Contacts of the helix formed by residues 3 - 22 (chain B) in PDB entry 2B5A
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 ASN 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 4.3 0.2 + - - -
2B ILE* 1.3 72.7 - - - +
4B GLU* 1.3 58.8 + - - +
5B ILE* 3.2 10.9 + - - +
6B GLU* 2.9 53.3 + - - +
7B ILE* 3.0 29.0 + - - +
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Residues in contact with GLU 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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53A ILE* 3.5 50.3 - - + +
57A LYS* 4.2 14.4 + - - +
2B ILE* 3.9 13.0 - - + +
3B ASN* 1.3 69.9 + - - +
5B ILE* 1.3 66.9 + - + +
7B ILE 3.3 1.0 + - - -
8B LYS* 3.0 33.7 + - - +
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Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 3.2 6.7 + - - +
4B GLU* 1.3 77.8 - - + +
6B GLU* 1.3 60.8 + - + +
8B LYS* 3.3 16.4 + - - +
9B ARG* 2.9 63.5 + - + +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 2.9 41.6 + - - +
5B ILE* 1.3 78.4 - - + +
7B ILE* 1.3 58.2 + - + +
9B ARG* 4.0 4.8 - - - +
10B LYS* 2.9 33.3 + - - +
16C LYS* 3.2 27.3 + - - -
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.8 20.2 - - + -
53A ILE* 3.7 17.5 - - + -
56A HIS* 3.7 35.4 - - + +
2B ILE* 4.0 27.1 - - + -
3B ASN 3.0 18.7 + - - +
4B GLU 3.3 6.7 + - - +
6B GLU* 1.3 76.8 - - + +
8B LYS* 1.3 65.2 + - - +
10B LYS* 4.7 0.9 - - + -
11B PHE* 2.9 23.9 + - - +
73B MET* 3.6 14.5 - - + +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.0 12.7 - - + +
53A ILE* 4.0 22.0 - - + +
4B GLU* 3.0 35.2 + - - +
5B ILE* 3.9 14.2 - - - +
7B ILE* 1.3 76.2 - - - +
9B ARG* 1.3 63.6 + - - +
11B PHE* 3.8 2.6 - - - +
12B GLY* 3.1 17.3 + - - -
43B VAL 4.4 0.9 - - - +
46B GLY* 3.6 32.5 + - - +
47B ASP 6.0 1.0 - - - -
48B ARG 3.4 28.7 - - - +
49B ASN* 4.3 9.3 - - + +
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Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 2.9 42.6 + - + +
6B GLU* 4.0 4.3 - - - +
8B LYS* 1.3 77.7 - - - +
10B LYS* 1.3 57.9 + - - +
12B GLY* 3.3 1.6 + - - -
13B ARG* 2.9 38.7 + - + +
44B GLU 4.7 0.9 - - - +
45B ARG 4.2 6.0 + - - +
46B GLY* 4.2 9.8 + - - +
9C ARG* 3.4 53.4 - - - +
45C ARG* 2.9 41.1 + - - +
47C ASP* 5.1 5.5 + - - -
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 2.9 19.7 + - - +
7B ILE* 4.0 2.7 - - + +
9B ARG* 1.3 73.1 - - - +
11B PHE* 1.3 66.6 + - - +
13B ARG* 3.4 33.9 + - + +
14B THR* 2.7 39.8 + - - -
72B LYS 4.8 1.8 - - - -
73B MET* 2.8 45.3 + - + +
75B GLU 3.0 25.2 + - - -
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 28.7 - - + -
7B ILE 2.9 18.2 + - - +
8B LYS 3.8 2.9 - - - +
10B LYS* 1.3 77.1 - - - +
12B GLY* 1.3 58.3 + - - +
14B THR* 3.2 3.8 + - - -
15B LEU* 2.9 34.3 + - + +
43B VAL* 3.7 28.7 - - + -
50B ILE* 3.8 28.0 - - + -
55B ILE* 4.1 21.1 - - + -
58B ILE* 5.7 4.0 - - + -
59B CYS* 6.1 1.3 - - - -
69B PHE* 3.2 38.3 - + - -
70B PHE* 4.0 13.9 - + - -
73B MET* 3.7 12.2 - - - +
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Residues in contact with GLY 12 (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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8B LYS 3.1 12.2 + - - -
9B ARG 3.3 2.6 + - - -
11B PHE* 1.3 80.0 - - - +
13B ARG* 1.3 56.3 + - - +
15B LEU* 3.4 4.8 + - - +
16B LYS* 3.0 26.9 + - - +
43B VAL 3.3 25.6 - - - -
44B GLU* 3.4 21.7 - - - +
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 2.9 23.5 + - + +
10B LYS* 3.5 36.1 - - + +
12B GLY* 1.3 76.1 - - - +
14B THR* 1.3 60.0 + - - +
16B LYS* 3.4 6.9 + - - +
17B LYS* 3.0 29.3 + - - +
44B GLU 3.9 4.9 + - - +
13C ARG* 3.5 59.9 - - - +
76C GLU* 4.1 11.9 + - - +
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 2.7 29.7 + - - -
11B PHE 3.6 4.3 - - - -
13B ARG* 1.3 73.6 - - - +
15B LEU* 1.3 65.9 + - - +
17B LYS* 3.2 9.0 + - + +
18B ILE* 2.9 44.8 + - + +
69B PHE* 3.8 19.5 - - + +
72B LYS* 4.2 6.4 + - + -
73B MET* 3.4 37.5 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 2.9 19.7 + - + +
12B GLY* 3.6 6.1 - - - +
13B ARG 3.3 0.2 - - - -
14B THR* 1.3 77.2 - - - +
16B LYS* 1.3 63.5 + - - +
18B ILE* 4.8 0.2 - - - -
19B ARG* 2.9 27.2 + - - +
29B LEU* 4.0 11.4 - - + -
40B ILE* 4.7 4.5 - - + -
43B VAL* 4.0 22.0 - - + -
44B GLU* 3.6 26.2 - - + +
58B ILE* 3.5 43.1 - - + -
62B LEU* 3.8 15.7 - - + -
69B PHE* 3.7 18.3 - - + -
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Residues in contact with LYS 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 GLY 3.0 16.4 + - - +
13B ARG* 3.7 7.0 - - - +
14B THR 3.3 0.2 - - - -
15B LEU* 1.3 76.0 - - - +
17B LYS* 1.3 62.2 + - - +
19B ARG* 3.8 19.2 - - - +
20B THR* 2.8 42.2 + - + +
44B GLU* 3.7 27.5 + - + +
3C ASN* 4.0 10.5 - - - +
6C GLU* 2.8 33.9 + - - +
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Residues in contact with LYS 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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13B ARG 3.0 18.5 + - - +
14B THR* 3.6 8.7 - - + +
16B LYS* 1.3 78.0 - - - +
18B ILE* 1.3 61.0 + - + +
20B THR* 2.9 18.9 + - - +
21B GLN* 2.9 50.2 + - + +
72B LYS* 6.4 2.2 - - + -
75B GLU* 5.4 5.7 + - - -
76C GLU 5.6 3.4 + - - -
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Residues in contact with ILE 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 THR* 2.9 35.8 + - + +
15B LEU* 4.0 3.1 - - - +
17B LYS* 1.3 72.2 - - + +
19B ARG* 1.3 67.3 + - - +
21B GLN* 3.3 13.4 + - - +
22B LYS* 3.0 48.6 + - + +
62B LEU* 4.2 13.7 - - + -
64B ILE* 3.9 16.4 - - + -
69B PHE* 3.4 31.0 - - + -
72B LYS* 3.7 28.9 - - + -
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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 LEU* 2.9 16.9 + - + +
16B LYS* 3.8 20.2 - - - +
18B ILE* 1.3 78.4 - - - +
20B THR* 1.3 79.4 + - - +
22B LYS* 3.2 2.9 + - - -
23B GLY 3.1 4.7 + - - -
24B VAL* 2.7 74.2 + - + +
25B SER* 3.7 15.1 - - - +
26B GLN* 3.5 28.8 - - - +
29B LEU* 3.9 17.3 - - + -
44B GLU* 2.7 42.2 + - - -
62B LEU* 4.3 21.7 - - + +
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Residues in contact with THR 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 LYS* 2.8 40.9 + - + +
17B LYS* 2.9 16.3 + - - +
19B ARG* 1.3 97.7 - - - +
21B GLN* 1.3 67.3 + - - +
23B GLY* 3.0 14.0 + - - +
24B VAL 4.6 3.6 - - - +
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Residues in contact with GLN 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 LYS* 2.9 59.4 + - + +
18B ILE* 3.5 17.1 - - + +
20B THR* 1.3 78.9 + - - +
22B LYS* 1.3 61.3 + - + +
23B GLY* 3.4 2.8 + - - -
72B LYS* 4.9 10.7 + - - +
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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 ILE* 3.0 32.7 + - + +
19B ARG* 3.8 4.7 - - - +
20B THR 3.2 0.2 - - - -
21B GLN* 1.3 78.7 - - + +
23B GLY* 1.3 62.8 + - - +
24B VAL* 3.3 15.3 + - + +
62B LEU* 2.8 42.3 + - + +
63B ASP* 3.4 16.1 + - - +
64B ILE* 4.5 8.6 - - - +
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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