Contacts of the helix formed by residues 3 - 24 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 3.3 6.0 + - - -
2B PRO* 1.3 75.6 - - - +
4B LYS* 1.3 67.9 + - - +
5B LEU* 3.1 2.5 - - - -
6B ALA* 2.9 24.7 + - - +
7B LEU* 3.2 7.7 - - - +
69B LEU 3.5 13.2 - - - -
70B GLU* 3.5 21.5 + - - -
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Residues in contact with LYS 4 (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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25A MET* 3.5 36.7 - - + +
26A SER* 2.7 36.1 + - - +
27A TYR* 3.9 4.9 - - - +
29A ASP* 3.9 15.6 + - + +
30A ALA* 6.2 1.3 - - + -
38A LEU* 5.9 1.6 - - + -
3B SER* 1.3 71.8 - - - +
5B LEU* 1.3 55.1 + - - +
7B LEU* 3.1 14.7 + - - +
8B ILE* 2.8 31.1 + - - +
68B TYR* 3.1 25.6 - - + +
69B LEU* 2.9 26.5 - - + +
71B GLY* 6.1 0.2 - - - -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.1 1.3 - - - -
4B LYS* 1.3 69.8 - - - +
6B ALA* 1.3 64.3 + - - +
7B LEU 3.1 0.2 - - - -
8B ILE* 3.1 20.9 - - + +
9B GLN* 2.8 49.3 + - + +
60B LEU* 4.7 6.1 - - + -
66B VAL* 3.8 34.1 - - + +
69B LEU* 2.7 30.6 + - + +
70B GLU* 3.3 24.0 - - + +
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Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 3.8 15.7 - - + -
3B SER* 2.9 28.8 + - - +
5B LEU* 1.3 84.7 - - - +
7B LEU* 1.3 54.8 + - - +
9B GLN* 4.0 3.0 - - - +
10B GLU* 3.0 36.8 + - - +
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Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.1 51.4 - - + +
22A ALA* 4.9 2.2 - - - +
25A MET* 4.6 12.8 - - + -
2B PRO* 4.1 21.8 - - + +
3B SER 3.2 19.3 - - - +
4B LYS* 3.1 11.6 + - - +
5B LEU 3.1 0.4 - - - -
6B ALA* 1.3 75.0 - - - +
8B ILE* 1.3 61.6 + - + +
10B GLU* 3.0 18.0 + - - +
11B LEU* 2.9 34.8 + - + +
14B ARG* 5.5 0.7 - - - +
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 5.1 0.7 - - + -
25A MET* 3.5 32.1 - - + -
41A LEU* 3.9 17.3 - - + -
4B LYS 2.8 11.7 + - - +
5B LEU* 3.1 33.0 - - + +
7B LEU* 1.3 74.0 - - + +
9B GLN* 1.3 87.6 + - + +
11B LEU* 3.6 10.8 - - + +
12B PRO* 3.4 4.9 - - - +
56B VAL* 3.2 40.4 - - + +
59B LEU* 4.3 5.4 - - + -
60B LEU* 4.5 5.8 - - + -
69B LEU* 3.5 31.6 - - + -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 2.8 40.6 + - + +
6B ALA* 4.1 3.6 - - - +
8B ILE* 1.3 81.8 - - + +
10B GLU* 1.3 57.6 + - - +
12B PRO* 3.0 22.6 - - - +
13B ASP* 4.5 1.4 + - - +
56B VAL* 3.7 5.9 - - - +
60B LEU* 3.3 40.3 - - - +
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Residues in contact with GLU 10 (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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2B PRO* 5.1 3.3 - - - +
6B ALA* 3.0 24.5 + - - +
7B LEU* 3.0 33.0 + - - +
9B GLN* 1.3 75.5 - - - +
11B LEU* 1.3 55.3 + - + +
12B PRO 3.2 1.1 - - - -
13B ASP* 2.8 13.4 + - + +
14B ARG* 2.6 77.1 + - + +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.0 30.4 - - - +
19A VAL* 4.4 1.8 - - + -
21A ALA* 4.6 2.9 - - + -
22A ALA* 3.6 38.4 - - + +
41A LEU* 4.5 13.5 - - + -
45A LEU* 4.7 11.7 - - + -
7B LEU 2.9 28.9 + - - +
8B ILE* 3.6 17.7 - - + +
10B GLU* 1.3 76.0 - - + +
12B PRO* 1.4 63.2 - - + +
14B ARG* 3.2 9.5 + - - +
15B ILE* 2.8 33.1 + - - +
52B VAL* 4.6 9.4 - - + +
56B VAL* 4.4 11.0 - - + -
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Residues in contact with PRO 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE 3.4 8.1 - - - +
9B GLN* 3.0 21.1 - - - +
11B LEU* 1.4 94.5 - - + +
13B ASP* 1.3 57.1 + - - +
15B ILE* 3.3 12.3 - - + +
16B GLN* 2.8 28.6 + - - +
49B LYS 5.7 0.4 - - - +
52B VAL* 5.1 3.6 - - + -
53B GLY* 4.2 19.3 - - - +
56B VAL* 4.0 18.6 - - + -
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Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN 4.5 1.1 + - - +
10B GLU* 2.8 19.5 + - + +
12B PRO* 1.3 73.4 - - - +
14B ARG* 1.3 58.0 + - - +
16B GLN* 3.1 28.0 + - - +
17B THR* 2.8 46.3 + - - -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 4.9 0.7 - - - +
17A THR* 2.7 28.1 + - + +
18A ALA* 3.3 31.2 - - - +
20A GLU* 2.7 30.1 + - - -
21A ALA* 3.5 19.9 - - - +
7B LEU* 5.5 0.6 - - - +
10B GLU* 2.6 54.6 + - + +
11B LEU* 3.4 11.4 - - - +
13B ASP* 1.3 76.0 + - - +
15B ILE* 1.3 50.3 + - - +
17B THR* 3.3 8.5 + - - -
18B ALA* 2.7 31.4 + - - +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 39.5 - - + -
18A ALA* 3.8 3.6 - - + +
19A VAL* 5.5 0.7 - - + -
52A VAL* 5.2 1.3 - - + -
11B LEU 2.8 17.7 + - - +
12B PRO* 3.3 16.2 - - + +
14B ARG* 1.3 70.5 - - - +
16B GLN* 1.3 70.4 + - - +
17B THR 3.2 0.2 - - - -
18B ALA* 3.5 7.0 - - + -
19B VAL* 3.0 18.3 + - + -
45B LEU* 4.7 15.3 - - + -
48B ALA* 5.0 3.6 - - + -
49B LYS* 3.6 49.4 - - + +
52B VAL* 4.8 16.4 - - + -
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Residues in contact with GLN 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 PRO 2.8 16.1 + - - +
13B ASP* 3.2 31.6 + - - +
15B ILE* 1.3 78.5 - - - +
17B THR* 1.3 57.8 + - - +
19B VAL* 3.7 1.9 - - - +
20B GLU* 2.9 35.4 + - + +
49B LYS* 3.8 25.1 + - + +
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Residues in contact with THR 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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14A ARG* 2.7 36.6 + - + +
13B ASP* 2.8 24.9 + - - -
14B ARG* 3.5 10.9 - - - -
16B GLN* 1.3 75.5 + - - +
18B ALA* 1.3 56.4 + - - +
19B VAL 3.2 0.9 - - - -
20B GLU* 3.1 20.6 - - + +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.0 24.0 - - - +
14A ARG* 3.1 46.2 + - + +
15A ILE* 4.0 7.6 - - + +
14B ARG 2.7 18.4 + - - +
15B ILE* 3.3 26.7 - - + +
17B THR* 1.3 75.7 - - - +
19B VAL* 1.3 58.0 + - + +
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Residues in contact with VAL 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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11A LEU* 4.0 9.0 - - + -
15B ILE 3.0 7.2 + - - +
16B GLN 4.2 0.2 - - - +
18B ALA* 1.3 77.7 - - + +
20B GLU* 1.3 61.6 + - - +
21B ALA 3.1 3.1 - - - -
22B ALA* 3.0 14.8 + - + -
23B MET* 2.8 49.6 + - + +
45B LEU* 3.5 38.1 - - + +
49B LYS* 3.2 42.8 - - + +
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Residues in contact with GLU 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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14A ARG* 2.6 29.3 + - - -
16B GLN* 2.9 18.0 + - + +
17B THR* 3.1 29.6 - - + +
19B VAL* 1.3 77.2 - - - +
21B ALA* 1.3 69.9 + - - +
23B MET* 3.8 8.2 - - - +
24B GLY* 2.8 31.9 + - - -
49B LYS* 6.0 0.7 - - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.2 40.5 - - + +
11A LEU* 4.7 4.9 - - + -
14A ARG* 3.4 30.3 - - - +
20B GLU* 1.3 88.8 + - - +
22B ALA* 1.3 57.6 + - - +
24B GLY* 3.6 2.3 - - - -
25B MET* 3.0 20.8 + - - +
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Residues in contact with ALA 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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7A LEU* 4.6 3.4 - - + -
8A ILE* 5.2 0.7 - - + -
11A LEU* 3.7 31.2 - - + -
19B VAL* 3.0 15.2 + - + +
21B ALA* 1.3 77.7 - - - +
23B MET* 1.3 65.4 + - + +
25B MET* 3.1 27.8 - - + +
41B LEU* 3.8 18.3 - - + +
42B HIS* 3.0 17.4 + - - -
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 2.8 49.3 + - + +
20B GLU* 3.8 7.4 - - - +
22B ALA* 1.3 80.4 - - + +
24B GLY* 1.3 58.5 + - - +
25B MET 3.1 4.0 + - - +
41B LEU* 3.6 20.6 - - + +
42B HIS* 3.2 57.4 + - + +
45B LEU* 4.3 2.2 - - + -
46B ASN* 4.0 21.3 - - - +
49B LYS* 4.6 9.6 - - - +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 2.8 19.4 + - - -
21B ALA 3.6 3.8 - - - -
23B MET* 1.3 71.5 - - - +
25B MET* 1.3 63.5 + - - +
26B SER* 3.5 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
------------------------------------------------------------
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