - + -
7A LEU* 4.9 1.1 - - + -
12A ARG* 3.9 14.6 - - - -
15A MSE 2.9 55.2 + - + +
16A ASP* 3.8 25.1 - - - +
18A LEU* 1.3 75.8 - - - +
20A SER* 1.3 60.7 + - - +
21A ARG 3.2 2.5 + - - +
71A PRO* 4.0 15.0 - - + -
73A HIS 2.9 22.9 + - - -
74A GLY* 4.0 2.9 - - - -
75A ARG* 3.3 52.0 - - + +
78A LEU* 4.0 21.5 - - + -
91B GLU* 5.6 1.6 - - - +
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Residues in contact with SER 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 3.1 12.6 + - - -
17A HIS* 2.4 31.3 + - - -
19A TRP* 1.3 76.4 - - - +
21A ARG* 1.3 83.8 + - - +
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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