Contacts of the helix formed by residues 4 - 21 (chain N) in PDB entry 1JJ2
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 4 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6560 G 2.8 24.8 + - - +
6570 G 3.5 7.7 + - - -
27C ARG* 3.1 38.3 + - - +
29C ASP* 3.9 4.9 - - - -
2N LYS* 4.8 1.7 - - - +
3N THR* 1.3 72.8 + - - +
5N PRO* 1.3 69.9 - - - +
6N ARG* 2.8 23.5 + - - +
7N LEU* 3.6 24.3 - - + +
8N SER* 3.0 20.8 + - - -
37N ARG* 6.0 0.6 - - - +
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Residues in contact with PRO 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL 5.8 3.4 - - - +
27C ARG* 4.0 6.1 - - - -
28C SER* 4.3 18.6 - - - +
29C ASP* 3.1 23.8 - - + +
3N THR 3.1 9.2 - - - +
4N ASN* 1.3 88.8 - - - +
6N ARG* 1.3 57.3 + - + +
8N SER* 3.3 8.9 - - - -
9N SER* 3.0 31.4 + - - -
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Residues in contact with ARG 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 3.4 41.4 - - - +
26C VAL 5.1 7.2 + - - +
27C ARG* 4.3 17.9 - - - +
4N ASN* 2.8 17.3 + - - +
5N PRO* 1.3 75.9 - - + +
7N LEU* 1.3 59.9 + - - +
8N SER 3.0 1.3 - - - -
9N SER* 3.0 8.0 + - - +
10N LEU* 2.8 30.0 + - - +
99N GLU* 5.3 10.4 + - - +
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Residues in contact with LEU 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6560 G 4.0 17.7 - - - +
2N LYS* 4.0 31.6 - - + +
4N ASN* 3.4 23.3 + - + +
6N ARG* 1.3 78.1 - - - +
8N SER* 1.3 61.6 + - - +
10N LEU* 3.5 7.2 + - + +
11N ILE* 3.1 33.5 + - + +
33N LEU* 4.2 30.7 - - + +
37N ARG* 5.6 3.1 - - + +
40N HIS* 4.8 7.9 - - + -
79N VAL* 4.5 17.9 - - + -
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Residues in contact with SER 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N LYS* 5.1 11.8 - - - +
4N ASN 3.0 14.4 + - - -
5N PRO* 3.3 13.9 - - - -
6N ARG 3.0 0.2 - - - -
7N LEU* 1.3 79.9 - - - +
9N SER* 1.3 60.9 + - - +
11N ILE* 3.2 11.8 + - - +
12N ALA* 3.1 20.8 + - - +
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Residues in contact with SER 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N PRO 3.0 15.2 + - - -
6N ARG* 3.0 9.2 + - - -
8N SER* 1.3 72.9 - - - +
10N LEU* 1.3 67.1 + - - +
12N ALA* 3.2 7.1 + - - +
13N ASP* 2.9 36.0 + - - +
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Residues in contact with LEU 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ARG 2.8 15.8 + - - +
7N LEU* 3.7 9.4 - - + +
9N SER* 1.3 75.3 - - - +
11N ILE* 1.3 59.4 + - - +
13N ASP* 3.1 7.7 + - + +
14N LEU* 2.8 47.3 + - + +
33N LEU* 4.1 13.5 - - + -
79N VAL* 4.4 18.4 - - + +
98N LEU* 4.1 27.8 - - + -
99N GLU* 3.9 44.9 - - + +
102N ILE* 4.2 8.7 - - + -
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Residues in contact with ILE 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2N LYS* 4.7 11.2 - - + -
7N LEU* 3.1 24.8 + - + +
8N SER* 3.4 10.5 - - - +
9N SER 3.2 0.2 - - - -
10N LEU* 1.3 79.8 - - - +
12N ALA* 1.3 63.2 + - - +
14N LEU* 3.3 10.5 + - - +
15N LYS* 3.2 37.2 + - - +
30N ALA* 4.1 6.1 - - + +
33N LEU* 3.8 48.9 - - + +
34N GLU* 4.0 26.5 - - + +
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Residues in contact with ALA 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12770 C 3.3 50.2 - - - +
8N SER 3.1 12.2 + - - +
9N SER* 3.7 9.6 - - - +
11N ILE* 1.3 78.4 - - - +
13N ASP* 1.3 65.7 + - - +
15N LYS* 3.3 4.3 + - - +
16N SER* 3.1 19.6 + - - -
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Residues in contact with ASP 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N SER* 2.9 29.5 + - - +
10N LEU* 3.5 8.6 - - + +
12N ALA* 1.3 77.2 - - - +
14N LEU* 1.3 65.7 + - - +
16N SER* 3.3 8.4 + - - -
17N ALA* 3.2 23.7 + - - +
99N GLU* 5.3 6.8 - - + +
102N ILE* 4.0 15.4 - - + +
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Residues in contact with LEU 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N LEU* 2.8 32.7 + - + +
11N ILE* 3.5 6.7 - - - +
13N ASP* 1.3 76.1 - - - +
15N LYS* 1.3 61.1 + - - +
17N ALA* 3.5 0.5 + - - +
18N ALA* 3.2 18.5 + - - +
26N TRP* 3.3 51.6 - - + +
29N VAL* 3.8 16.2 - - + -
30N ALA* 3.9 11.0 - - + +
33N LEU* 3.8 28.5 - - + -
98N LEU* 4.3 6.3 - - + -
102N ILE* 3.2 31.0 - - + -
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Residues in contact with LYS 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12770 C 3.5 17.7 + - - +
12780 A 2.7 35.9 + - - +
12790 U 5.6 1.4 + - - -
11N ILE* 3.2 22.9 + - - +
12N ALA* 3.5 7.4 - - - +
13N ASP 3.1 0.4 - - - -
14N LEU* 1.3 73.8 - - - +
16N SER* 1.3 65.5 + - - +
17N ALA 3.0 1.6 - - - -
18N ALA* 3.1 6.7 + - - +
19N ARG* 3.0 50.3 + - - +
27N GLY* 5.4 2.7 - - - -
30N ALA* 4.1 14.1 - - + -
31N GLU* 6.4 0.9 - - - -
34N GLU* 3.0 35.7 + - - -
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Residues in contact with SER 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12770 C 3.2 30.2 + - - -
12N ALA 3.1 10.8 + - - -
13N ASP* 3.6 13.0 - - - -
15N LYS* 1.3 79.0 - - - +
17N ALA* 1.3 57.7 + - - +
19N ARG* 4.0 1.4 - - - +
20N SER* 3.0 38.5 + - - -
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Residues in contact with ALA 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N ASP 3.2 9.4 + - - +
14N LEU 3.8 4.7 - - - +
15N LYS 3.0 0.8 - - - -
16N SER* 1.3 75.1 - - - +
18N ALA* 1.3 59.5 + - - +
19N ARG 3.2 2.0 - - - -
20N SER* 5.0 0.7 - - - -
21N SER* 3.1 37.8 + - - +
23N GLY 4.3 0.2 + - - -
26N TRP* 3.8 14.6 - - + -
102N ILE* 3.5 32.3 - - + -
106N PRO* 3.6 11.2 - - + +
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Residues in contact with ALA 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LEU 3.2 8.9 + - - +
15N LYS* 3.1 6.1 + - - +
17N ALA* 1.3 78.7 - - - +
19N ARG* 1.3 60.8 + - + +
21N SER 3.1 8.7 - - - +
22N GLY 4.4 0.5 - - - -
23N GLY* 3.0 33.9 - - - +
24N ALA* 5.0 0.7 - - - -
26N TRP* 3.9 3.7 - - + +
27N GLY* 3.3 37.7 - - - +
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Residues in contact with ARG 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12760 U 3.3 56.1 + - - +
12770 C 2.6 42.7 + - - +
12780 A 2.7 42.8 + - - -
15N LYS* 3.0 32.3 + - - +
16N SER* 4.0 2.7 - - - +
18N ALA* 1.3 79.9 - - + +
20N SER* 1.3 69.5 + - - +
21N SER 3.3 4.3 - - - +
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Residues in contact with SER 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12760 U 5.0 5.2 + - - -
16N SER* 3.0 21.8 + - - -
17N ALA* 5.0 0.4 - - - -
19N ARG* 1.3 83.0 - - - +
21N SER* 1.3 66.3 + - - +
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Residues in contact with SER 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N ALA* 3.1 9.1 + - - +
18N ALA 3.1 20.4 - - - +
19N ARG 3.3 2.4 - - - +
20N SER* 1.3 85.8 - - - +
22N GLY* 1.3 60.0 + - - +
23N GLY 3.1 2.5 - - - -
106N PRO* 2.9 53.1 - - - +
107N GLU* 3.7 10.6 + - - -
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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