Contacts of the helix formed by residues 3 - 14 (chain N) in PDB entry 1NJI
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 3 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A A 3.4 18.1 + - - -
243A A 3.1 25.4 - - - -
377A C 5.5 1.0 - - - -
34H ASN* 3.8 1.6 - - - -
37H THR* 4.7 0.2 - - - -
38H LYS* 3.3 9.2 - - - +
1N ALA 3.3 1.4 + - - -
2N ARG* 1.3 76.3 - - - +
4N ALA* 1.3 63.2 + - - +
5N TYR* 3.1 14.6 + - - +
6N SER* 2.6 44.5 + - - -
7N TYR* 3.3 4.5 - - - -
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Residues in contact with ALA 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H THR* 3.9 15.3 - - + +
34H ASN* 2.8 32.2 + - + +
37H THR* 3.4 27.1 - - - +
59H ILE 5.3 0.4 - - - +
62H HIS* 4.1 6.2 - - + +
2N ARG 4.0 1.0 + - - -
3N SER* 1.3 70.2 - - - +
5N TYR* 1.3 58.2 + - + +
7N TYR* 2.8 40.9 + - - +
8N ILE* 3.7 6.7 + - + +
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Residues in contact with TYR 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A A 3.5 34.4 + - - -
243A A 5.0 0.9 - - - -
263A U 5.4 0.9 - - - -
264A G 2.7 48.6 + + - +
34H ASN* 4.0 22.4 + - + -
3N SER* 3.3 15.9 - - - +
4N ALA* 1.3 78.4 - - + +
6N SER* 1.3 52.9 + - - +
7N TYR 2.7 1.2 + - - -
8N ILE* 2.7 40.6 + - + +
9N ARG* 3.2 8.7 + - - +
46N LEU* 3.6 19.1 - - + -
47N ASP* 3.8 24.0 - - + +
50N ARG* 3.6 23.9 + - - -
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Residues in contact with SER 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A A 4.8 3.1 - - - -
2N ARG* 3.1 32.6 + - - +
3N SER* 2.6 34.3 + - - -
5N TYR* 1.3 74.6 - - - +
7N TYR* 1.3 57.0 + - - +
9N ARG* 3.6 33.6 + - - +
10N GLU* 2.9 29.9 + - - +
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Residues in contact with TYR 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR* 3.9 8.7 - - + -
41H GLU* 2.9 28.7 + - - -
58H GLU 5.8 1.3 - - - +
61H MET* 5.7 0.4 - - - +
62H HIS* 3.5 48.5 - + + +
66H LEU* 3.8 24.0 - - + +
2N ARG* 3.3 46.1 + - + +
3N SER 3.3 12.6 - - - -
4N ALA* 2.8 20.0 + - - +
5N TYR 2.7 1.4 + - - -
6N SER* 1.3 80.0 + - - +
8N ILE* 1.3 64.1 + - + +
10N GLU* 3.6 3.6 - - + +
11N ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU* 3.7 42.2 - - + +
59H ILE* 4.4 19.1 - - + +
61H MET* 5.8 0.7 - - - -
62H HIS* 6.0 1.1 - - + +
4N ALA* 4.3 6.1 - - + +
5N TYR* 2.7 31.0 + - + +
7N TYR* 1.3 72.6 - - + +
9N ARG* 1.3 60.7 + - - +
11N ALA* 3.2 4.5 + - - +
12N TRP* 3.1 35.0 + - + -
45N ARG* 4.4 10.5 - - - -
46N LEU* 3.7 29.8 - - + +
47N ASP* 3.7 20.6 - - - +
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Residues in contact with ARG 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A A 6.3 1.4 - - - -
378A A 2.4 38.4 + - - -
379A G 3.9 24.6 + - - -
380A A 3.0 34.7 + - + +
5N TYR* 3.2 5.3 + - - +
6N SER* 3.6 30.6 + - - +
8N ILE* 1.3 76.6 - - - +
10N GLU* 1.3 68.3 + - - +
12N TRP* 3.2 14.9 + - - +
13N LYS* 3.2 29.5 + - + +
45N ARG* 5.9 2.2 - - - +
47N ASP* 3.1 26.4 + - + +
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Residues in contact with GLU 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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2N ARG* 4.0 20.3 + - - +
6N SER* 2.9 19.9 + - - +
7N TYR* 3.6 5.8 - - + +
9N ARG* 1.3 79.2 + - - +
11N ALA* 1.3 65.4 + - - +
13N LYS* 3.3 51.5 + - - +
14N ARG* 4.3 2.4 + - - +
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Residues in contact with ALA 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H MET* 4.0 27.4 - - + -
7N TYR 3.0 12.6 + - - +
8N ILE* 3.4 9.4 - - - +
10N GLU* 1.3 79.1 - - - +
12N TRP* 1.3 62.7 + - + +
13N LYS 3.1 5.0 + - - -
14N ARG* 3.3 21.3 + - - +
15N PRO 3.9 0.3 - - - -
20N ILE* 4.0 16.3 - - + +
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Residues in contact with TRP 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A A 3.8 8.4 + - - +
381A G 5.4 6.5 - - - +
58H GLU* 3.0 34.9 + - + +
8N ILE* 3.1 26.1 + - + +
9N ARG* 3.2 7.3 + - - +
11N ALA* 1.3 77.8 - - + +
13N LYS* 1.3 63.5 + - - +
14N ARG 3.1 0.4 - - - -
15N PRO* 3.3 29.7 - - + +
20N ILE* 3.1 23.8 - - + +
24N MET* 3.8 14.6 - - + -
27N ARG* 3.9 10.5 - - - -
31N TRP* 5.5 0.2 - + - -
44N THR* 4.2 5.1 + - + -
45N ARG* 3.5 56.1 + - + +
119N SER 4.4 1.3 - - - -
120N VAL* 3.7 42.0 - - + -
121N GLY* 4.1 4.0 - - - -
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Residues in contact with LYS 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A A 3.6 66.0 + - + +
381A G 3.7 14.0 - - - +
408A A 5.2 2.1 + - - +
409A U 2.6 39.6 + - - -
9N ARG* 3.2 27.0 + - + +
10N GLU* 3.3 43.8 + - - +
11N ALA 3.1 1.2 + - - -
12N TRP* 1.3 79.7 - - - +
14N ARG* 1.3 69.3 + - + +
15N PRO* 3.5 5.4 - - - +
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Residues in contact with ARG 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A A 5.5 3.8 + - + -
381A G 4.4 7.4 - - - +
407A A 3.6 37.4 + - - +
408A A 4.1 21.8 + - - -
10N GLU 5.4 1.6 - - - +
11N ALA 3.3 12.3 + - - +
12N TRP 3.1 0.2 - - - -
13N LYS* 1.3 90.6 - - + +
15N PRO* 1.3 56.5 - - - +
16N LYS 2.9 11.5 + - - -
17N GLU* 3.0 45.3 + - + +
20N ILE* 3.9 2.9 - - - +
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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