Contacts of the helix formed by residues 3 - 24 (chain A) in PDB entry 2B9Z
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 SER 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 3.4 8.0 + - - -
2A PRO* 1.3 74.6 - - - +
4A LYS* 1.3 69.4 + - - +
5A LEU* 3.1 1.6 - - - -
6A ALA* 2.9 17.5 + - - +
7A LEU* 3.1 16.0 + - - +
69A LEU 3.6 13.0 - - - -
70A GLU* 4.0 16.8 + - - -
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Residues in contact with LYS 4 (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 SER* 1.3 72.7 - - - +
5A LEU* 1.3 54.5 + - - +
7A LEU* 3.2 14.4 + - - +
8A ILE* 2.8 32.1 + - - +
68A TYR* 3.1 25.8 - - + +
69A LEU* 3.0 26.0 - - + +
25B MET* 3.4 40.1 - - + +
26B SER* 2.7 34.6 + - - +
27B TYR* 4.0 5.6 - - - +
29B ASP* 3.8 15.7 + - - +
38B LEU* 5.8 1.6 - - + -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.1 0.8 - - - -
4A LYS* 1.3 70.1 - - - +
6A ALA* 1.3 63.7 + - - +
7A LEU 3.0 1.1 - - - -
8A ILE* 3.1 21.2 - - + +
9A GLN* 2.8 48.6 + - + +
60A LEU* 5.1 2.5 - - + -
66A VAL* 3.7 24.7 - - + +
69A LEU* 2.7 29.5 + - + +
70A GLU* 3.3 37.5 - - + +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 3.8 15.7 - - + -
3A SER* 2.9 26.5 + - - +
5A LEU* 1.3 83.1 - - - +
7A LEU* 1.3 57.0 + - - +
9A GLN* 3.9 3.6 - - - +
10A GLU* 3.0 36.2 + - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 3.9 25.1 - - + +
3A SER 3.1 21.1 + - - +
4A LYS* 3.3 15.9 - - - +
5A LEU 3.0 0.2 - - - -
6A ALA* 1.3 74.5 - - - +
8A ILE* 1.3 61.0 + - + +
10A GLU* 3.2 14.6 + - - +
11A LEU* 2.8 35.8 + - + +
14A ARG* 5.4 1.6 - - - +
21B ALA* 3.2 51.1 - - + +
22B ALA* 4.2 4.3 - - - +
25B MET* 4.6 9.9 - - + -
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 2.8 15.7 + - - +
5A LEU* 3.1 45.8 - - + +
7A LEU* 1.3 73.2 - - - +
9A GLN* 1.3 75.0 + - + +
11A LEU* 3.5 10.8 - - + +
12A PRO* 3.2 10.0 - - - +
56A VAL* 3.2 27.4 - - + +
59A LEU* 4.1 10.5 - - + -
60A LEU* 4.3 15.3 - - + -
69A LEU* 3.4 28.5 - - + -
22B ALA* 5.2 0.4 - - + -
25B MET* 3.8 22.0 - - + -
41B LEU* 4.0 19.7 - - + -
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 2.8 40.2 + - + +
6A ALA* 4.0 4.0 - - - +
8A ILE* 1.3 80.9 - - + +
10A GLU* 1.3 57.8 + - - +
12A PRO* 3.0 21.2 - - - +
13A ASP* 4.5 1.7 + - - +
56A VAL* 4.3 3.1 - - - +
60A LEU* 3.5 40.9 - - - +
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Residues in contact with GLU 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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2A PRO* 4.8 5.0 - - - +
6A ALA* 3.0 35.7 + - - +
7A LEU* 3.2 20.5 + - - +
9A GLN* 1.3 74.2 - - - +
11A LEU* 1.3 55.4 + - - +
12A PRO 3.2 1.3 - - - -
13A ASP* 2.8 12.1 + - + +
14A ARG* 2.6 77.5 + - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 2.8 27.6 + - - +
8A ILE* 3.5 17.5 - - + +
10A GLU* 1.3 75.1 - - - +
12A PRO* 1.4 62.7 - - + +
14A ARG* 3.2 9.5 + - - +
15A ILE* 2.8 32.2 + - - +
52A VAL* 4.8 8.0 - - + +
56A VAL* 4.2 12.6 - - + -
18B ALA* 3.0 29.0 - - - +
19B VAL* 4.0 13.2 - - + -
21B ALA* 4.7 2.9 - - + -
22B ALA* 3.7 36.6 - - + +
41B LEU* 4.2 15.3 - - + -
45B LEU* 5.0 2.5 - - + -
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Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE 3.2 12.1 - - - +
9A GLN* 3.0 20.4 - - - +
11A LEU* 1.4 92.7 - - + +
13A ASP* 1.3 56.1 + - - +
15A ILE* 3.3 10.7 - - + +
16A GLN* 2.8 29.7 + - - +
49A LYS 5.5 1.8 - - - +
52A VAL* 5.1 3.6 - - + -
53A GLY* 5.1 11.7 - - - +
56A VAL* 3.8 24.2 - - + -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN 4.5 1.5 + - - +
10A GLU* 2.8 18.4 + - + +
12A PRO* 1.3 73.6 - - - +
14A ARG* 1.3 55.2 + - - +
16A GLN* 3.2 26.0 + - - +
17A THR* 2.8 47.3 + - - -
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Residues in contact with ARG 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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7A LEU* 5.1 1.6 - - - +
10A GLU* 2.6 57.3 + - + +
11A LEU* 3.4 10.8 - - - +
13A ASP* 1.3 74.0 + - - +
15A ILE* 1.3 51.2 + - - +
17A THR* 3.2 9.3 + - - -
18A ALA* 2.7 32.1 + - - +
14B ARG 4.9 0.5 - - - +
17B THR* 2.7 25.9 + - + +
18B ALA* 3.1 30.7 + - - +
20B GLU* 2.6 27.1 + - - -
21B ALA* 3.4 23.5 - - - +
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Residues in contact with ILE 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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11A LEU 2.8 14.5 + - - +
12A PRO* 3.3 14.1 - - + +
14A ARG* 1.3 73.0 - - - +
16A GLN* 1.3 64.0 + - - +
17A THR 3.0 1.3 - - - -
18A ALA* 3.6 3.6 - - + -
19A VAL* 2.9 51.2 + - + +
45A LEU* 5.4 0.7 - - + -
48A ALA* 4.7 5.4 - - + -
49A LYS* 3.5 44.2 - - + +
52A VAL* 4.6 14.8 - - + -
15B ILE* 3.5 37.9 - - + -
18B ALA* 4.0 3.5 - - + +
52B VAL* 5.4 0.9 - - + -
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Residues in contact with GLN 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 PRO 2.8 19.7 + - - +
13A ASP* 3.4 25.9 + - - +
15A ILE* 1.3 77.2 - - - +
17A THR* 1.3 56.9 + - - +
20A GLU* 2.8 32.8 + - + +
49A LYS* 3.5 27.9 + - + +
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Residues in contact with THR 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 ASP* 2.8 29.0 + - - -
14A ARG* 3.3 11.8 - - - +
16A GLN* 1.3 74.8 + - - +
18A ALA* 1.3 58.9 + - - +
19A VAL 3.0 3.6 + - - -
20A GLU* 3.1 20.8 - - + +
14B ARG* 2.7 39.1 + - + +
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Residues in contact with ALA 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 ARG 2.7 19.0 + - - +
15A ILE* 3.4 19.7 - - + +
17A THR* 1.3 73.2 - - - +
19A VAL* 1.3 58.8 + - + +
11B LEU* 3.0 27.4 - - - +
14B ARG* 3.3 46.7 + - + +
15B ILE* 3.8 11.2 - - + +
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Residues in contact with VAL 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 ILE* 2.9 38.1 + - + +
16A GLN 3.8 0.2 - - - -
18A ALA* 1.3 83.1 - - + +
20A GLU* 1.3 63.1 + - - +
21A ALA 3.1 2.7 - - - -
22A ALA* 3.0 6.6 + - + -
23A MET* 2.9 48.1 + - + +
45A LEU* 3.6 34.1 - - + +
49A LYS* 3.6 18.8 - - + -
11B LEU* 4.4 6.1 - - + -
15B ILE* 5.5 1.3 - - + -
52B VAL* 5.6 0.4 - - + -
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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 GLN* 2.8 18.4 + - + +
17A THR* 3.1 30.4 - - + +
19A VAL* 1.3 76.5 - - - +
21A ALA* 1.3 68.8 + - - +
23A MET* 3.7 8.7 - - - +
24A GLY* 2.8 29.1 + - - -
49A LYS* 5.7 1.3 - - - +
14B ARG* 2.7 28.4 + - - -
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Residues in contact with ALA 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 VAL 3.1 0.2 - - - -
20A GLU* 1.3 88.8 - - - +
22A ALA* 1.3 56.3 + - - +
24A GLY* 3.4 1.7 + - - -
25A MET 3.0 21.1 + - - -
7B LEU* 3.1 40.0 - - + +
11B LEU* 4.6 6.3 - - + -
14B ARG* 3.5 32.7 - - - +
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Residues in contact with ALA 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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19A VAL* 3.0 10.0 + - + +
21A ALA* 1.3 76.4 - - - +
23A MET* 1.3 69.7 + - + +
25A MET* 3.1 27.9 - - + +
41A LEU* 4.1 17.3 - - + -
42A HIS* 3.0 18.4 + - - -
45A LEU* 5.6 0.2 - - + -
7B LEU* 4.6 3.1 - - + -
8B ILE* 5.1 1.1 - - + -
11B LEU* 3.6 33.2 - - + -
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Residues in contact with MET 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 VAL* 2.9 42.6 + - + +
20A GLU* 3.7 9.6 - - - +
22A ALA* 1.3 84.6 - - + +
24A GLY* 1.3 59.0 + - - +
25A MET 3.1 3.2 + - - +
27A TYR* 4.8 0.5 - - - -
41A LEU* 4.0 1.1 - - + +
42A HIS* 3.3 72.7 - - + +
45A LEU* 3.9 11.9 - - + -
46A ASN* 4.2 11.9 - - - -
49A LYS* 4.2 14.1 - - - +
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Residues in contact with GLY 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 2.8 16.9 + - - -
21A ALA 3.6 3.4 - - - -
23A MET* 1.3 74.3 - - - +
25A MET* 1.3 63.6 + - - +
26A SER* 3.4 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
------------------------------------------------------------
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