Contacts of the strand formed by residues 62 - 69 (chain J) in PDB entry 1N33
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 62 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1188A A 6.1 3.4 - - - -
1367A C 3.6 14.7 + - - -
1368A G 3.4 27.6 + - - -
111I ARG* 3.7 5.8 + - - -
114I TYR* 4.5 12.5 - + - -
46J ARG* 5.3 4.5 - - + -
47J PHE 3.6 3.6 - - - -
48J THR* 2.6 37.7 + - + -
60J ARG* 4.6 0.2 - - + -
61J GLU* 1.3 80.3 + - - +
63J PHE* 1.3 64.9 + - - +
58N LYS* 3.4 8.2 + - - +
59N ALA* 2.6 46.4 + - + +
61N TRP* 3.1 30.1 - + + -
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Residues in contact with PHE 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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46J ARG* 3.5 1.6 - - - +
47J PHE* 2.5 58.1 + - + +
48J THR 5.6 0.4 - - - -
49J VAL* 5.7 4.5 - - + -
61J GLU* 3.5 28.0 - - + -
62J HIS* 1.3 80.2 - - - +
64J GLU* 1.3 61.4 + - - +
44N LEU* 4.2 16.6 - - + -
45N ARG* 3.3 30.1 - - + -
48N ALA* 3.8 23.6 - - + -
49N HIS* 4.0 7.6 - + - -
56N VAL* 4.5 10.5 - - + -
57N ARG 3.0 23.3 - - - +
58N LYS* 3.3 28.3 - - + -
59N ALA* 3.4 5.6 - - - +
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Residues in contact with GLU 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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1114A C 4.9 7.1 + - - -
44J VAL* 4.1 6.5 - - + -
45J ARG 3.2 9.9 - - - +
46J ARG* 3.0 27.8 + - - +
47J PHE* 4.0 6.2 - - - -
63J PHE* 1.3 75.0 - - - +
65J LEU* 1.3 66.3 + - - +
66J ARG* 2.6 56.2 + - - +
55N GLY 4.7 0.3 - - - +
56N VAL* 3.7 17.3 - - - +
57N ARG* 3.4 31.6 + - + +
58N LYS 5.0 1.1 - - - +
59N ALA* 3.4 21.2 - - - +
60N SER 4.7 4.5 + - - +
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Residues in contact with LEU 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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29C TYR* 4.1 6.5 - - + -
11J PHE* 3.6 38.6 - - + -
43J ARG 3.9 3.3 - - - +
44J VAL* 4.2 1.2 - - - +
45J ARG* 3.2 33.9 + - + +
47J PHE* 4.1 9.9 - - + -
64J GLU* 1.3 82.8 - - - +
66J ARG* 1.3 62.2 + - - +
67J THR* 3.3 6.1 + - - +
36N PHE* 3.7 33.2 - - + -
37N PHE* 4.5 0.2 - - + -
55N GLY 3.8 12.1 - - - -
56N VAL* 3.6 31.6 - - + +
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Residues in contact with ARG 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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1115A C 5.4 10.1 + - - -
11J PHE* 3.0 32.9 - - - +
42J THR* 3.9 17.1 - - + +
44J VAL* 4.1 24.1 - - + +
46J ARG* 4.9 6.9 - - - +
64J GLU* 2.6 59.1 + - - +
65J LEU* 1.3 72.5 - - - +
67J THR* 1.3 61.3 + - - +
68J HIS* 3.7 29.0 + - + +
55N GLY 4.5 4.8 + - - +
57N ARG* 5.1 13.2 - - + +
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Residues in contact with THR 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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23C TYR* 3.9 23.1 - - + +
26C LYS* 5.2 10.6 + - - +
9J ARG* 3.7 26.5 - - + +
10J GLY 3.6 4.7 - - - +
11J PHE* 3.4 21.8 - - - -
42J THR* 2.9 20.4 - - - +
43J ARG* 3.5 21.4 + - + +
45J ARG* 5.8 1.7 - - - +
65J LEU* 3.3 9.1 + - - +
66J ARG* 1.3 69.9 - - - +
68J HIS* 1.3 64.7 + - - +
69J ASN* 3.8 4.0 + - - -
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Residues in contact with HIS 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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1152A A 2.4 34.4 + - - +
8J LEU 4.6 0.2 - - - -
9J ARG* 3.4 20.1 - - - -
10J GLY 3.0 12.6 + - - +
11J PHE 3.5 17.3 + - - -
12J ASP* 3.4 7.8 - - - -
13J HIS* 3.2 38.0 + - + +
16J LEU* 5.1 8.3 - - + -
42J THR* 3.4 17.6 + - - +
66J ARG* 3.7 37.7 + - + -
67J THR* 1.3 78.9 - - - +
69J ASN* 1.3 65.3 + - - +
70J ARG* 5.4 3.1 - - - +
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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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1151A A 5.8 0.5 - - - +
1280A A 5.0 2.0 + - - -
7J LYS* 6.1 0.3 - - - +
8J LEU 3.2 4.4 - - - +
9J ARG* 2.7 41.6 + - - +
39J PRO* 2.4 25.4 + - - +
40J LEU* 3.0 33.1 + - + +
41J PRO 2.7 25.3 + - - -
42J THR* 4.2 1.4 + - - +
43J ARG* 4.5 5.1 - - - +
67J THR* 3.8 10.5 + - - +
68J HIS* 1.3 73.5 - - - +
70J ARG* 1.3 81.4 + - - +
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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