Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 4JCY
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 GLU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.7 0.7 - - - -
66A THR* 3.3 10.1 - - - +
67A PRO* 1.3 97.9 - - + +
69A ASP* 1.3 60.4 + - - +
70A ASP* 3.2 15.3 - - - +
71A LEU* 3.2 17.2 + - + +
72A ALA* 2.9 30.7 + - - +
60B PRO* 3.9 26.9 - - - +
61B VAL* 4.7 1.6 + - - +
62B SER* 4.8 0.9 + - - -
78B TRP* 4.1 13.9 - - + -
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Residues in contact with ASP 69 (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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4A ARG* 5.8 1.7 + - - -
5A ARG* 2.9 29.9 + - - +
67A PRO 3.3 5.9 + - - +
68A GLU* 1.3 71.3 - - - +
70A ASP* 1.3 63.5 + - - +
72A ALA* 3.4 2.8 + - - +
73A GLN* 3.1 22.7 + - - +
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Residues in contact with ASP 70 (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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68A GLU* 3.8 11.1 - - - +
69A ASP* 1.3 71.9 + - - +
71A LEU* 1.3 68.3 + - - +
73A GLN* 3.4 6.8 + - - +
74A ILE* 3.1 28.1 + - - +
78B TRP* 3.5 26.2 + - - +
83B GLU* 5.1 3.5 - - - +
86B ARG* 4.6 10.9 + - - +
90B ASN* 4.3 26.7 + - - +
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Residues in contact with LEU 71 (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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66A THR* 3.8 17.5 - - + -
68A GLU* 3.2 22.1 + - + +
70A ASP* 1.3 79.0 + - - +
72A ALA* 1.3 61.2 + - - +
74A ILE* 3.1 18.1 + - + +
75A ILE* 2.9 38.0 + - + +
60B PRO* 4.1 10.5 - - + -
62B SER* 4.1 11.4 - - - +
71B LEU* 6.4 0.2 - - + -
74B ILE* 5.5 1.6 - - + -
75B ILE* 4.2 23.8 - - + -
78B TRP* 3.9 53.4 - - + -
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Residues in contact with ALA 72 (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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5A ARG* 3.5 34.5 - - - +
63A TYR* 3.5 28.7 - - + -
66A THR* 3.5 13.1 - - + +
68A GLU 2.9 16.1 + - - +
69A ASP 3.6 4.0 - - - +
71A LEU* 1.3 77.1 - - - +
73A GLN* 1.3 55.9 + - - +
75A ILE* 3.3 5.0 + - - +
76A LEU 3.0 22.7 + - - -
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Residues in contact with GLN 73 (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 TYR* 5.4 0.2 - - - -
69A ASP 3.1 16.7 + - - +
70A ASP* 3.7 7.6 - - - +
71A LEU 3.2 0.2 - - - -
72A ALA* 1.3 74.1 - - - +
74A ILE* 1.3 59.5 + - + +
76A LEU* 3.2 22.9 + - - +
77A THR* 2.9 45.5 + - - +
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Residues in contact with ILE 74 (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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70A ASP 3.1 13.5 + - - +
71A LEU* 3.1 16.3 + - + +
73A GLN* 1.3 74.6 - - + +
75A ILE* 1.3 60.1 + - + +
77A THR* 3.3 5.6 + - - -
78A TRP* 2.8 35.5 + - + +
71B LEU* 5.5 1.6 - - + -
74B ILE* 4.5 21.8 - - + -
78B TRP* 3.5 37.7 - - + +
89B ILE* 3.8 27.6 - - + +
90B ASN* 4.4 13.9 - - - +
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Residues in contact with ILE 75 (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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60A PRO* 3.6 29.2 - - + +
62A SER* 3.9 13.7 - - - +
63A TYR* 4.1 18.2 - - + +
66A THR* 3.3 31.9 - - + +
71A LEU* 2.9 26.2 + - + +
72A ALA* 3.5 7.9 - - - +
73A GLN 3.2 0.2 - - - -
74A ILE* 1.3 77.0 - - + +
76A LEU* 1.3 60.5 + - - +
78A TRP* 3.5 6.5 + - - +
79A ASN* 3.1 22.7 + - - +
62B SER* 4.3 0.2 - - - +
71B LEU* 4.1 22.4 - - + -
75B ILE* 4.2 14.4 - - + -
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Residues in contact with LEU 76 (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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12A ARG* 3.5 33.7 - - - +
59A ILE* 3.9 28.7 - - + -
60A PRO* 4.6 4.7 - - + -
63A TYR* 3.4 35.4 - - + +
72A ALA 3.0 7.9 + - - +
73A GLN* 3.5 25.4 - - - +
75A ILE* 1.3 78.1 - - - +
77A THR* 1.3 62.2 + - - +
79A ASN* 3.3 18.4 - - + +
80A GLU* 3.8 12.5 + - - +
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Residues in contact with THR 77 (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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73A GLN* 2.9 33.2 + - - +
74A ILE* 3.8 5.4 - - - -
76A LEU* 1.3 72.1 - - - +
78A TRP* 1.3 67.5 + - - +
80A GLU* 3.0 18.7 + - - +
81A LEU* 3.5 25.0 + - + +
92B TYR 5.5 6.5 - - - +
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Residues in contact with TRP 78 (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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60A PRO* 4.4 8.1 - - + -
74A ILE* 2.8 26.9 + - + +
75A ILE* 3.7 7.4 - - - +
77A THR* 1.3 72.7 - - - +
79A ASN* 1.3 72.4 + - - +
81A LEU* 3.2 23.2 + - + +
86A ARG* 3.1 72.1 + - + +
89A ILE* 5.4 4.3 - - + -
90A ASN* 5.2 1.4 - - - +
68B GLU* 4.2 21.1 - - + -
70B ASP* 3.5 30.6 + - - -
71B LEU* 3.8 45.0 - - + +
74B ILE* 3.6 30.6 - - + +
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Residues in contact with ASN 79 (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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58A LYS 3.0 24.9 - - - +
59A ILE* 3.9 2.8 - - - +
60A PRO* 3.5 31.4 - - + +
75A ILE 3.1 14.2 + - - +
76A LEU* 3.3 14.8 - - + +
77A THR 3.2 0.4 - - - -
78A TRP* 1.3 80.4 - - - +
80A GLU* 1.3 63.8 + - + +
81A LEU 4.4 1.0 - - - +
86A ARG* 3.3 20.2 + - - +
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Residues in contact with GLU 80 (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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76A LEU 4.1 10.9 - - - +
77A THR* 3.0 12.0 + - + +
79A ASN* 1.3 84.6 - - - +
81A LEU* 1.3 65.7 + - + +
82A ASN 3.7 1.6 + - - -
85A GLU* 4.5 1.7 - - - +
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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