Contacts of the helix formed by residues 65 - 80 (chain A) in PDB entry 6AF6
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 GLY 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU 3.8 1.6 + - - -
64A LEU* 1.3 72.6 - - - +
66A ALA* 1.3 60.5 + - - -
67A LEU 3.4 2.2 - - - -
68A ASP* 3.3 15.5 + - - -
69A THR* 2.9 31.1 + - - -
243A TRP* 4.5 4.0 - - - -
309A ASP* 3.6 14.1 - - - -
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Residues in contact with ALA 66 (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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65A GLY* 1.3 67.3 - - - -
67A LEU* 1.3 59.7 + - - +
69A THR 3.3 0.5 + - - -
70A ALA* 2.9 30.5 + - - +
243A TRP* 4.0 22.9 - - + -
247A CYS* 3.7 13.4 - - - -
305A CYS* 3.8 22.2 - - + +
308A HIS* 3.9 18.4 + - + +
309A ASP* 2.7 18.7 + - - +
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Residues in contact with LEU 67 (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 LEU* 5.7 4.0 - - + -
9A GLN* 3.6 26.9 - - - +
66A ALA* 1.3 78.6 - - - +
68A ASP* 1.4 57.6 + - - +
70A ALA* 3.2 4.4 + - + +
71A LEU* 2.9 40.3 + - + +
302A TYR* 3.8 46.0 - - + +
305A CYS* 3.6 12.3 - - + +
306A TRP* 4.4 25.4 - - + +
309A ASP* 2.9 17.8 + - - +
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Residues in contact with ASP 68 (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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8A SER* 5.4 0.9 + - - -
9A GLN* 3.6 29.5 + - - +
12A ILE* 3.9 24.5 - - + +
63A GLU 5.1 0.3 - - - +
64A LEU* 3.9 19.5 - - + +
65A GLY* 3.3 23.9 + - - +
66A ALA 3.3 0.2 - - - -
67A LEU* 1.4 78.8 - - - +
69A THR* 1.3 62.6 + - - +
71A LEU* 3.3 10.2 + - - +
72A MET* 3.0 25.8 + - - +
309A ASP* 5.8 0.7 - - - -
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Residues in contact with THR 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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53A GLY* 3.6 17.0 - - - -
64A LEU* 3.6 19.4 - - - +
65A GLY 2.9 22.3 + - - -
66A ALA 3.7 4.3 - - - -
68A ASP* 1.3 74.5 - - - +
70A ALA* 1.3 63.3 + - - +
72A MET* 3.2 7.2 + - + +
73A ILE* 3.0 41.7 + - + +
93A LEU* 4.2 17.5 - - + -
243A TRP* 4.2 9.7 - - + -
247A CYS* 4.0 16.2 - - + -
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Residues in contact with ALA 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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66A ALA 2.9 17.6 + - - +
67A LEU* 3.6 9.0 - - + +
69A THR* 1.3 77.6 - - - +
71A LEU* 1.3 57.1 + - - +
73A ILE 3.2 0.5 + - - -
74A GLU* 2.8 29.2 + - - +
247A CYS* 4.3 10.7 - - - -
250A ALA* 3.2 24.8 - - + +
301A LEU* 4.5 7.9 - - + -
302A TYR* 5.6 3.4 - - + -
305A CYS* 3.8 20.9 - - - -
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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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5A LEU* 4.1 25.4 - - + -
9A GLN* 3.9 40.2 - - + +
12A ILE* 4.8 4.7 - - + -
13A TYR* 3.4 30.1 - - + -
67A LEU* 2.9 30.1 + - + +
68A ASP* 3.5 10.5 - - - +
70A ALA* 1.3 76.8 - - - +
72A MET* 1.3 62.1 + - - +
74A GLU* 3.4 5.5 + - - +
75A ALA* 3.0 18.4 + - - +
302A TYR* 3.8 34.1 - - + +
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Residues in contact with MET 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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12A ILE* 3.2 30.7 - - + +
16A ALA* 3.7 8.0 - - + +
48A TYR* 3.6 33.0 - - + +
49A GLY* 3.9 27.4 - - - +
50A PHE* 3.6 23.9 - - + -
53A GLY 6.0 0.2 - - - -
64A LEU* 3.5 26.9 - - - -
68A ASP 3.0 8.8 + - - +
69A THR* 3.2 10.3 + - + +
71A LEU* 1.3 75.6 - - - +
73A ILE* 1.3 60.6 - - + +
75A ALA* 3.3 5.4 + - - +
76A LEU 3.1 21.3 + - - -
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Residues in contact with ILE 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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50A PHE* 4.9 9.4 - - + +
69A THR* 3.0 36.7 + - + +
70A ALA 3.2 3.8 + - - +
72A MET* 1.3 77.2 - - + +
74A GLU* 1.3 65.8 + - - +
76A LEU* 3.2 7.2 + - - +
77A GLY 2.9 18.5 + - - -
90A CYS* 3.8 33.9 - - + -
93A LEU* 4.4 11.9 - - + -
94A CYS* 5.1 0.9 - - - -
247A CYS* 3.7 26.7 - - + +
248A LEU* 3.9 2.7 - - - +
251A LEU* 3.5 32.6 - - + +
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Residues in contact with GLU 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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13A TYR* 4.2 19.5 + - + +
70A ALA 2.8 16.8 + - - +
71A LEU* 3.7 8.2 - - - +
73A ILE* 1.3 76.3 - - - +
75A ALA* 1.3 62.5 + - - +
77A GLY 3.1 1.9 + - - -
78A LYS* 3.0 19.8 + - + +
250A ALA* 3.4 18.6 - - + +
253A VAL* 3.9 13.4 - - + +
254A GLY* 3.3 27.9 - - - +
257A ALA* 5.5 0.5 - - - +
298A ARG* 2.8 30.1 + - - -
301A LEU* 5.6 0.7 - - - +
302A TYR* 2.6 36.3 + - - -
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Residues in contact with ALA 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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13A TYR* 3.4 44.3 - - + +
16A ALA* 3.6 3.4 - - + -
17A TYR* 3.6 22.1 - - + +
20A ALA* 4.0 1.9 - - - +
71A LEU 3.0 14.2 + - - +
72A MET 3.4 9.6 - - - +
74A GLU* 1.3 77.3 - - - +
76A LEU* 1.3 56.3 + - - +
78A LYS 3.3 0.6 + - - +
79A GLY* 2.8 28.6 + - - -
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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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16A ALA 4.9 0.4 + - - -
20A ALA* 3.9 13.9 - - + -
24A LEU* 3.4 32.3 - - + -
50A PHE* 3.8 33.1 - - + -
72A MET 3.1 13.0 + - - +
73A ILE* 3.4 9.2 - - - +
75A ALA* 1.3 76.8 - - - +
77A GLY* 1.3 62.1 + - - +
80A SER* 3.2 26.2 + - - +
86A SER* 3.4 38.6 + - - +
89A LEU* 4.8 5.6 - - + -
90A CYS* 4.2 14.8 - - - -
251A LEU* 3.9 7.0 - - + -
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Residues in contact with GLY 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 ILE 2.9 11.5 + - - -
74A GLU 3.1 2.6 + - - -
76A LEU* 1.3 79.4 - - - +
78A LYS* 1.3 59.2 + - - +
80A SER 3.8 11.0 - - - +
83A ILE* 5.9 4.0 - - - +
86A SER* 5.6 0.2 - - - -
251A LEU* 3.5 33.1 - - - +
254A GLY 3.6 7.0 - - - -
255A GLY* 3.6 13.5 + - - -
258A ARG* 4.6 4.0 - - - -
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Residues in contact with LYS 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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13A TYR* 3.4 23.0 + - - +
17A TYR* 3.9 23.9 + - + +
74A GLU 3.0 15.0 + - - +
75A ALA 3.9 3.4 - - - +
77A GLY* 1.3 77.5 - - - +
79A GLY* 1.3 59.5 + - - +
254A GLY* 3.3 20.8 - - - +
257A ALA* 4.1 19.9 - - + +
258A ARG* 3.1 35.1 + - + +
261A GLU* 2.9 39.3 + - - -
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Residues in contact with GLY 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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17A TYR* 3.6 17.0 - - - -
20A ALA* 3.6 11.9 - - - +
21A CYS* 3.6 16.4 - - - -
25A ASP* 3.5 17.5 - - - +
75A ALA 2.8 17.2 + - - -
78A LYS* 1.3 79.6 - - - +
80A SER* 1.3 58.2 + - - +
258A ARG* 3.5 9.5 + - - -
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Residues in contact with SER 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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20A ALA* 3.8 16.8 - - - -
24A LEU* 3.8 22.3 + - - +
25A ASP* 3.7 3.9 - - - -
76A LEU* 3.2 21.5 + - - +
77A GLY* 3.8 13.6 - - - +
78A LYS 3.6 0.4 - - - -
79A GLY* 1.3 77.9 - - - +
81A ARG* 1.3 61.5 + - - +
82A ASP* 3.1 27.4 + - - +
83A ILE* 4.4 4.2 + - - +
85A LEU* 5.8 0.2 - - - +
86A SER* 4.7 4.4 + - - -
258A ARG* 4.4 3.7 - - - -
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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