Contacts of the helix formed by residues 84 - 96 (chain A) in PDB entry 3JRE
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 ASN 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ALA* 4.4 0.2 - - - -
83A ILE* 1.3 73.4 - - - +
85A ARG* 1.3 68.4 + - - +
86A GLY* 3.3 16.1 + - - -
87A THR* 3.0 11.5 + - - +
88A LEU* 2.9 20.8 + - - +
17C T 2.9 64.1 + - + +
18C G 2.9 45.3 + - - +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLN* 4.9 16.0 + - + +
75A THR* 4.0 30.5 - - + +
78A ALA* 4.0 14.7 - - + +
83A ILE 3.7 1.8 + - - -
84A ASN* 1.3 77.1 - - - +
86A GLY* 1.3 58.7 + - - +
88A LEU* 3.5 4.5 + - + +
89A ARG* 3.0 34.3 + - + +
19C A 5.5 4.2 + - - +
20C G 3.4 10.5 + - - -
21C C 5.3 1.0 - - - +
6D T 3.9 24.3 + - - +
7D G 2.7 41.2 + - - -
8D C 3.1 19.3 - - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASN* 3.1 11.9 + - - -
85A ARG* 1.3 76.7 - - - +
87A THR* 1.3 65.7 + - - +
88A LEU 3.1 0.9 - - - -
89A ARG* 3.1 13.0 + - - +
90A LYS* 3.1 23.3 + - - +
17C T 5.2 4.7 - - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 3.6 22.4 - - + -
84A ASN* 3.0 14.8 + - - +
86A GLY* 1.3 75.8 - - - +
88A LEU* 1.3 62.0 + - - -
90A LYS* 3.2 12.0 + - + +
91A LYS* 3.0 42.1 + - + +
16C A 3.2 32.8 + - - +
17C T 2.8 27.5 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.9 21.8 - - + -
66A VAL* 6.2 1.1 - - + -
67A MET* 5.1 5.4 - - + -
74A GLN* 3.2 34.8 - - + +
77A ALA* 3.6 11.4 - - + -
78A ALA* 3.3 24.2 - - + +
81A MET* 5.2 5.2 - - - -
83A ILE* 4.0 15.0 - - + -
84A ASN 2.9 11.8 + - - +
85A ARG 3.6 10.8 - - - +
86A GLY 3.1 0.4 - - - -
87A THR* 1.3 76.3 - - - +
89A ARG* 1.3 64.0 + - - +
91A LYS* 3.4 2.8 + - - -
92A LEU* 3.1 40.8 + - + +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN* 3.2 32.2 + - - +
85A ARG* 3.0 28.0 - - + +
86A GLY* 3.1 11.6 + - - +
88A LEU* 1.3 76.3 - - - +
90A LYS* 1.3 55.3 + - - +
92A LEU* 2.8 26.9 + - - +
93A LYS* 2.9 14.6 + - - +
6D T 3.8 6.0 - - - +
7D G 2.6 75.2 + - - +
8D C 4.7 10.9 + - - +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.1 9.7 + - - +
87A THR* 3.4 13.5 - - + +
89A ARG* 1.3 79.0 - - - +
91A LYS* 1.3 59.5 + - + +
93A LYS* 3.2 9.9 + - - +
94A LYS* 2.9 31.6 + - - +
15C A 3.4 27.4 + - - +
16C A 2.4 34.1 + - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 5.7 3.2 - - - +
59A GLU* 3.2 35.9 + - - +
63A LEU* 4.4 20.4 - - + -
83A ILE* 4.6 10.3 - - + -
87A THR* 3.0 40.2 + - + +
88A LEU* 4.0 4.7 - - - +
90A LYS* 1.3 75.5 - - + +
92A LEU* 1.3 63.6 + - - +
94A LYS* 3.4 17.1 + - + +
95A TYR* 3.2 33.4 + - + -
51B TYR* 4.1 17.6 + - + -
16C A 3.8 19.3 + - - -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.4 13.0 - - + -
67A MET* 4.2 25.4 - - + -
74A GLN* 4.1 22.7 - - - +
88A LEU* 3.1 36.3 + - + +
89A ARG* 2.8 8.3 + - - +
91A LYS* 1.3 77.1 - - - +
93A LYS* 1.3 57.5 + - - +
95A TYR* 3.3 2.1 + - - -
96A GLY 2.9 22.7 + - - -
97A MET* 3.1 59.1 + - + +
98A ASN* 3.6 10.8 - - + +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG 2.9 11.5 + - - +
90A LYS* 3.3 14.1 - - + +
92A LEU* 1.3 74.8 - - - +
94A LYS* 1.3 65.6 + - - +
96A GLY* 2.9 16.7 + - - -
98A ASN* 2.9 33.2 + - - +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 3.3 25.6 + - - +
55A LEU* 6.1 1.4 - - - +
59A GLU* 5.0 4.9 - - - +
90A LYS* 2.9 20.3 + - - +
91A LYS* 3.6 21.5 - - + +
93A LYS* 1.3 74.4 - - - +
95A TYR* 1.3 90.9 + - + +
96A GLY 3.6 0.2 + - - -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 5.7 0.5 + - - -
55A LEU* 5.3 1.0 - - - +
56A ALA* 3.5 29.5 + - + +
59A GLU* 2.8 44.5 + - + +
60A GLN* 3.6 41.5 + - + +
63A LEU* 3.5 16.4 - - + -
91A LYS* 3.2 25.9 + - + +
92A LEU 3.3 0.2 + - - -
93A LYS 3.1 0.4 - - - -
94A LYS* 1.3 101.8 - - + +
96A GLY* 1.3 66.1 + - - +
97A MET* 4.1 20.0 - - + +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 2.9 8.4 + - - -
93A LYS* 2.9 17.9 + - - -
94A LYS 3.6 0.2 + - - -
95A TYR* 1.3 81.2 - - - +
97A MET* 1.3 57.1 + - - +
98A ASN* 4.0 7.9 - - - -
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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
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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