Contacts of the helix formed by residues 71 - 93 (chain B) in PDB entry 2QE9
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 THR 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.6 16.8 - - + +
39B LEU* 3.8 7.9 - - - -
69B TYR 3.4 0.8 - - - -
70B GLN* 1.3 86.7 - - + +
72B LEU* 1.3 64.3 + - - +
73B ASN* 3.7 7.0 + - - +
74B LYS* 3.2 35.6 + - + +
75B VAL* 3.0 26.0 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.6 33.4 - - + +
19B CYS* 3.4 28.7 - - + +
20B HIS* 3.5 44.9 - - + +
22B LEU 5.9 0.2 - - - +
24B THR* 5.5 1.8 + - - -
27B LEU* 3.9 16.3 - - + +
39B LEU* 3.7 19.4 - - + +
42B LEU* 4.8 0.9 - - + -
71B THR* 1.3 71.8 - - - +
73B ASN* 1.3 64.4 + - - +
75B VAL* 3.3 2.3 + - - +
76B LYS* 2.8 33.7 + - + +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS* 5.2 7.6 - - - -
71B THR* 3.3 7.7 + - - +
72B LEU* 1.3 86.1 - - - +
74B LYS* 1.3 58.6 + - + +
76B LYS* 3.5 6.7 + - - +
77B SER* 2.9 33.8 + - - +
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 3.1 29.3 + - - +
69B TYR* 3.5 32.6 - - + -
70B GLN* 4.6 4.3 - - + +
71B THR* 3.2 28.2 + - + +
73B ASN* 1.3 74.8 - - + +
75B VAL* 1.3 61.5 + - - +
77B SER* 3.4 7.5 + - - -
78B LEU 3.0 22.9 + - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.9 12.1 - - + -
39B LEU* 3.6 24.7 - - + +
42B LEU* 4.0 6.1 - - + -
43B PHE* 3.9 23.8 - - + +
46B ILE* 3.5 24.9 - - + +
69B TYR* 3.5 27.8 - - + +
71B THR 3.0 20.9 + - - +
72B LEU* 3.8 3.4 - - - +
74B LYS* 1.3 73.0 - - - +
76B LYS* 1.3 65.5 + - - +
78B LEU* 3.3 7.8 + - - +
79B SER 3.1 18.7 + - - -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 5.9 0.2 - - - +
16B PHE* 4.0 39.0 - - + -
72B LEU* 2.8 21.1 + - + +
73B ASN* 3.8 7.6 - - - +
75B VAL* 1.3 77.5 - - - +
77B SER* 1.3 60.8 + - - +
79B SER* 3.4 4.9 - - - -
80B ASN* 3.2 32.3 + - - +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 6.3 0.2 - - - -
73B ASN* 2.9 19.4 + - - +
74B LYS* 3.7 7.6 - - - -
75B VAL 3.3 0.4 - - - -
76B LYS* 1.3 74.3 - - - +
78B LEU* 1.3 59.3 + - - +
80B ASN* 3.2 12.3 + - - +
81B THR* 2.9 33.1 + - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.5 38.6 - - + +
46B ILE* 4.0 15.5 - - + -
47B ASP* 5.8 1.3 - - - +
64B VAL* 4.1 7.4 - - + -
69B TYR* 3.6 35.6 - - + +
74B LYS 3.0 14.2 + - - +
75B VAL* 3.3 10.1 + - - +
77B SER* 1.3 71.0 - - - +
79B SER* 1.3 67.6 + - - +
81B THR* 3.2 19.5 + - + +
82B PHE* 3.4 48.8 + - + -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 2.9 31.5 + - - +
13B ASP* 5.1 1.9 + - - -
16B PHE* 3.7 13.0 - - - -
46B ILE* 3.6 28.9 - - - +
75B VAL 3.1 7.7 + - - -
76B LYS 3.4 10.1 - - - -
78B LEU* 1.3 75.7 - - - +
80B ASN* 1.3 66.2 + - - +
82B PHE* 3.6 2.6 + - - +
83B ARG* 3.5 29.6 + - - +
86B ILE* 5.9 0.3 - - - +
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 5.0 6.8 - - - +
16B PHE* 6.1 0.2 - - - -
76B LYS* 3.2 26.1 + - - +
77B SER* 3.2 11.8 + - - +
79B SER* 1.3 82.5 + - - +
81B THR* 1.3 63.8 + - - +
82B PHE 3.3 0.5 + - - -
83B ARG* 3.5 21.0 + - - +
84B THR* 4.6 4.2 + - - +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 2.9 17.9 + - - -
78B LEU* 3.2 15.8 + - + +
80B ASN* 1.3 77.7 - - - +
82B PHE* 1.3 76.2 + - + +
83B ARG 3.8 0.2 + - - -
84B THR* 4.4 8.5 + - - -
85B GLU* 5.1 2.1 + - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.9 16.6 - - + -
47B ASP* 5.6 2.7 - - - -
50B TYR* 3.4 70.2 - + + -
64B VAL* 4.1 19.5 - - + -
78B LEU* 3.4 48.0 + - + +
79B SER 4.3 2.0 - - - +
80B ASN 3.3 0.4 - - - -
81B THR* 1.3 89.1 - - + +
83B ARG* 1.3 65.0 + - - +
84B THR 3.4 1.6 - - - -
85B GLU* 3.2 9.4 + - - +
86B ILE* 2.9 31.5 + - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TRP* 3.4 66.2 + - - +
12B ARG* 3.6 20.2 - - - +
13B ASP* 4.8 12.3 + - - -
49B GLU* 5.6 0.4 + - - -
79B SER* 3.5 21.4 + - - +
80B ASN* 3.5 18.2 + - - +
82B PHE* 1.3 76.0 - - - +
84B THR* 1.3 64.3 + - + +
86B ILE* 3.2 9.4 + - - +
87B ILE* 2.9 50.3 + - + +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN 4.6 3.7 + - - +
81B THR 4.4 8.1 + - - -
83B ARG* 1.3 84.1 - - + +
85B GLU* 1.3 64.6 + - - +
87B ILE* 3.4 10.5 + - + +
88B ASP* 3.0 34.5 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 2.6 37.5 + - + -
53B ILE* 5.6 0.2 - - + -
54B ARG* 3.5 6.4 + - - -
57B GLN* 2.7 39.1 + - - +
59B LYS* 3.5 11.7 + - - +
81B THR 5.1 1.5 + - - +
82B PHE* 3.2 12.6 + - - +
84B THR* 1.3 79.2 + - - +
86B ILE* 1.3 58.1 - - - +
88B ASP* 3.3 8.4 + - + +
89B VAL* 3.0 35.3 + - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 5.1 0.7 - - + -
9B TRP* 3.6 28.3 - - + -
12B ARG* 6.1 0.2 - - - +
46B ILE 5.5 0.2 - - - +
49B GLU* 3.4 33.7 - - + +
50B TYR* 4.1 17.9 - - + -
53B ILE* 3.9 32.5 - - + +
79B SER 5.9 0.7 - - - +
82B PHE* 2.9 34.2 + - + +
83B ARG* 3.2 12.3 + - - +
85B GLU* 1.3 74.9 - - - +
87B ILE* 1.3 56.6 + - - +
89B VAL* 3.4 2.3 + - - +
90B LEU* 3.0 42.4 + - + +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MSE 5.8 5.6 - - + -
9B TRP* 3.7 26.0 - - + -
83B ARG* 2.9 41.6 + - + +
84B THR* 3.8 11.2 - - + +
85B GLU 3.3 0.2 - - - -
86B ILE* 1.3 73.2 - - - +
88B ASP* 1.3 60.5 + - - +
90B LEU* 3.3 8.7 + - - +
91B GLN* 2.9 54.6 + - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.0 25.7 + - - +
85B GLU* 3.3 7.5 + - + +
87B ILE* 1.3 77.7 - - - +
89B VAL* 1.3 54.5 + - + +
91B GLN* 3.3 17.8 + - - +
92B THR* 2.7 39.2 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.5 42.2 - - + +
56B ILE* 3.8 22.0 - - + -
57B GLN* 3.3 40.6 - - + +
85B GLU* 3.0 22.5 + - + +
86B ILE 3.7 0.2 - - - +
88B ASP* 1.3 72.7 - - + +
90B LEU* 1.3 66.8 + - + +
92B THR* 3.3 6.0 + - - -
93B HIS* 3.1 33.2 + - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2B PHE* 3.2 21.2 - - + -
2B MSE 3.7 39.0 - - + -
5B PHE* 4.0 18.4 - - + -
9B TRP* 4.0 11.0 - - + -
53B ILE* 3.8 16.4 - - + -
56B ILE* 5.7 0.4 - - + -
86B ILE* 3.0 36.5 + - + +
87B ILE* 3.3 5.4 + - - +
89B VAL* 1.3 76.3 - - + +
91B GLN* 1.3 60.0 + - - +
93B HIS* 3.2 16.9 + - - +
118B LEU* 3.6 34.8 - - + -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B PHE* 4.1 16.2 - - + -
2B MSE 6.3 1.8 - - + -
87B ILE* 2.9 36.9 + - + +
88B ASP* 3.6 19.4 - - - +
90B LEU* 1.3 74.8 - - + +
92B THR* 1.3 58.9 + - - +
94B SER* 2.7 25.9 + - - -
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 2.7 25.7 + - - +
89B VAL* 3.5 8.5 - - - -
91B GLN* 1.3 75.7 - - - +
93B HIS* 1.3 74.4 + - + +
94B SER 3.5 1.9 + - - -
95B ASP* 6.0 1.2 - - - +
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Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3B TYR* 6.1 0.3 - - - -
-2B PHE* 4.6 3.3 - - - -
56B ILE* 3.6 42.8 + - + +
57B GLN* 4.7 5.1 - - - +
89B VAL* 3.1 31.9 + - + +
90B LEU* 3.4 8.9 - - + +
91B GLN 3.2 0.2 - - - -
92B THR* 1.3 94.7 + - + +
94B SER* 1.3 56.6 + - - +
95B ASP* 3.5 3.1 - - - +
100B GLU* 2.8 36.1 + - - -
114B ARG* 3.3 39.8 + - + +
118B LEU* 5.3 2.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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