Contacts of the strand formed by residues 65 - 79 (chain C) in PDB entry 1QD6
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 ASP 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C TYR* 2.5 35.5 + - + +
43C THR 3.2 10.3 - - - +
44C GLN* 3.4 18.8 + - - +
63C ARG* 3.6 24.7 + - - +
64C LYS* 1.3 78.6 + - - +
66C GLU* 1.3 67.4 + - - +
99C GLN* 4.5 7.1 - - - -
100C LEU 4.9 0.7 + - - -
101C SER* 2.6 28.4 + - - -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.8 6.2 - - - -
43C THR* 2.7 44.4 + - - +
48C LEU* 4.1 3.4 - - - -
63C ARG 4.4 2.5 - - - +
64C LYS 3.9 0.6 + - - -
65C ASP* 1.3 78.6 - - - +
67C VAL* 1.3 64.0 + - - +
97C TRP* 3.5 12.2 - - + +
98C TRP 3.5 11.4 - - - +
99C GLN* 2.7 33.0 + - - +
100C LEU 5.1 0.7 - - - +
110C ARG* 2.7 45.4 + - - +
258C ARG* 2.5 33.1 + - - +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.4 31.9 - - + -
41C ILE 3.5 8.3 - - - +
42C TYR* 3.6 24.7 - - + -
66C GLU* 1.3 72.8 - - - +
68C LYS* 1.3 64.3 + - - +
69C PHE* 4.4 4.6 - - + -
96C SER 3.6 1.0 - - - +
97C TRP* 3.4 5.4 - - - -
98C TRP* 2.8 57.1 + - + +
100C LEU* 3.7 31.6 - - + +
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Residues in contact with LYS 68 (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 TYR* 3.5 24.9 + - + +
40C LEU* 3.6 0.7 - - - +
41C ILE* 2.8 40.2 + - + +
43C THR* 3.8 20.2 - - + +
66C GLU 3.7 1.4 + - - -
67C VAL* 1.3 74.6 - - - +
69C PHE* 1.3 66.8 + - - +
95C LYS* 5.4 7.4 - - + +
96C SER 3.3 7.6 - - - +
97C TRP* 3.4 37.6 - - + +
224C GLU* 4.1 8.9 + - - -
240C GLN* 3.0 29.4 - - - +
242C TYR* 4.7 2.2 - - - +
247C GLU* 2.8 31.2 + - - +
258C ARG* 4.7 1.6 - - - -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.2 18.4 - - - +
40C LEU* 3.6 17.9 - - + -
67C VAL* 4.4 7.9 - - + -
68C LYS* 1.3 79.7 - - - +
70C GLN* 1.3 62.5 + - - +
71C LEU* 3.9 28.5 - - + -
94C GLN* 4.0 10.5 - - - -
95C LYS* 3.4 3.6 - - - +
96C SER* 2.9 59.2 + - - -
98C TRP* 5.1 3.6 - - + -
109C PHE* 3.8 22.0 - + - -
92D TYR* 3.9 17.5 - - - -
270D HDS 3.7 38.1 - - + -
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Residues in contact with GLN 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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36C ASP* 3.7 10.6 - - - +
37C THR* 2.7 48.1 + - - +
38C ASN* 3.4 3.8 - - - -
39C TYR* 3.0 56.9 + - + +
69C PHE* 1.3 75.8 - - - +
71C LEU* 1.3 71.9 + - - +
72C SER 4.2 0.2 - - - -
93C THR* 3.8 14.8 - - + -
94C GLN 3.1 11.4 - - - +
95C LYS* 2.6 39.3 + - + +
211C LYS* 4.4 3.4 + - - +
270D HDS 4.3 0.2 - - - +
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Residues in contact with LEU 71 (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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38C ASN* 3.3 7.6 - - - +
69C PHE* 3.9 7.9 - - + -
70C GLN* 1.3 75.0 - - - +
72C SER* 1.3 61.4 + - - +
73C LEU* 5.7 2.7 - - + -
92C TYR* 3.7 6.4 - - + +
93C THR* 3.3 2.8 - - - +
94C GLN* 2.8 60.0 + - + +
71D LEU* 4.6 12.6 - - + -
73D LEU* 5.0 15.3 - - + -
75D PHE* 5.5 0.2 - - + -
92D TYR* 3.6 31.0 - - + -
94D GLN* 4.3 1.6 - - - +
270D HDS 3.4 42.6 - - + -
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Residues in contact with SER 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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34C PRO* 3.5 3.3 - - - +
35C TYR* 3.2 16.9 + - - +
36C ASP* 2.5 44.4 + - - +
37C THR 3.6 10.8 - - - -
38C ASN* 2.8 23.4 + - - +
71C LEU* 1.3 76.7 - - - +
73C LEU* 1.3 62.8 + - - +
92C TYR 3.2 4.5 - - - -
93C THR* 2.9 21.0 + - - -
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Residues in contact with LEU 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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32C LEU* 4.3 22.9 - - + -
33C TYR 3.4 9.0 - - - +
35C TYR* 3.6 3.9 - - - +
38C ASN* 5.0 0.7 - - - +
71C LEU* 5.7 2.5 - - + -
72C SER* 1.3 78.6 - - - +
74C ALA* 1.3 60.1 + - - +
75C PHE* 3.5 33.5 - - + -
91C SER* 3.1 6.4 - - - -
92C TYR* 2.9 35.5 + - + +
270C HDS 5.8 0.7 - - + -
32D LEU* 3.3 33.7 - - + -
38D ASN* 4.5 11.2 - - + +
71D LEU* 5.3 13.2 - - + -
73D LEU* 4.3 20.0 - - + -
265D LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 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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18A ILE* 4.7 0.4 - - + -
22A MET* 3.9 23.8 - - + -
33C TYR* 2.8 33.7 + - + +
34C PRO 3.8 18.4 - - - +
35C TYR* 3.8 16.6 - - + +
73C LEU* 1.3 74.8 - - - +
75C PHE* 1.3 70.0 + - - +
76C PRO* 3.8 2.2 - - - +
90C ALA 3.4 6.3 - - - +
91C SER* 4.2 0.4 - - - +
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Residues in contact with PHE 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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22A MET* 4.8 1.6 - - - -
73C LEU* 3.5 37.2 - - + -
74C ALA* 1.3 79.6 - - - +
76C PRO* 1.3 68.4 - - - +
77C LEU* 3.3 8.4 + - + +
89C GLY* 3.5 0.6 - - - -
90C ALA* 2.6 54.4 + - + -
91C SER 4.0 7.9 - - - -
92C TYR* 3.9 25.1 - + + -
270C HDS 3.8 36.3 - - + -
235D VAL* 6.0 0.4 - - + -
265D LEU* 3.4 48.0 - - + -
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Residues in contact with PRO 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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22A MET* 4.1 23.1 - - + +
33C TYR* 3.6 39.5 - - + -
74C ALA 3.8 1.8 - - - +
75C PHE* 1.3 84.2 - - - +
77C LEU* 1.3 61.0 + - - +
79C ARG* 3.9 18.6 - - + +
87C VAL* 4.1 18.4 - - + -
88C LEU 4.1 4.3 - - - +
89C GLY* 4.5 1.6 - - - -
232D THR* 5.0 1.0 + - - -
234D HIS* 4.1 16.1 - - + +
235D VAL* 3.8 15.6 - - - +
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Residues in contact with LEU 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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75C PHE* 3.5 14.8 - - + +
76C PRO* 1.3 75.8 - - - +
78C TRP* 1.3 63.5 + - - +
79C ARG 4.2 0.4 - - - -
88C LEU* 2.9 21.8 + - + +
89C GLY* 3.9 22.7 - - - +
90C ALA* 4.0 12.3 - - + -
118C LEU* 4.2 14.6 - - + -
270C HDS 4.5 15.9 - - + -
232D THR* 4.0 22.2 - - - +
235D VAL* 3.9 27.1 - - + +
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Residues in contact with TRP 78 (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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76C PRO 3.8 0.2 - - - -
77C LEU* 1.3 80.2 - - - +
79C ARG* 1.3 77.5 + - - +
80C GLY 3.7 2.5 + - - -
81C ILE* 3.7 46.4 + - + +
87C VAL* 3.3 4.2 - - - -
88C LEU* 2.9 53.4 + - + -
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Residues in contact with ARG 79 (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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22A MET 2.7 21.3 + - - +
23A LEU* 3.6 23.9 + - + +
24A GLN 2.8 25.5 + - - -
25A GLU* 3.4 22.4 - - - +
33C TYR* 2.8 24.2 + - - -
76C PRO* 3.9 12.9 - - + +
77C LEU 4.2 0.2 - - - -
78C TRP* 1.3 84.4 + - - +
80C GLY* 1.3 59.0 + - - +
86C SER 3.8 5.2 - - - +
87C VAL* 4.2 14.1 - - + -
233D LYS* 4.8 13.3 - - - +
234D HIS* 3.9 9.3 + - - -
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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