Contacts of the helix formed by residues 4 - 21 (chain A) in PDB entry 1NSH
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 THR 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 3.5 24.7 - - - +
2A ARG 3.1 1.7 - - - +
3A PRO* 1.3 80.9 - - - +
5A GLU* 1.3 58.4 + - - +
6A THR* 3.3 15.1 + - - -
7A GLU* 2.6 63.9 + - + +
8A ARG* 3.1 6.8 + - - +
42B GLU* 3.9 17.1 + - - +
43B LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PRO 3.5 3.3 + - - +
4A THR* 1.3 73.2 + - - +
6A THR* 1.3 62.8 + - - +
8A ARG* 2.9 36.6 + - - +
9A CYS* 3.1 19.8 + - - +
12B SER* 3.8 6.1 + - - +
16B VAL* 5.9 0.4 - - - -
19B LYS* 6.1 4.3 - - - +
42B GLU* 5.8 2.9 - - - +
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Residues in contact with THR 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.0 1.9 + - - -
5A GLU* 1.3 75.5 - - - +
7A GLU* 1.3 55.8 + - - +
9A CYS* 2.8 38.0 + - - -
10A ILE* 2.6 23.8 - - + +
16B VAL* 3.8 5.2 - - + +
38B PHE* 3.6 24.9 - - + -
42B GLU* 3.1 39.7 + - - +
43B LEU* 3.5 29.6 - - + -
80B ILE* 5.1 0.9 - - + -
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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
----------------------------------------------------------
1A SER* 3.1 23.6 - - - +
2A ARG* 2.8 40.7 - - - +
4A THR* 2.6 38.5 + - + +
6A THR* 1.3 75.0 - - - +
8A ARG* 1.3 58.0 + - - -
9A CYS 3.2 0.2 + - - -
10A ILE* 3.4 5.5 + - - +
11A GLU* 3.4 20.6 + - - +
43B LEU* 4.7 2.4 - - + +
45B ALA* 4.5 5.6 - - + +
46B PHE* 4.0 16.8 - - - -
88B HIS* 3.5 25.3 + - - -
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Residues in contact with ARG 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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2A ARG 4.5 8.5 - - - +
3A PRO* 4.3 17.7 + - + +
4A THR 3.1 6.5 + - - +
5A GLU* 2.9 33.3 + - - +
7A GLU* 1.3 79.2 - - - +
9A CYS* 1.3 62.6 + - - +
11A GLU* 4.1 5.9 - - - +
12A SER* 3.1 24.8 + - - -
12B SER* 4.2 3.1 + - - +
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Residues in contact with CYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU 3.1 12.3 + - - +
6A THR* 2.8 30.8 + - - +
8A ARG* 1.3 75.5 - - - +
10A ILE* 1.3 71.9 + - - +
12A SER* 3.2 14.6 - - - -
13A LEU 3.6 1.0 + - - -
12B SER* 2.8 37.2 + - - +
13B LEU* 2.7 37.7 - - - +
16B VAL* 3.5 22.7 - - + -
80B ILE* 4.7 0.2 - - - -
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 2.6 42.8 + - + +
7A GLU* 3.6 10.3 - - - +
9A CYS* 1.3 76.1 - - - +
11A GLU* 1.3 63.9 + - - +
12A SER 2.9 1.4 + - - -
13A LEU* 3.2 10.4 + - - +
14A ILE* 2.8 26.1 + - + +
13B LEU* 4.0 4.3 - - - -
43B LEU* 3.3 25.1 - - + -
46B PHE* 3.8 20.4 - - + -
80B ILE* 3.0 28.9 - - + -
84B ALA* 3.2 36.3 - - + -
88B HIS* 4.2 3.6 - - + -
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.4 12.9 + - - +
8A ARG* 4.2 6.1 - - - +
10A ILE* 1.3 78.9 - - - +
12A SER* 1.3 62.1 + - - +
14A ILE* 3.4 9.2 - - - +
15A ALA* 3.3 32.6 + - - +
88B HIS* 3.5 16.1 - - + -
89B GLU* 2.7 35.9 - - - +
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Residues in contact with SER 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG 3.1 15.4 + - - -
9A CYS* 3.2 14.6 - - - -
10A ILE 2.9 1.6 + - - -
11A GLU* 1.3 81.0 - - - +
13A LEU* 1.3 58.9 + - - -
15A ALA* 4.0 2.4 - - - +
16A VAL* 3.0 25.6 + - - +
5B GLU* 3.8 5.9 + - - +
8B ARG* 4.2 1.9 + - - +
9B CYS* 2.8 40.5 + - - +
12B SER* 4.8 0.7 - - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A CYS 3.6 1.5 + - - +
10A ILE 3.2 6.4 + - - +
12A SER* 1.3 77.7 - - - +
14A ILE* 1.3 60.4 + - - +
16A VAL* 2.6 28.4 - - + +
17A PHE* 3.7 4.2 + - - +
76A PHE* 4.9 1.0 - - - +
77A LEU* 3.3 34.4 - - + +
80A ILE* 3.1 40.8 - - + -
81A GLY* 5.6 0.2 - - - -
9B CYS* 2.7 54.5 - - - +
10B ILE* 3.7 3.1 - - - +
13B LEU* 4.0 19.7 - - + -
77B LEU* 4.9 1.6 - - + -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 2.8 43.5 + - + +
11A GLU* 3.4 11.2 - - - +
13A LEU* 1.3 77.0 - - + +
15A ALA* 1.3 54.2 + - - +
17A PHE* 3.5 7.7 + - - +
18A GLN* 2.7 42.1 + - + +
77A LEU* 5.6 7.6 - - + -
84B ALA* 3.8 14.8 - - + +
88B HIS* 3.6 24.5 - - + +
89B GLU* 4.0 15.7 - - + +
90B SER* 3.7 30.7 - - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.3 27.4 + - - +
12A SER* 4.0 2.7 - - - +
13A LEU 3.2 0.4 - - - -
14A ILE* 1.3 77.5 - - + +
16A VAL* 1.3 59.9 + - - +
17A PHE 2.9 1.8 - - - -
18A GLN* 3.8 11.0 - - + -
19A LYS* 2.6 44.8 + - - +
89B GLU* 5.2 3.8 - - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 3.0 17.5 + - - +
13A LEU* 2.6 36.6 - - + +
15A ALA* 1.3 77.7 - - - +
17A PHE* 1.3 68.9 + - - +
19A LYS* 4.0 2.0 - - - +
20A TYR* 3.9 7.3 + - - +
38A PHE* 3.3 41.1 - - + -
76A PHE* 3.3 35.2 - - + -
80A ILE* 4.9 0.4 - - + -
5B GLU 5.9 0.2 - - - -
6B THR* 3.8 6.5 - - + +
9B CYS* 3.5 24.9 - - + -
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Residues in contact with PHE 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 LEU 4.2 4.5 - - - +
14A ILE* 3.5 10.1 + - + +
15A ALA 2.9 0.2 - - - -
16A VAL* 1.3 80.9 - - - +
18A GLN* 1.3 87.7 + - - +
20A TYR* 3.1 5.0 + - - +
21A ALA* 2.6 57.6 + - + +
28A VAL* 3.3 27.4 - - - -
29A THR 3.5 11.4 - - - -
30A LEU* 3.7 6.1 - - + +
72A ASP 2.7 28.0 - - - -
73A PHE* 4.1 7.6 - - - +
76A PHE* 3.4 37.9 - + + -
90B SER* 3.1 20.2 - - - -
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Residues in contact with GLN 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 ILE* 2.7 30.6 + - + +
15A ALA* 3.8 7.9 - - + +
17A PHE* 1.3 107.3 - - - +
19A LYS* 1.3 54.4 + - - +
21A ALA* 3.8 6.5 + - - +
22A GLY 2.5 45.8 + - - +
27A SER 5.1 5.9 + - - -
89B GLU* 3.5 13.7 - - + +
90B SER* 2.6 38.8 + - - +
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Residues in contact with LYS 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 ALA* 2.6 29.4 + - - +
16A VAL* 4.0 6.7 - - - +
18A GLN* 1.3 75.5 - - - +
20A TYR* 1.3 66.9 + - + +
22A GLY 3.7 3.6 + - - -
23A LYS* 3.2 44.0 - - + +
38A PHE* 5.0 6.9 - - + -
42A GLU* 4.5 14.3 + - - +
5B GLU* 6.1 3.8 - - - +
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Residues in contact with TYR 20 (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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16A VAL 3.9 3.3 + - - +
17A PHE 3.1 3.1 + - - +
19A LYS* 1.3 83.1 - - + +
21A ALA* 1.3 58.0 - - - +
22A GLY 3.1 8.5 + - - -
23A LYS* 4.8 13.5 + - - +
30A LEU* 3.2 30.8 - - + +
34A GLU* 2.7 54.8 - - + +
37A SER* 2.6 34.2 + - - -
38A PHE* 3.3 45.2 + + + -
41A THR* 4.0 8.9 - - + +
42A GLU* 5.3 1.6 - - + -
76A PHE* 4.9 0.9 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.6 50.8 + - + +
18A GLN* 3.1 7.4 + - - +
20A TYR* 1.3 73.3 - - - +
22A GLY* 1.3 53.8 + - - +
26A HIS* 4.9 1.7 - - - +
27A SER* 3.8 18.7 + - - +
29A THR 2.8 31.7 - - - +
30A LEU* 3.4 8.1 - - + +
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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
------------------------------------------------------------
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