Contacts of the helix formed by residues 4 - 18 (chain 3) 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 4 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23 LYS 4.0 1.2 + - - -
33 LYS* 1.3 76.9 - - - +
53 LYS* 1.3 65.9 + - - +
63 ALA* 3.8 6.9 + - - +
73 THR* 3.3 25.8 + - - -
83 LYS* 3.1 22.2 + - - +
120A A 5.8 0.2 - - - -
121A U 4.5 9.1 + - - -
122A C 5.7 3.6 - - - -
1486A A 5.9 1.3 - - - +
1675A C 4.4 5.8 - - - -
1676A G 4.4 3.4 - - - -
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Residues in contact with LYS 5 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 SER* 1.3 74.8 - - - +
63 ALA* 1.3 63.6 + - - +
83 LYS* 3.3 4.2 + - - +
93 LYS* 3.0 35.7 + - + +
122A C 3.4 21.2 + - - +
123A U 2.8 34.2 + - - +
1674A C 4.4 0.8 + - - -
1675A C 3.1 49.7 + - - +
1676A G 4.0 7.4 - - - +
30T ASP* 2.8 42.6 + - - -
31T ARG* 4.9 1.6 - - - +
56T ASN* 3.7 16.2 - - + +
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Residues in contact with ALA 6 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 SER* 3.3 3.2 + - - +
53 LYS* 1.3 76.9 - - - +
73 THR* 1.3 65.1 + - - +
93 LYS* 3.1 7.7 + - - +
103 ARG* 3.1 29.2 + - - +
121A U 3.3 40.8 - - - +
122A C 3.4 36.8 + - - +
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Residues in contact with THR 7 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 LYS* 3.8 19.4 - - + -
43 SER* 3.3 25.4 + - - -
63 ALA* 1.3 78.1 - - - +
83 LYS* 1.3 58.4 + - - +
103 ARG* 3.2 18.5 + - - +
113 LEU* 2.9 42.1 + - + +
493 GLU* 3.3 22.1 + - - +
120A A 3.7 14.4 + - - -
121A U 4.8 0.3 + - - -
1417A G 5.3 4.9 - - - +
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Residues in contact with LYS 8 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33 LYS* 4.2 13.9 - - + -
43 SER 3.1 17.9 + - - +
53 LYS* 3.5 7.2 - - - +
73 THR* 1.3 76.4 - - - +
93 LYS* 1.3 66.6 + - + +
113 LEU* 3.4 5.5 + - - +
123 ALA* 2.9 24.5 + - - +
1446A U 4.7 11.9 + - - -
1676A G 3.4 18.6 + - - +
1677A U 2.6 39.1 + - - +
55T GLN* 5.5 1.2 - - - +
56T ASN* 2.8 31.5 + - + +
57T THR 3.9 11.6 - - - +
58T MET* 3.6 32.0 - - - +
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Residues in contact with LYS 9 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53 LYS* 3.0 29.4 + - + +
63 ALA* 3.4 6.3 - - - +
83 LYS* 1.3 76.1 - - + +
103 ARG* 1.3 60.0 + - + +
123 ALA* 3.1 9.7 + - - +
133 LYS* 2.9 27.6 + - - +
53A C 4.2 34.5 + - - +
54A G 4.9 2.6 + - - -
122A C 3.1 45.0 + - - +
30T ASP* 4.1 21.4 + - - +
60T GLY* 4.9 21.7 - - - +
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Residues in contact with ARG 10 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 LYS* 4.1 18.8 - - - +
63 ALA* 3.1 19.1 + - - +
73 THR* 3.5 21.5 + - - +
93 LYS* 1.3 74.0 - - + +
113 LEU* 1.3 66.9 + - - +
133 LYS* 3.1 5.8 + - - +
143 LEU* 2.9 29.4 + - + +
493 GLU* 3.0 47.0 + - - +
52A A 4.7 3.9 + - - +
53A C 3.7 31.9 + - - +
120A A 3.5 7.3 + - - -
121A U 2.3 72.3 + - - -
122A C 5.5 2.1 + - - +
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Residues in contact with LEU 11 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33 LYS* 4.8 11.0 - - + +
73 THR* 2.9 33.0 + - + +
83 LYS* 3.8 4.7 - - - +
103 ARG* 1.3 75.2 - - - +
123 ALA* 1.3 63.1 + - - +
143 LEU* 3.1 23.3 + - + +
153 ASP* 2.9 22.3 + - - +
473 THR* 4.3 11.7 - - + +
483 ASP 5.8 0.7 - - - +
493 GLU* 5.0 8.7 - - - +
1417A G 3.5 66.8 + - + +
1418A U 4.9 2.6 + - - -
58T MET* 4.2 13.4 - - + +
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Residues in contact with ALA 12 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LYS 2.9 13.3 + - - +
93 LYS 3.2 11.0 - - - +
113 LEU* 1.3 76.6 - - - +
133 LYS* 1.3 64.0 + - - +
153 ASP* 3.0 6.9 + - - +
163 ASN* 3.0 21.2 + - - +
54A G 5.8 0.7 - - - +
57T THR 4.8 0.2 - - - +
58T MET* 3.3 40.2 - - - +
59T ASP 3.9 4.6 - - - +
60T GLY* 3.7 17.3 - - - +
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Residues in contact with LYS 13 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 LYS 2.9 10.9 + - - +
103 ARG* 3.4 9.9 - - - +
123 ALA* 1.3 74.7 - - - +
143 LEU* 1.3 60.4 + - + +
163 ASN* 2.8 11.0 + - + +
173 GLN* 2.8 54.7 + - + +
53A C 3.4 48.0 - - - +
54A G 2.7 49.4 + - - +
61A G 5.3 2.4 + - - -
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Residues in contact with LEU 14 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 ARG* 2.9 19.6 + - + +
113 LEU* 3.4 21.1 - - + +
133 LYS* 1.3 77.7 - - + +
153 ASP* 1.3 63.0 + - - +
173 GLN* 3.5 23.8 + - + +
183 ASN* 3.3 20.4 + - - +
403 ARG* 3.5 26.2 + - - +
473 THR* 3.7 33.4 - - + -
483 ASP 5.1 2.9 - - - +
493 GLU* 5.5 4.7 - - - +
53A C 6.2 0.2 - - - +
1418A U 5.2 0.2 - - - +
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Residues in contact with ASP 15 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 LEU 2.9 12.0 + - - +
123 ALA* 3.0 11.4 + - - +
143 LEU* 1.3 76.0 - - - +
163 ASN* 1.3 62.1 + - - +
183 ASN* 3.0 29.1 - - - +
193 SER* 4.1 0.7 + - - -
403 ARG* 4.1 0.4 - - - +
1418A U 4.1 41.7 + - + +
1419A U 5.1 1.7 + - - -
8076A MG 4.2 9.2 - - - -
58T MET* 4.7 14.0 - - + +
59T ASP* 5.4 2.4 - - - +
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Residues in contact with ASN 16 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 ALA 3.0 10.9 + - - +
133 LYS* 2.8 13.7 + - + +
153 ASP* 1.3 76.3 + - - +
173 GLN* 1.3 62.6 + - + +
183 ASN 2.9 6.0 + - - -
193 SER* 3.2 16.3 + - - -
54A G 5.6 1.6 + - - +
60A A 3.2 39.4 + - - +
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Residues in contact with GLN 17 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133 LYS* 2.8 45.8 + - + +
143 LEU* 3.5 32.3 + - + +
153 ASP 3.3 0.2 - - - -
163 ASN* 1.3 72.0 - - + +
183 ASN* 1.3 56.6 + - - +
193 SER 3.1 5.1 + - - -
363 ASN* 3.7 9.5 + - - +
383 LYS* 4.6 26.2 - - + +
60A A 3.5 27.1 + - - +
61A G 2.8 32.4 + - - +
62A C 5.5 2.0 + - - -
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Residues in contact with ASN 18 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 LEU 3.3 10.9 + - - +
153 ASP* 3.0 20.8 - - - +
163 ASN 2.9 1.2 - - - -
173 GLN* 1.3 78.1 - - - +
193 SER* 1.3 61.8 + - - +
363 ASN* 4.9 0.7 - - - +
383 LYS 4.2 1.8 + - - -
393 ARG* 3.6 14.5 - - - +
403 ARG* 2.7 57.0 + - - +
1418A U 5.1 2.4 + - - -
1441A G 5.3 5.0 + - - -
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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