Contacts of the helix formed by residues 3 - 21 (chain A) in PDB entry 3NSO
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 ARG 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 77.0 - - - +
4A PRO* 1.3 73.5 - - + +
5A LEU 4.5 0.4 - - - +
6A GLU* 3.1 28.6 + - + +
7A GLN* 3.1 24.9 + - - +
40B LYS* 3.1 22.9 + - - +
41B GLU* 3.6 31.6 + - - +
43B ALA* 3.8 14.3 - - - +
44B THR* 4.0 21.8 - - - +
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Residues in contact with PRO 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA 3.9 6.3 - - - +
3A ARG* 1.3 88.7 - - + +
5A LEU* 1.3 57.9 + - - +
7A GLN* 3.4 11.9 + - + +
8A ALA* 3.0 28.6 + - - +
11B ALA* 4.3 15.4 - - + +
15B THR* 5.5 3.8 - - - +
41B GLU* 5.3 7.2 - - - +
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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 ARG* 3.3 1.4 - - - +
4A PRO* 1.3 76.8 - - - +
6A GLU* 1.3 61.6 + - - +
8A ALA* 3.2 2.0 + - + +
9A VAL* 2.8 37.9 + - + +
11B ALA* 4.5 1.6 - - - +
12B ILE* 3.6 34.3 - - + +
15B THR* 3.9 21.9 + - + +
37B LEU* 3.8 20.4 - - + -
41B GLU* 3.7 34.9 + - + +
42B LEU* 4.2 10.8 - - + -
75B TYR* 3.8 12.8 - - - +
79B LEU* 4.0 17.0 - - + -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.1 33.3 + - + +
5A LEU* 1.3 77.4 - - - +
7A GLN* 1.3 63.6 + - + +
9A VAL 3.4 0.2 + - - -
10A ALA* 3.0 25.3 + - - +
41B GLU 3.4 13.9 + - - +
42B LEU* 3.4 13.8 - - + -
43B ALA 3.3 9.0 + - - -
44B THR* 2.7 48.9 + - - +
45B TRP* 3.6 22.1 + - - +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.6 29.9 + - + +
3A ARG 3.1 21.9 + - - +
4A PRO* 3.7 10.8 - - + +
6A GLU* 1.3 76.2 - - + +
8A ALA* 1.3 63.4 + - - +
10A ALA* 3.5 6.1 + - - +
11A ALA* 2.9 24.1 + - - +
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO 3.0 17.7 + - - +
5A LEU* 3.2 5.6 + - - +
7A GLN* 1.3 78.5 - - - +
9A VAL* 1.3 58.7 + - - +
11A ALA* 3.1 1.8 + - - -
12A ILE* 2.9 31.1 + - - +
8B ALA* 3.4 41.6 - - - +
11B ALA* 3.8 9.9 - - + -
12B ILE* 4.0 10.5 - - + -
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Residues in contact with VAL 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 40.6 + - + +
6A GLU 4.2 0.9 - - - +
8A ALA* 1.3 69.0 - - - +
10A ALA* 1.3 67.0 + - - +
12A ILE* 3.1 20.6 + - + +
13A VAL* 3.2 13.7 + - - +
12B ILE* 4.6 3.8 - - + -
42B LEU* 4.5 7.0 - - + -
45B TRP* 3.6 17.9 - - + -
79B LEU* 4.2 33.4 - - + +
83B CYS* 3.2 32.3 - - - -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 3.0 18.5 + - - +
7A GLN* 3.7 6.3 - - - +
9A VAL* 1.3 76.6 - - - +
11A ALA* 1.3 56.8 + - - +
13A VAL* 3.2 8.3 + - - +
14A CYS* 2.9 27.0 + - - +
45B TRP* 4.0 14.8 - - + -
87B HIS* 4.9 9.8 + - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN 2.9 18.4 + - - +
8A ALA* 3.1 5.4 + - - +
10A ALA* 1.3 74.1 - - - +
12A ILE* 1.3 64.5 + - - +
14A CYS* 3.1 9.2 + - - +
15A THR* 3.0 28.2 + - - -
4B PRO* 4.3 18.8 - - + +
5B LEU* 4.8 1.3 - - - -
8B ALA* 3.8 15.3 - - + -
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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 ALA 2.9 18.2 + - - +
9A VAL* 3.1 17.7 + - + +
11A ALA* 1.3 75.5 - - - +
13A VAL* 1.4 60.7 + - - +
16A PHE 3.2 8.8 + - - -
72A PHE* 4.2 6.3 - - + -
75A TYR* 2.7 45.7 + - + +
76A VAL* 4.0 18.4 - - + -
79A LEU* 4.0 15.5 - - + -
5B LEU* 3.9 19.5 - - + -
8B ALA* 4.2 6.5 - - + -
9B VAL* 4.7 3.6 - - + -
12B ILE* 4.1 33.9 - - + -
79B LEU* 5.9 1.3 - - + -
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL 3.2 9.6 + - - +
10A ALA 3.6 6.1 - - - +
12A ILE* 1.4 72.8 - - - +
14A CYS* 1.3 67.9 + - - +
16A PHE* 3.1 3.2 + - - +
17A GLN* 2.8 25.2 + - - +
72A PHE* 3.8 16.4 - - + -
83B CYS* 3.5 33.9 - - + -
87B HIS* 3.5 43.7 - - + +
89B TYR* 4.2 9.9 - - + -
90B PHE* 4.1 15.3 - - + -
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Residues in contact with CYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 2.9 14.0 + - - +
11A ALA* 3.1 12.8 + - - +
13A VAL* 1.3 77.4 - - - +
15A THR* 1.3 62.3 + - - +
17A GLN* 3.2 14.8 + - - +
18A GLU* 3.0 25.9 + - - +
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.0 14.1 + - - -
14A CYS* 1.3 76.6 - - - +
16A PHE* 1.3 65.5 + - - +
18A GLU* 3.1 21.1 + - - +
19A TYR* 3.2 17.8 + - + -
37A LEU* 3.9 30.5 - - + +
41A GLU* 4.0 18.6 + - + -
75A TYR* 3.6 15.3 - - - +
4B PRO* 5.5 4.7 - - - +
5B LEU* 3.9 21.5 + - + +
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 3.2 4.3 + - - +
13A VAL 3.1 8.8 + - - +
15A THR* 1.3 78.1 - - - +
17A GLN* 1.3 55.9 + - - +
19A TYR* 3.2 2.6 + - - +
20A ALA* 2.7 53.4 + - + +
26A LYS 3.9 8.3 - - - -
27A TYR 3.4 28.5 - - - -
28A LYS* 4.2 2.7 - - - -
29A LEU* 3.8 25.8 - - + -
37A LEU* 4.8 4.5 - - - -
70A VAL 4.6 0.4 - - - -
71A ASP 4.2 2.7 - - - -
72A PHE* 3.7 35.9 - + + -
75A TYR* 3.5 42.2 + + + -
89B TYR* 4.2 6.3 - + - -
90B PHE* 4.1 20.6 - + - -
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Residues in contact with GLN 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 VAL* 2.8 15.4 + - - +
14A CYS* 3.4 15.8 - - - +
16A PHE* 1.3 78.4 - - - +
18A GLU* 1.3 56.9 + - - +
21A GLY* 2.8 32.1 + - - -
87B HIS* 5.4 3.3 - - - -
89B TYR* 3.6 53.4 - - + +
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Residues in contact with GLU 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 CYS* 3.0 14.6 + - - +
15A THR* 3.1 22.8 + - - +
17A GLN* 1.3 79.3 - - - +
19A TYR* 1.3 76.7 + - + +
21A GLY 4.6 0.5 - - - -
22A ARG* 3.6 19.7 + - - +
41A GLU* 4.5 10.3 - - - +
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Residues in contact with TYR 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 THR* 3.2 15.5 + - + +
16A PHE 3.2 4.9 + - - +
18A GLU* 1.3 91.8 + - + +
20A ALA* 1.3 65.4 + - - +
21A GLY 3.2 1.3 - - - -
22A ARG* 3.2 59.1 + - - +
23A CYS 5.6 0.2 - - - +
29A LEU* 3.7 19.8 - - + +
33A GLU* 4.0 16.3 - - + +
36A GLU* 3.9 7.6 - - - -
37A LEU* 3.7 47.3 - - + -
40A LYS* 3.9 18.5 - - - +
41A GLU* 2.6 35.7 + - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 2.7 38.9 + - + +
19A TYR* 1.3 74.1 - - - +
21A GLY* 1.3 58.7 + - - +
22A ARG 3.2 1.3 + - - -
23A CYS 3.6 15.6 - - - +
25A ASP 3.7 11.1 - - - +
26A LYS* 3.5 25.1 - - - +
28A LYS 3.5 18.0 - - - +
29A LEU* 3.5 13.4 - - + +
33A GLU* 5.6 0.7 - - - -
89B TYR* 4.5 0.7 - - - +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 2.8 20.6 + - - -
18A GLU 4.6 1.1 - - - -
20A ALA* 1.3 76.8 - - - +
22A ARG* 1.3 65.7 + - - +
23A CYS* 3.3 1.5 - - - -
26A LYS* 4.8 7.2 - - - -
89B TYR* 4.4 9.1 + - - -
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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