Contacts of the helix formed by residues 59 - 71 (chain Q) 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 ARG 59 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1548A U 3.0 51.6 + - - -
1549A C 3.3 15.9 + - - -
1565A C 3.6 0.2 + - - -
1566A C 2.7 19.3 + - - +
1704A G 3.0 22.3 + - - +
1705A C 2.8 41.8 + - - -
1798A C 5.3 0.6 + - - -
57Q ASN 4.0 6.1 - - - +
58Q SER* 1.3 74.8 - - - +
60Q GLY* 1.3 58.0 + - - +
61Q ARG 3.5 1.8 - - - -
62Q ALA* 3.1 9.2 + - + +
63Q ARG* 2.9 45.2 + - - +
66Q GLN* 2.6 33.4 - - - +
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Residues in contact with GLY 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1564A C 5.3 0.2 - - - -
1565A C 3.7 37.3 + - - -
2738A G 4.7 5.4 - - - -
2739A A 6.3 0.4 - - - -
58Q SER* 3.3 4.8 - - - +
59Q ARG* 1.3 77.4 - - - +
61Q ARG* 1.3 63.5 + - - +
63Q ARG* 3.1 15.0 + - - +
64Q GLU* 3.1 19.0 + - - +
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Residues in contact with ARG 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2736A U 3.4 41.5 + - - +
2737A C 2.6 46.3 + - - +
2738A G 3.3 11.8 + - - +
2739A A 2.8 41.7 + - - +
58Q SER* 3.7 17.2 + - - -
60Q GLY* 1.3 75.5 - - - +
62Q ALA* 1.3 62.2 + - - +
64Q GLU* 3.5 12.0 + - - +
65Q ARG* 3.2 37.6 + - - +
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Residues in contact with ALA 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705A C 4.1 16.6 - - - +
1706A G 5.3 0.4 + - - +
58Q SER 5.3 1.1 + - - +
59Q ARG* 3.1 32.2 + - + +
60Q GLY 3.1 0.6 - - - -
61Q ARG* 1.3 79.1 - - - +
63Q ARG* 1.3 57.6 + - - +
65Q ARG* 3.2 20.4 + - - +
66Q GLN* 2.8 47.7 + - - +
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Residues in contact with ARG 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A C 3.0 38.6 + - - +
1550A A 4.9 13.5 + - - -
1565A C 2.9 36.4 + - - +
1566A C 3.4 33.3 + - - -
59Q ARG* 2.9 24.4 + - + +
60Q GLY* 3.1 9.3 + - - +
62Q ALA* 1.3 73.9 - - - +
64Q GLU* 1.3 65.4 + - - +
66Q GLN* 3.1 13.8 + - - +
67Q LYS* 2.9 35.4 + - + +
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Residues in contact with GLU 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2739A A 5.2 12.1 + - - +
60Q GLY 3.1 16.2 + - - +
61Q ARG* 3.9 13.8 - - - +
62Q ALA 3.3 0.2 - - - -
63Q ARG* 1.3 76.0 - - + +
65Q ARG* 1.3 63.0 + - - +
67Q LYS* 3.1 15.6 + - + +
68Q LYS* 3.1 42.1 + - - +
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Residues in contact with ARG 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705A C 2.9 32.7 + - - -
1706A G 3.0 19.2 + - - +
2735A U 3.4 30.1 + - - -
2736A U 5.6 1.8 + - - -
61Q ARG* 3.2 25.7 + - - +
62Q ALA* 3.2 23.5 + - - +
63Q ARG 3.2 0.2 - - - -
64Q GLU* 1.3 76.2 - - - +
66Q GLN* 1.3 65.5 + - + +
67Q LYS 3.2 0.2 + - - -
68Q LYS* 3.2 4.3 + - - +
69Q ARG* 2.9 58.9 + - - +
74Q GLN* 3.5 22.4 - - - +
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Residues in contact with GLN 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A C 3.8 17.7 + - - +
1705A C 4.6 4.0 + - - -
1706A G 5.5 8.4 + - - +
1798A C 3.3 53.6 + - - +
59Q ARG* 2.6 32.9 - - - +
62Q ALA* 2.8 33.3 + - - +
63Q ARG* 3.5 10.5 - - - +
65Q ARG* 1.3 73.5 - - - +
67Q LYS* 1.3 57.3 + - + +
69Q ARG* 3.8 4.9 - - - +
70Q ALA* 2.9 30.4 + - - +
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Residues in contact with LYS 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550A A 5.8 3.6 - - - -
63Q ARG* 2.9 23.5 + - + +
64Q GLU* 3.3 16.0 - - + +
65Q ARG 3.1 0.2 - - - -
66Q GLN* 1.3 75.3 - - + +
68Q LYS* 1.3 66.6 + - + +
70Q ALA* 3.1 6.8 + - - +
71Q LYS* 2.9 25.1 + - - +
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Residues in contact with LYS 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1787A C 2.9 38.1 + - - +
1788A U 3.7 26.5 + - - +
64Q GLU* 3.1 32.2 + - - +
65Q ARG* 3.6 5.8 - - - +
67Q LYS* 1.3 77.7 - - + +
69Q ARG* 1.3 52.7 + - - +
71Q LYS* 3.1 9.5 + - - +
72Q GLY 3.1 9.4 + - - -
73Q HIS* 2.7 39.0 + - + +
74Q GLN* 3.9 25.6 - - + +
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Residues in contact with ARG 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706A G 3.7 5.9 + - - -
1707A G 3.0 42.1 + - - -
1786A C 5.8 0.8 + - - -
1798A C 5.0 6.5 + - - -
1800A G 5.6 1.1 - - - +
65Q ARG* 2.9 50.4 + - - +
66Q GLN* 4.0 6.3 - - - +
68Q LYS* 1.3 72.1 - - - +
70Q ALA* 1.3 66.5 + - - +
72Q GLY* 3.0 8.7 + - - -
73Q HIS 3.2 19.3 - - - +
74Q GLN* 3.6 28.3 + - + +
75Q LYS* 3.2 35.9 + - + +
79Q SER* 5.5 4.2 + - - -
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Residues in contact with ALA 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1798A C 3.5 38.0 + - + +
66Q GLN 2.9 19.8 + - - +
67Q LYS* 3.1 7.3 + - - +
69Q ARG* 1.3 76.2 - - - +
71Q LYS* 1.3 57.6 + - - +
72Q GLY* 3.2 3.8 + - - -
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Residues in contact with LYS 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1789A G 3.7 35.4 + - - +
1790A C 3.0 78.3 + - + -
1791A U 4.9 2.1 - - - +
67Q LYS 2.9 12.5 + - - +
68Q LYS* 3.1 8.5 + - - +
70Q ALA* 1.3 75.9 - - - +
72Q GLY* 1.3 56.2 + - - +
73Q HIS* 3.8 19.5 - - + -
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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