Contacts of the helix formed by residues 63 - 77 (chain C) in PDB entry 4JCQ
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 63 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 3.6 22.8 + - - -
30C ILE* 2.7 25.5 + - - +
31C ASN* 4.0 11.9 - - + +
32C GLN* 5.5 1.1 - - + +
62C GLY* 1.3 74.8 - - - -
64C VAL* 1.3 65.3 + - - +
65C GLU* 3.4 25.6 - - - +
66C ALA* 3.2 10.1 + - + +
67C GLY* 3.1 18.0 + - - -
92C ALA* 4.3 1.8 - - - +
121C GLY 3.8 3.4 - - - -
122C VAL 3.2 23.8 + - - -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY 3.8 1.2 + - - -
63C HIS* 1.3 71.8 - - - +
65C GLU* 1.3 69.6 + - + +
67C GLY* 3.1 3.0 + - - +
68C ASP* 2.8 48.0 + - - +
92C ALA* 4.9 7.6 - - - -
117C GLN* 6.1 0.2 - - - +
118C PRO* 6.3 0.2 - - + -
120C GLY 5.0 0.7 - - - +
121C GLY* 3.2 25.6 + - - +
139C MET* 3.9 26.5 - - + -
142C ARG* 3.8 13.7 - - - +
143C ILE* 3.8 20.6 - - + -
112D ARG* 4.6 6.7 - - - +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 4.4 14.8 - - + +
63C HIS* 3.4 27.9 - - - +
64C VAL* 1.3 91.4 + - + +
66C ALA* 1.3 60.7 + - - +
68C ASP* 4.0 9.0 - - - -
69C THR* 3.1 21.5 + - - -
121C GLY 5.0 0.3 - - - +
122C VAL 6.1 0.2 - - - -
58D ASN* 3.2 18.4 + - - +
87D GLY* 3.5 12.7 - - - +
88D TRP* 3.4 64.6 - - + +
112D ARG* 5.9 1.6 - - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.8 7.9 - - + -
31C ASN* 3.4 41.1 - - - +
32C GLN* 3.8 7.4 - - + +
35C ALA* 3.9 9.4 - - + +
63C HIS* 3.2 14.0 + - + +
65C GLU* 1.3 79.0 - - - +
67C GLY* 1.3 64.8 + - - +
69C THR* 3.4 2.9 + - - -
70C ILE* 3.2 28.6 + - - +
58D ASN* 4.3 4.7 - - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.5 14.5 - - - +
63C HIS 3.1 12.5 + - - -
64C VAL 3.5 3.4 - - - -
66C ALA* 1.3 74.7 - - - +
68C ASP* 1.3 58.9 + - - +
70C ILE 3.5 0.3 + - - -
71C HIS* 2.9 31.8 + - - +
92C ALA* 4.6 9.6 - - - -
95C THR* 4.7 5.7 - - - +
96C ILE* 3.7 16.4 - - - +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 2.8 28.6 + - - +
65C GLU* 3.6 10.1 - - - +
66C ALA 3.3 0.2 - - - -
67C GLY* 1.3 76.7 - - - +
69C THR* 1.3 56.2 + - - +
71C HIS* 3.5 5.6 + - - +
72C ASP* 3.0 36.1 + - - +
95C THR* 4.4 12.8 - - - +
142C ARG* 2.8 45.2 + - - -
143C ILE* 5.2 1.6 - - - +
86D THR* 4.7 1.1 - - - -
87D GLY* 4.1 5.9 - - - +
110D ASN* 3.5 25.8 - - + +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA* 4.5 3.8 - - + -
39C SER* 4.0 7.2 - - - +
65C GLU 3.1 2.6 + - - -
66C ALA* 3.7 7.9 - - - -
67C GLY 3.3 0.4 - - - -
68C ASP* 1.3 75.2 - - - +
70C ILE* 1.3 58.9 + - - +
72C ASP* 3.3 2.1 + - - +
73C MET* 2.8 37.6 + - + +
27D TYR* 3.3 40.2 - - + +
58D ASN* 2.6 30.6 + - - -
86D THR* 2.8 29.3 + - + +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.9 13.7 - - + -
30C ILE* 4.2 5.4 - - + -
34C LEU* 3.7 30.3 - - + -
35C ALA* 3.8 24.5 - - + +
38C VAL* 4.0 19.3 - - + -
39C SER* 5.5 0.7 - - - +
42C LEU* 5.4 0.2 - - + -
66C ALA 3.2 17.0 + - - +
69C THR* 1.3 73.0 - - + +
71C HIS* 1.3 65.6 + - - +
73C MET* 3.3 5.9 + - - +
74C ILE* 3.0 30.9 + - + +
96C ILE* 3.7 43.3 - - + -
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY 2.9 18.8 + - - +
68C ASP* 3.6 7.2 - - - +
70C ILE* 1.3 78.7 - - - +
72C ASP* 1.3 84.7 + - - +
74C ILE* 3.4 2.1 + - - -
75C LYS* 3.4 44.5 + - + +
95C THR* 3.1 32.5 - - + +
96C ILE* 4.3 3.7 - - - +
98C LEU 4.6 1.0 + - - -
99C ALA* 3.5 38.0 - - + +
146C LEU* 3.7 28.1 - - + +
110D ASN* 3.7 15.5 + - - -
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ASP 3.0 18.6 + - - +
69C THR 3.9 1.3 - - - +
71C HIS* 1.3 98.6 + - - +
73C MET* 1.3 60.4 + - - +
75C LYS* 3.3 7.0 + - - +
76C PHE* 2.8 30.7 + - - +
86D THR* 4.7 1.6 + - - +
108D LEU* 3.4 34.0 - - + +
109D PRO* 3.4 11.6 - - + +
110D ASN* 2.9 43.0 + - - +
184D GLU 4.7 1.2 - - - +
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Residues in contact with MET 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C SER* 3.7 27.1 - - - +
42C LEU* 4.2 15.0 - - + -
43C LEU* 3.9 39.3 - - + -
69C THR* 2.8 27.1 + - + +
70C ILE* 3.3 6.0 + - - +
72C ASP* 1.3 73.8 - - - +
74C ILE* 1.3 65.1 + - - +
76C PHE* 3.7 15.0 - - + +
77C ILE* 3.2 35.3 + - + +
25D LEU* 6.2 0.2 - - + -
27D TYR* 4.6 3.1 - - - -
56D PHE* 3.8 28.9 - - + -
86D THR* 5.8 0.2 - - - -
108D LEU* 4.2 9.6 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.1 12.6 - - + -
55C ILE* 3.9 27.8 - - + -
70C ILE* 3.0 23.1 + - + +
71C HIS 3.5 6.7 - - - +
72C ASP 3.3 0.2 - - - -
73C MET* 1.3 78.8 - - - +
75C LYS* 1.3 59.2 + - - +
77C ILE* 3.5 18.6 - - - +
79C PRO 4.8 0.9 - - - +
81C VAL* 3.8 31.0 - - + +
83C VAL* 5.2 3.8 - - + -
96C ILE* 3.9 36.8 - - + +
99C ALA* 3.7 25.1 - - + +
100C ALA* 4.4 2.0 - - - +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C HIS* 3.4 37.9 + - + +
72C ASP* 3.3 9.9 + - - +
73C MET 3.3 0.2 - - - -
74C ILE* 1.3 75.8 - - - +
76C PHE* 1.3 62.0 + - - +
77C ILE 3.8 4.9 - - - +
98C LEU 4.9 3.6 + - - -
99C ALA* 3.3 28.9 - - - +
101C GLU* 4.8 11.9 + - - +
149C GLU* 5.3 7.3 + - - -
184D GLU* 3.7 34.0 + - + +
185D ASN* 3.1 25.7 + - - +
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Residues in contact with PHE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASP 2.8 18.0 + - - +
73C MET* 3.3 26.4 + - + +
75C LYS* 1.3 77.2 - - - +
77C ILE* 1.3 69.1 + - + +
56D PHE* 3.8 19.5 - + - -
84D VAL* 5.7 0.2 - - + -
108D LEU* 3.9 20.9 - - + -
183D ILE* 3.8 19.7 - - + -
184D GLU 3.4 10.8 - - - +
185D ASN* 3.5 27.4 + - - +
186D ARG* 3.3 60.6 + - - +
189D LEU* 3.9 24.5 - - + -
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.9 32.8 - - + +
43C LEU* 4.6 1.1 - - + -
46C GLU* 3.4 28.7 - - + +
53C ILE* 3.8 29.4 - - + -
73C MET* 3.2 32.5 + - + +
74C ILE 3.5 11.3 - - - +
75C LYS 3.8 6.9 - - - +
76C PHE* 1.3 83.5 - - + +
78C LYS* 1.3 63.2 + - - +
79C PRO* 3.8 12.4 - - + +
81C VAL* 3.9 17.5 - - + -
185D ASN* 5.4 0.5 + - - -
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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