Contacts of the helix formed by residues 86 - 104 (chain A) in PDB entry 1QN6
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 SER 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.6 1.1 - - - -
28A ILE* 3.4 17.7 - - - +
84A ALA* 3.4 1.5 - - - +
85A LYS* 1.3 81.0 - - - +
87A GLU* 1.3 67.9 + - - +
88A ASP* 3.6 6.7 + - - +
89A PHE* 2.9 40.7 + - - +
90A SER* 3.0 23.2 + - - -
178A ARG* 4.3 9.9 - - - -
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Residues in contact with GLU 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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25A LEU* 3.8 8.5 - - - +
28A ILE* 4.4 3.8 - - + -
86A SER* 1.3 70.7 - - - +
88A ASP* 1.3 70.0 + - - +
90A SER* 3.1 5.0 + - - -
91A LYS* 3.0 22.9 + - - +
113A PHE* 4.8 0.5 - - - -
115A ILE* 3.9 35.4 - - + +
118A ILE* 3.8 17.2 - - + +
177A MET* 5.3 0.3 - - - -
178A ARG* 2.8 59.6 + - - +
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 3.4 6.3 + - - +
87A GLU* 1.3 83.5 + - - +
89A PHE* 1.3 62.2 + - + +
91A LYS* 3.3 7.9 + - - +
92A MET* 3.0 36.3 + - - +
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Residues in contact with PHE 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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67A PRO* 3.6 23.3 - - + +
84A ALA* 3.9 12.8 - - + -
85A LYS* 4.4 12.3 - - + +
86A SER* 2.9 39.2 + - - +
88A ASP* 1.3 77.1 - - + +
90A SER* 1.3 57.5 + - - +
92A MET* 3.4 27.5 + - + +
93A ALA* 2.9 30.8 + - - +
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Residues in contact with SER 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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28A ILE* 3.6 24.5 + - - +
30A SER* 2.8 29.5 + - - -
81A CYS* 4.0 8.9 - - - -
84A ALA* 3.6 11.0 - - - +
86A SER 3.0 13.4 + - - -
87A GLU 3.1 9.6 + - - -
89A PHE* 1.3 78.3 - - - +
91A LYS* 1.3 57.1 + - - +
93A ALA* 3.5 4.7 + - - +
94A ALA* 3.0 28.6 + - - +
113A PHE* 4.0 1.3 - - - -
115A ILE* 4.4 3.6 - - - -
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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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87A GLU 3.0 13.1 + - - +
88A ASP* 3.3 8.5 + - - +
90A SER* 1.3 73.0 - - - +
92A MET* 1.3 60.2 + - - +
94A ALA* 3.5 1.6 + - - +
95A ARG* 2.9 55.9 + - - +
110A PHE* 3.8 26.5 - - + -
113A PHE* 3.5 35.6 - - + +
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Residues in contact with MET 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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67A PRO* 4.1 13.7 - - + -
88A ASP* 3.0 28.1 + - + +
89A PHE* 3.5 34.5 - - + +
91A LYS* 1.3 75.1 - - - +
93A ALA* 1.3 64.8 + - - +
95A ARG* 3.2 25.4 + - - +
96A LYS* 3.1 34.4 + - - +
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Residues in contact with ALA 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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64A ILE* 4.2 5.3 - - + +
67A PRO* 4.0 16.1 - - + +
69A THR* 3.4 37.2 - - + +
81A CYS* 4.0 5.4 - - - -
89A PHE 2.9 17.3 + - - +
90A SER 3.8 4.0 - - - +
92A MET* 1.3 72.4 - - - +
94A ALA* 1.3 66.8 + - - +
96A LYS* 3.0 13.4 + - - +
97A TYR* 3.0 19.9 + - - -
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Residues in contact with ALA 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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30A SER* 4.8 0.2 - - - +
32A VAL* 4.7 2.2 - - + -
79A MET* 3.2 28.5 - - + +
81A CYS* 4.3 10.0 - - + -
90A SER 3.0 18.6 + - - +
91A LYS 3.6 5.4 - - - +
93A ALA* 1.3 75.9 - - - +
95A ARG* 1.3 57.0 + - - +
97A TYR* 3.5 3.5 + - - -
98A ALA* 3.0 25.3 + - - +
110A PHE* 3.5 19.2 - - + -
113A PHE* 3.9 12.6 - - + -
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Residues in contact with ARG 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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91A LYS* 2.9 44.1 + - - +
92A MET* 3.3 33.2 - - - +
93A ALA 3.1 0.2 - - - -
94A ALA* 1.3 75.2 - - - +
96A LYS* 1.3 65.3 + - + +
98A ALA* 3.2 5.4 + - + +
99A ARG* 3.0 22.9 + - - +
110A PHE* 3.4 38.6 - - + -
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Residues in contact with LYS 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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64A ILE* 3.9 17.3 - - + -
66A GLU* 3.1 31.4 + - - +
67A PRO* 4.1 8.9 - - - +
92A MET* 3.1 21.6 + - - +
93A ALA 3.0 7.4 + - - +
95A ARG* 1.3 75.5 - - + +
97A TYR* 1.3 58.5 + - - +
99A ARG* 3.2 7.2 + - - +
100A ILE* 2.8 39.1 + - + +
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Residues in contact with TYR 97 (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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62A MET* 3.9 30.9 - - + +
63A ARG* 3.5 2.6 - - - -
64A ILE* 3.3 33.4 + - + -
69A THR* 2.8 49.1 + - - -
70A THR* 3.4 1.0 + - - -
71A ALA* 3.5 33.0 - - + -
73A ILE* 5.1 2.2 - - + -
79A MET* 3.6 20.9 - - + -
81A CYS* 4.2 9.0 - - - -
93A ALA 3.0 30.3 + - - -
94A ALA* 3.7 7.2 - - - +
96A LYS* 1.3 75.6 - - - +
98A ALA* 1.3 63.4 + - - +
100A ILE* 3.2 7.5 + - + +
101A VAL* 2.9 29.3 + - - +
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Residues in contact with ALA 98 (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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34A LEU* 3.9 28.3 - - + -
79A MET* 4.4 0.6 - - - +
94A ALA 3.0 15.5 + - - +
95A ARG* 3.4 10.3 - - + +
96A LYS 3.2 0.2 - - - -
97A TYR* 1.3 75.9 - - - +
99A ARG* 1.3 56.0 + - - +
101A VAL* 3.4 6.1 + - - +
102A GLN* 2.9 38.5 + - - +
108A ALA* 4.1 2.0 - - + +
109A LYS 4.3 4.9 - - - +
110A PHE* 4.1 15.7 - - + -
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Residues in contact with ARG 99 (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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95A ARG 3.0 13.6 + - - +
96A LYS* 3.7 8.3 - - - +
98A ALA* 1.3 74.0 - - - +
100A ILE* 1.3 61.8 + - + +
102A GLN* 2.6 48.7 + - - +
103A LYS* 2.8 71.4 + - - +
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Residues in contact with ILE 100 (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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47A ALA* 5.6 2.0 - - + -
49A ASN* 4.3 16.4 - - - +
62A MET* 3.9 26.5 - - + -
64A ILE* 4.0 27.1 - - + -
96A LYS* 2.8 21.6 + - + +
97A TYR* 3.2 13.9 + - + +
99A ARG* 1.3 76.6 - - + +
101A VAL* 1.3 63.7 + - + +
103A LYS* 3.3 10.8 + - + +
104A LEU* 3.1 31.9 + - + +
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Residues in contact with VAL 101 (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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34A LEU* 4.5 10.8 - - + -
38A LEU* 3.8 31.4 - - + -
43A ILE* 4.7 14.4 - - + -
62A MET* 5.3 0.2 - - + -
73A ILE* 4.0 26.2 - - + -
97A TYR 2.9 20.0 + - - +
98A ALA* 3.6 5.8 - - - +
100A ILE* 1.3 78.4 - - + +
102A GLN* 1.3 65.3 + - - +
104A LEU* 3.2 20.1 + - - +
106A PHE* 3.4 20.0 + - + -
108A ALA* 4.1 11.9 - - + -
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Residues in contact with GLN 102 (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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98A ALA* 2.9 26.0 + - - +
99A ARG* 2.6 61.2 + - - +
101A VAL* 1.3 75.3 - - - +
103A LYS* 1.3 53.6 + - - +
105A GLY* 2.8 28.4 + - - -
106A PHE 3.4 13.9 + - - +
108A ALA* 2.8 37.4 + - + +
109A LYS* 4.5 7.4 - - - +
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Residues in contact with LYS 103 (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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99A ARG* 2.8 57.1 + - + +
100A ILE* 3.6 9.2 - - + +
102A GLN* 1.3 72.2 - - - +
104A LEU* 1.3 61.3 + - + +
105A GLY* 3.0 4.6 + - - -
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Residues in contact with LEU 104 (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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43A ILE* 3.6 45.5 - - + +
46A GLN* 3.1 52.5 + - + +
47A ALA* 4.3 9.9 - - + +
62A MET* 5.2 0.2 - - + -
100A ILE* 3.1 25.4 + - + +
101A VAL* 3.3 17.0 - - + +
102A GLN 3.0 1.2 - - - -
103A LYS* 1.3 79.4 - - + +
105A GLY* 1.3 56.3 + - - +
106A PHE* 3.7 15.6 + - + -
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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