Contacts of the helix formed by residues 3 - 22 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 4.0 9.6 - - - +
1C MET 3.4 6.8 + - - +
2C ILE* 1.3 74.4 - - - +
4C GLU* 1.3 61.7 + - - +
5C ILE* 3.4 11.1 + - - +
6C GLU* 3.0 47.2 + - + +
7C ILE* 3.0 27.6 + - - +
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Residues in contact with GLU 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.9 11.5 + - + +
3C ASN* 1.3 68.5 + - - +
5C ILE* 1.3 69.8 + - + +
7C ILE* 3.3 7.8 + - - +
8C LYS* 2.9 39.4 + - - +
53D ILE* 3.6 46.0 - - + +
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Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.8 30.5 - - + +
3C ASN* 3.3 8.4 + - - +
4C GLU* 1.3 77.0 - - + +
6C GLU* 1.3 57.8 + - - +
8C LYS* 3.8 13.7 - - - +
9C ARG* 2.8 69.6 + - + +
46C GLY 5.5 1.3 - - - +
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Residues in contact with GLU 6 (chain C).
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 33.5 + - - -
3C ASN* 3.0 34.7 + - - +
5C ILE* 1.3 77.7 - - - +
7C ILE* 1.3 60.4 + - + +
9C ARG* 4.1 4.2 - - - +
10C LYS* 2.8 39.2 + - + +
13C ARG* 4.9 6.3 + - - +
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.7 26.7 - - + -
3C ASN 3.0 21.9 + - - +
4C GLU* 3.7 9.0 - - - +
6C GLU* 1.3 79.5 - - + +
8C LYS* 1.3 62.8 + - - +
10C LYS* 3.4 6.3 + - - +
11C PHE* 3.0 22.9 + - - +
73C MET* 5.0 2.0 - - - +
52D LEU* 3.7 28.9 - - + +
53D ILE* 4.5 16.6 - - + -
56D HIS* 3.8 43.7 - - + +
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLU* 2.9 36.1 + - - +
5C ILE* 4.0 11.1 - - - +
7C ILE* 1.3 75.1 - - - +
9C ARG* 1.3 58.1 + - - +
11C PHE* 3.3 4.3 + - - +
12C GLY* 3.0 23.2 + - - -
43C VAL 4.3 1.6 - - - +
46C GLY* 3.5 30.6 + - - +
47C ASP* 5.0 6.1 + - - +
48C ARG 3.6 31.8 - - - +
49C ASN* 3.7 12.0 - - + +
52D LEU* 4.1 11.0 - - + -
53D ILE* 4.2 21.6 - - + +
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Residues in contact with ARG 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.4 51.6 - - - +
44B GLU 5.4 0.2 + - - -
45B ARG* 2.8 42.8 + - - +
47B ASP* 4.8 5.7 + - - -
5C ILE* 2.8 48.9 + - + +
6C GLU* 4.1 3.6 - - - +
8C LYS* 1.3 72.3 - - - +
10C LYS* 1.3 52.8 + - - +
12C GLY* 3.2 0.7 + - - -
13C ARG* 2.7 54.4 + - + +
44C GLU 4.6 0.9 - - - +
45C ARG 3.9 15.8 + - - +
46C GLY* 3.9 12.4 + - - +
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLU* 2.8 24.0 + - + +
7C ILE* 3.7 6.5 - - - +
9C ARG* 1.3 72.8 - - - +
11C PHE* 1.3 66.1 + - - +
13C ARG* 3.4 24.5 + - - +
14C THR* 2.8 30.4 + - - +
73C MET* 3.2 43.8 + - + +
74C GLU* 4.4 6.7 + - - +
76C GLU* 3.3 24.0 - - - +
77C ASN 4.1 11.2 - - - +
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE 3.0 7.6 + - - +
8C LYS 3.6 8.1 - - - +
10C LYS* 1.3 76.5 - - - +
12C GLY* 1.3 59.3 + - - +
14C THR* 3.2 4.2 + - - -
15C LEU* 2.8 31.9 + - + -
43C VAL* 3.7 29.4 - - + -
50C ILE* 3.8 21.8 - - + -
55C ILE* 4.0 20.9 - - + -
58C ILE* 5.4 4.5 - - + -
59C CYS* 5.9 0.7 - - - -
69C PHE* 3.3 39.7 - + - -
70C PHE* 4.0 14.1 - + - -
73C MET* 3.6 18.0 - - + -
52D LEU* 3.6 36.3 - - + -
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Residues in contact with GLY 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS 3.0 12.2 + - - -
9C ARG 3.6 2.0 - - - -
11C PHE* 1.3 78.8 - - - +
13C ARG* 1.3 56.3 + - - +
15C LEU* 3.3 4.2 + - - +
16C LYS* 3.0 27.9 + - - +
43C VAL 3.3 17.5 + - - -
44C GLU* 3.3 30.0 - - - +
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Residues in contact with ARG 13 (chain C).
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* 3.5 52.8 - - - +
6C GLU* 4.9 7.1 + - - +
9C ARG* 2.7 46.8 + - + +
10C LYS* 3.6 24.2 - - - +
12C GLY* 1.3 71.8 - - - +
14C THR* 1.3 56.8 + - - +
16C LYS* 3.4 6.5 + - - +
17C LYS* 3.0 30.7 + - - +
44C GLU 3.9 2.7 + - - +
76C GLU* 2.8 46.3 + - - +
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Residues in contact with THR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS* 2.8 20.9 + - - +
11C PHE 3.5 4.3 - - - -
13C ARG* 1.3 73.1 - - - +
15C LEU* 1.3 62.9 + - - +
17C LYS* 3.3 11.8 + - + +
18C ILE* 2.9 50.0 + - + +
69C PHE* 3.8 27.8 - - + +
72C LYS* 4.4 4.7 - - + +
73C MET* 3.6 27.2 - - + +
76C GLU* 4.8 6.1 + - - +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 2.8 17.5 + - + +
12C GLY* 3.6 9.2 - - - +
14C THR* 1.3 78.1 - - - +
16C LYS* 1.3 58.1 + - - +
18C ILE* 4.9 0.4 - - - -
19C ARG* 2.9 34.7 + - + +
29C LEU* 3.9 12.6 - - + -
40C ILE* 4.7 3.6 - - + -
43C VAL* 4.0 22.7 - - + -
44C GLU* 3.7 26.0 - - + +
58C ILE* 3.6 39.3 - - + -
62C LEU* 3.8 17.9 - - + -
69C PHE* 3.7 17.6 - - + -
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.2 26.5 + - - -
12C GLY 3.0 16.4 + - - +
13C ARG* 3.8 6.5 - - - +
15C LEU* 1.3 76.4 - - - +
17C LYS* 1.3 53.7 + - - +
19C ARG* 3.9 20.4 - - - +
20C THR* 2.7 52.6 + - + +
44C GLU* 3.8 22.0 + - + +
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 3.0 18.2 + - - +
14C THR* 3.4 13.2 - - + +
16C LYS* 1.3 76.9 - - - +
18C ILE* 1.3 63.5 + - + +
20C THR* 3.1 6.4 + - - -
21C GLN* 3.0 31.6 + - + +
72C LYS* 6.1 5.6 - - + +
76C GLU* 5.7 10.3 - - - -
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C THR* 2.9 28.6 + - + +
15C LEU* 4.0 2.9 - - - +
17C LYS* 1.3 80.1 - - + +
19C ARG* 1.3 67.0 + - - +
21C GLN* 3.3 5.8 + - - +
22C LYS* 3.0 47.7 + - + +
62C LEU* 4.1 15.0 - - + -
64C ILE* 4.1 16.2 - - + -
69C PHE* 3.6 31.0 - - + -
72C LYS* 3.7 32.8 - - + -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 2.9 19.6 + - + +
16C LYS* 3.9 20.7 - - - +
18C ILE* 1.3 76.1 - - - +
20C THR* 1.3 80.5 + - - +
22C LYS* 3.2 5.0 + - - +
23C GLY 3.1 3.8 + - - -
24C VAL* 2.9 71.2 + - + +
25C SER* 3.7 14.7 - - - +
26C GLN* 3.5 27.4 - - - +
29C LEU* 3.9 17.5 - - + -
44C GLU* 2.6 40.2 + - - -
62C LEU* 4.2 19.9 - - + +
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 2.7 41.2 + - + +
17C LYS* 3.1 10.6 + - - -
19C ARG* 1.3 101.5 - - - +
21C GLN* 1.3 64.1 + - - +
23C GLY* 3.0 14.6 + - - +
24C VAL 4.7 2.7 - - - +
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 3.0 22.2 + - + +
18C ILE* 3.3 6.9 + - - +
20C THR* 1.3 77.6 + - - +
22C LYS* 1.3 63.8 + - + +
23C GLY* 3.4 1.0 + - - -
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.0 38.2 + - + +
19C ARG* 3.6 5.4 - - - +
20C THR 3.1 0.4 - - - -
21C GLN* 1.3 80.4 - - + +
23C GLY* 1.3 60.7 + - - +
24C VAL* 3.3 16.5 + - + +
62C LEU* 2.7 40.1 + - + +
63C ASP* 3.7 14.8 + - - +
64C ILE* 4.5 10.9 - - - +
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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