Contacts of the helix formed by residues 4 - 19 (chain A) in PDB entry 2NS0
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 1.3 75.1 - - - +
5A ASP* 1.3 64.9 + - - +
6A ARG* 3.7 9.6 + - - +
7A GLU* 3.0 45.6 + - - +
8A LEU* 3.2 15.6 + - - +
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Residues in contact with ASP 5 (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 VAL 4.0 1.6 + - - +
4A SER* 1.3 72.1 - - - +
6A ARG* 1.3 57.5 + - - +
8A LEU* 3.2 12.4 + - - +
9A GLU* 3.0 35.8 + - - +
45A PRO* 6.1 0.3 - - - +
52A ARG* 3.3 36.9 + - - +
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Residues in contact with ARG 6 (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 SER* 3.2 9.0 + - - +
5A ASP* 1.3 80.3 - - - +
7A GLU* 1.3 62.7 + - - +
9A GLU* 3.3 13.0 + - + +
10A GLU* 3.0 25.6 + - + +
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Residues in contact with GLU 7 (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 THR 4.3 4.4 - - - +
3A VAL* 3.3 27.5 - - + +
4A SER* 3.0 38.3 + - - +
6A ARG* 1.3 76.7 - - - +
8A LEU* 1.3 57.6 + - - +
10A GLU* 3.5 8.3 + - - +
11A CYS* 3.0 27.4 + - - +
34A VAL* 4.5 8.5 - - + +
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Residues in contact with LEU 8 (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 VAL* 3.7 28.3 - - + +
4A SER 3.2 15.8 + - - +
5A ASP* 3.6 13.2 - - - +
7A GLU* 1.3 74.2 - - - +
9A GLU* 1.3 65.8 + - - +
11A CYS* 3.3 4.6 + - - +
12A ILE* 3.0 27.4 + - - +
30A VAL* 4.0 5.3 - - + +
34A VAL* 4.0 22.0 - - + -
42A LEU* 4.7 3.8 - - + -
45A PRO* 3.6 43.1 - - + +
46A VAL* 4.1 17.7 - - + -
49A ALA* 3.8 14.6 - - + -
52A ARG* 5.6 0.4 - - - +
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Residues in contact with GLU 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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5A ASP* 3.0 22.8 + - - +
6A ARG* 3.3 10.0 + - - +
8A LEU* 1.3 76.9 - - - +
10A GLU* 1.3 60.6 + - - +
12A ILE* 3.4 6.0 + - - +
13A ARG* 3.1 42.0 + - - +
49A ALA* 4.1 14.8 - - + +
52A ARG* 2.6 39.0 + - - -
53A LEU* 3.8 31.8 - - + +
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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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6A ARG* 3.0 19.3 + - + +
7A GLU* 3.8 7.6 - - - +
9A GLU* 1.3 75.6 - - - +
11A CYS* 1.3 59.6 + - - +
13A ARG* 3.4 20.7 + - - +
14A ALA* 2.9 35.4 + - + +
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Residues in contact with CYS 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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7A GLU 3.0 17.4 + - - +
8A LEU 3.6 4.5 - - - +
9A GLU 3.2 0.2 - - - -
10A GLU* 1.3 75.4 - - - +
12A ILE* 1.3 59.2 + - - +
14A ALA* 3.7 6.0 - - - +
15A LEU* 2.9 37.3 + - - +
30A VAL* 3.7 21.8 - - + -
33A ALA* 3.6 31.0 - - - -
34A VAL* 3.8 16.6 - - + -
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Residues in contact with ILE 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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8A LEU 3.0 15.9 + - - +
9A GLU 3.6 6.1 - - - +
11A CYS* 1.3 74.4 - - - +
13A ARG* 1.3 58.9 + - - +
15A LEU* 3.4 1.2 + - - +
16A LEU* 2.9 49.4 + - + +
25A ILE* 4.1 8.9 - - + +
30A VAL* 3.8 23.8 - - + -
46A VAL* 4.2 5.6 - - + +
49A ALA* 3.8 16.8 - - + -
50A ALA* 3.5 36.6 - - + +
53A LEU* 3.9 19.7 - - + -
59A VAL* 4.4 3.1 - - + -
79A ILE* 4.1 16.6 - - + -
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Residues in contact with ARG 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 GLU* 3.1 34.7 + - - +
10A GLU* 3.7 21.7 + - - +
11A CYS 3.2 0.2 - - - -
12A ILE* 1.3 75.2 - - - +
14A ALA* 1.3 58.4 + - - +
17A ASP* 2.8 34.8 + - - +
53A LEU* 3.4 28.5 - - + +
58A GLU* 2.9 35.0 + - - -
81A TRP* 3.6 28.4 - - + -
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Residues in contact with ALA 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 GLU* 2.9 31.3 + - + +
11A CYS* 3.3 8.0 + - - +
13A ARG* 1.3 77.1 - - - +
15A LEU* 1.3 64.4 + - + +
17A ASP* 3.6 6.5 + - - +
18A ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 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 CYS* 2.9 27.6 + - - +
14A ALA* 1.3 77.2 - - + +
16A LEU* 1.3 65.0 + - - +
18A ALA* 3.2 15.0 + - + +
19A ARG* 3.6 17.1 + - - +
25A ILE* 4.0 19.1 - - + -
29A ASP* 3.4 42.4 - - + +
30A VAL* 3.6 16.6 - - + +
33A ALA* 4.2 12.1 - - + -
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Residues in contact with LEU 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 ILE* 2.9 27.1 + - + +
15A LEU* 1.3 75.3 - - - +
17A ASP* 1.3 64.4 + - - +
19A ARG* 3.0 20.8 + - + +
20A ALA 5.1 0.3 - - - +
23A ALA 4.6 3.6 - - - +
24A SER* 4.4 4.9 - - - -
25A ILE* 3.8 23.3 - - + +
59A VAL* 3.7 30.3 - - + -
79A ILE* 3.3 28.3 - - + +
80A ARG* 3.9 7.9 - - - -
81A TRP* 3.4 39.1 + - + +
101A GOL 3.2 10.4 + - - -
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Residues in contact with ASP 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 ARG 2.8 25.0 + - - +
14A ALA* 3.8 7.6 - - - +
16A LEU* 1.3 74.4 - - - +
18A ALA* 1.3 50.5 + - - +
81A TRP* 3.6 11.5 + - + +
101A GOL 2.2 61.9 + - - -
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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 ALA 3.2 15.0 + - - +
15A LEU* 3.2 9.5 + - + +
16A LEU 3.1 1.6 - - - -
17A ASP* 1.3 76.2 - - - +
19A ARG* 1.3 61.7 + - + +
101A GOL 3.7 8.0 + - - -
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Residues in contact with ARG 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 LEU* 3.6 12.2 + - - +
16A LEU* 3.0 13.2 + - + +
18A ALA* 1.3 81.5 - - + +
20A ALA* 1.3 58.9 + - - +
23A ALA* 3.9 18.1 - - + +
24A SER 2.6 34.6 + - - +
25A ILE* 3.5 17.5 - - - +
29A ASP* 3.3 25.3 + - - +
78A ARG* 4.2 8.3 - - - +
101A GOL 2.3 42.8 + - - -
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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