Contacts of the helix formed by residues 58 - 70 (chain J) 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 HIS 58 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J PRO* 5.2 4.3 - - + +
25J GLY 3.4 12.7 + - - -
26J LYS* 3.4 24.2 - - + -
27J LYS* 2.9 51.8 - - + +
28J ILE* 4.0 3.2 - - + +
56J ILE 3.7 1.0 + - - -
57J ARG* 1.3 71.3 - - - +
59J ASN* 1.3 87.2 + - - +
61J LEU* 3.5 13.7 - - - +
62J GLU* 3.1 24.6 + - - +
89J PRO* 4.1 7.0 - - + -
119J VAL 5.3 1.6 - - - -
120J GLY* 4.5 8.7 - - - -
121J THR* 3.1 40.6 + - - +
122J ALA* 4.2 0.6 - - - +
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Residues in contact with ASN 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2519A C 3.9 31.3 + - - +
2520A G 4.5 1.8 - - - +
27J LYS* 3.6 28.2 + - - +
57J ARG* 2.7 36.3 + - + +
58J HIS* 1.3 106.9 + - - +
60J ALA* 1.3 62.4 + - - +
62J GLU* 3.3 2.9 + - - +
63J ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2519A C 3.6 20.5 + - - +
2520A G 3.9 13.0 + - - +
56J ILE* 3.8 15.0 - - + -
57J ARG 2.8 11.0 + - - +
59J ASN* 1.3 76.5 - - - +
61J LEU* 1.3 67.1 + - - +
63J ALA* 3.9 0.2 - - - +
64J ALA* 2.8 28.2 + - - +
152J LYS 3.5 18.0 - - - +
153J VAL* 4.3 3.8 - - + -
154J THR 5.7 0.2 - - - +
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Residues in contact with LEU 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ILE* 3.4 27.6 - - + -
56J ILE* 3.0 49.6 - - + +
57J ARG 3.0 24.3 + - - +
58J HIS* 3.5 7.9 - - + +
60J ALA* 1.3 77.7 - - - +
62J GLU* 1.3 53.9 + - - +
64J ALA* 3.4 3.6 - - + +
65J ARG* 2.7 38.0 + - - +
85J ILE* 4.3 14.1 - - + -
87J LYS* 5.4 3.6 - - + +
89J PRO* 4.8 2.0 - - + -
123J ALA* 4.3 15.0 - - + +
131J ILE* 3.6 27.1 - - + -
132J PHE* 4.6 2.4 - - + -
153J VAL* 5.1 1.6 - - + -
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Residues in contact with GLU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J LYS* 2.7 30.2 - - + +
28J ILE* 2.8 9.9 - - - +
29J ALA* 2.5 35.7 + - - +
58J HIS 3.1 15.5 + - - +
59J ASN 3.7 3.4 - - - +
61J LEU* 1.3 79.7 - - - +
63J ALA* 1.3 56.1 + - - +
65J ARG* 3.2 18.4 + - - -
66J VAL* 2.8 61.3 + - + +
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Residues in contact with ALA 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2518A C 4.1 13.9 - - - +
2519A C 3.4 39.5 - - - +
59J ASN 3.1 15.2 + - - +
60J ALA 3.9 0.2 - - - +
62J GLU* 1.3 74.2 - - - +
64J ALA* 1.3 65.6 + - - +
66J VAL* 4.1 4.2 - - - +
67J ALA* 3.0 27.9 + - - +
70J ARG* 5.7 0.2 + - - -
152J LYS* 3.7 11.7 + - + +
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J ALA 2.8 19.8 + - - +
61J LEU* 3.4 4.5 - - + +
63J ALA* 1.3 79.5 - - - +
65J ARG* 1.3 63.5 + - - +
67J ALA* 3.7 3.2 - - - +
68J ALA* 3.1 22.2 + - - +
132J PHE* 4.2 16.4 - - + -
149J ALA* 3.8 28.3 - - - +
152J LYS* 4.3 6.4 - - + +
153J VAL* 3.9 15.9 - - + -
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Residues in contact with ARG 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ILE* 4.8 2.9 - - - -
29J ALA* 3.2 14.8 - - - +
30J GLN* 2.9 61.2 + - - +
33J MET* 3.4 38.7 - - + -
61J LEU 2.7 22.6 + - - +
62J GLU* 3.2 30.1 + - - +
64J ALA* 1.3 71.7 - - - +
66J VAL* 1.3 83.7 + - - +
68J ALA* 2.9 4.6 + - - +
69J ASN* 2.8 28.8 + - - +
83J PHE* 4.5 0.6 - - + -
85J ILE* 4.4 6.1 - - + -
132J PHE* 3.7 22.2 - - + -
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Residues in contact with VAL 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J GLU* 2.8 52.4 + - + +
63J ALA* 4.1 4.0 - - - +
65J ARG* 1.3 85.8 - - - +
67J ALA* 1.3 59.2 + - - +
68J ALA 2.9 0.5 + - - -
69J ASN* 5.0 0.9 - - - -
70J ARG* 2.6 75.4 + - + +
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Residues in contact with ALA 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2502A C 6.1 0.4 - - - +
63J ALA 3.0 21.2 + - - +
64J ALA 3.7 4.3 - - - +
66J VAL* 1.3 76.2 - - - +
68J ALA* 1.3 59.2 + - - +
70J ARG* 4.3 15.4 + - - +
71J TYR* 3.5 18.0 + - - +
145J ALA 4.6 1.8 - - - -
148J ARG* 4.1 29.5 + - + +
152J LYS* 3.7 26.0 - - + +
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Residues in contact with ALA 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J ALA 3.1 11.7 + - - +
65J ARG* 2.9 8.7 + - - +
66J VAL 2.9 0.8 + - - -
67J ALA* 1.3 76.6 - - - +
69J ASN* 1.3 61.4 + - - +
71J TYR* 3.1 6.6 + - - +
72J VAL* 2.9 22.1 + - - +
83J PHE* 3.7 25.8 - - + -
132J PHE* 5.6 0.4 - - + -
145J ALA* 3.2 35.9 - - + +
149J ALA* 4.0 8.7 - - + -
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Residues in contact with ASN 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J GLN* 5.0 6.1 + - - +
33J MET* 3.6 43.0 - - - +
65J ARG* 2.8 21.9 + - - +
66J VAL* 4.2 1.3 - - - +
68J ALA* 1.3 69.7 - - - +
70J ARG* 1.3 66.3 + - - +
71J TYR 2.9 1.8 - - - -
72J VAL* 2.8 31.9 + - - +
73J GLN* 3.2 15.2 + - - -
81J TYR* 2.9 31.0 + - - -
83J PHE* 3.9 8.7 - - + -
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Residues in contact with ARG 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504A A 3.0 65.8 + - - -
2505A G 5.7 0.2 - - - -
2517A A 4.8 10.9 + - - -
2518A C 5.5 1.0 + - - -
63J ALA 5.7 0.2 + - - -
66J VAL* 2.6 56.3 + - + +
67J ALA* 4.3 16.6 + - - +
69J ASN* 1.3 73.2 - - - +
71J TYR* 1.3 59.2 + - - +
73J GLN* 3.5 22.6 - - - +
148J ARG* 5.9 0.6 - - - +
152J LYS* 4.8 11.5 - - - +
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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