Contacts of the helix formed by residues 66 - 87 (chain B) in PDB entry 3QWR
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 ASN 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLY* 4.7 3.8 - - - +
62B GLY 3.1 16.6 + - - +
63B LEU* 4.0 0.4 - - - -
64B ARG 3.5 0.2 - - - -
65B ASP* 1.3 85.0 - - + +
67B SER* 1.3 61.4 + - - +
68B GLN* 3.5 3.3 + - + +
69B PHE* 4.3 30.3 + - + +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 4.6 26.0 - - - -
63B LEU* 3.6 25.8 + - - +
66B ASN* 1.3 69.8 - - - +
68B GLN* 1.3 65.2 + - - +
69B PHE 3.3 3.1 - - - -
70B CYS* 3.2 8.1 + - - +
71B LEU* 3.1 28.6 + - - +
168B LEU* 4.9 4.3 - - - -
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 3.5 3.6 - - + +
67B SER* 1.3 75.9 - - - +
69B PHE* 1.3 64.4 + - + +
71B LEU* 3.4 8.3 + - - +
72B GLN* 2.9 31.4 + - - +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 5.6 4.7 - - - -
56B ASP* 4.0 15.5 - - - +
57B GLY* 5.5 2.2 - - - -
66B ASN* 4.4 25.6 - - + +
67B SER 3.3 0.6 - - - -
68B GLN* 1.3 78.4 - - + +
70B CYS* 1.3 67.4 + - - +
72B GLN* 3.3 7.0 + - - +
73B ARG* 3.1 23.9 + - - +
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Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP 3.8 4.9 + - - -
57B GLY 3.5 16.8 + - - +
58B CYS* 2.1 52.7 - - - -
63B LEU* 5.6 3.8 - - + -
66B ASN 4.8 0.2 + - - -
67B SER* 3.2 12.8 + - - +
69B PHE* 1.3 80.2 - - - +
71B LEU* 1.3 57.8 + - + +
73B ARG* 3.1 6.5 + - - +
74B ILE* 2.9 34.8 + - - +
160B VAL* 3.7 24.0 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.5 35.2 - - + -
11B TRP* 4.1 20.0 - - + -
67B SER* 3.1 22.4 + - - +
68B GLN* 4.0 6.5 - - - +
70B CYS* 1.3 75.8 - - + +
72B GLN* 1.3 56.6 + - - +
74B ILE* 3.4 8.2 + - + +
75B HIS* 2.9 29.8 + - - +
116B LEU* 5.2 6.6 - - + +
160B VAL* 4.2 14.6 - - + -
161B PHE* 3.7 29.4 - - + -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN 2.9 18.6 + - - +
69B PHE* 3.6 6.5 - - - +
71B LEU* 1.3 75.3 - - - +
73B ARG* 1.4 58.3 + - - +
75B HIS* 3.3 8.6 + - - +
76B GLN* 3.0 30.2 + - - +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO 6.4 1.1 - - - -
51B HIS 4.5 8.4 + - - -
52B ILE* 3.4 27.1 - - + +
53B GLN* 4.3 8.5 + - - -
56B ASP* 3.2 48.9 + - + +
69B PHE 3.1 12.2 + - - +
70B CYS* 3.1 11.8 + - - +
72B GLN* 1.4 73.0 - - - +
74B ILE* 1.3 63.5 + - - +
76B GLN* 3.2 42.4 + - - +
77B GLY* 3.1 19.4 + - - -
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Residues in contact with ILE 74 (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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52B ILE* 4.5 10.1 - - + -
58B CYS* 4.6 0.7 - - - -
70B CYS* 2.9 27.7 + - - +
71B LEU* 3.7 9.9 - - + +
73B ARG* 1.3 72.8 - - - +
75B HIS* 1.3 67.1 + - - +
77B GLY 3.2 1.4 + - - -
78B LEU* 2.9 41.0 + - + +
153B PHE* 3.4 11.1 - - + -
156B VAL* 5.6 1.3 - - + -
157B ALA* 4.1 28.9 - - + +
160B VAL* 3.7 35.2 - - + -
161B PHE* 4.1 23.6 - - + -
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 2.9 17.6 + - - +
72B GLN* 3.3 8.8 + - - +
74B ILE* 1.3 77.0 - - - +
76B GLN* 1.3 62.2 + - - +
78B LEU* 3.2 10.6 + - - +
79B ILE* 3.1 45.6 + - + +
113B SER* 3.7 30.8 + - - -
116B LEU* 4.4 13.7 - - + -
117B GLN* 4.3 20.3 + - + +
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Residues in contact with GLN 76 (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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50B PRO* 5.4 10.1 - - - +
72B GLN 3.0 16.7 + - - +
73B ARG* 3.2 47.4 + - - +
74B ILE 3.2 0.2 - - - -
75B HIS* 1.3 76.7 + - - +
77B GLY* 1.3 67.5 + - - +
79B ILE* 3.4 7.0 + - - +
80B PHE* 3.0 24.2 + - + +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO* 5.4 5.4 - - - -
73B ARG 3.1 12.4 + - - -
74B ILE 3.2 0.4 + - - -
76B GLN* 1.3 79.6 - - - +
78B LEU* 1.3 61.2 + - - +
80B PHE* 3.0 9.1 + - - +
81B TYR* 3.0 28.7 + - - -
153B PHE* 3.6 28.3 - - - -
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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
----------------------------------------------------------
21B LEU* 4.4 3.8 - - + -
74B ILE* 2.9 33.7 + - + +
75B HIS* 3.2 10.3 + - - +
77B GLY* 1.3 75.6 - - - +
79B ILE* 1.3 57.7 + - - +
81B TYR* 3.4 2.7 + - - +
82B GLU* 3.0 29.5 + - - +
109B LEU* 3.7 34.8 - - + +
112B LEU* 3.9 38.1 - - + +
113B SER* 3.9 27.1 - - - +
116B LEU* 5.4 3.6 - - + -
153B PHE* 3.7 17.9 - - + -
154B VAL* 5.3 1.6 - - + -
157B ALA* 5.7 1.6 - - + -
161B PHE* 5.8 0.4 - - + -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.1 36.6 + - + +
76B GLN* 3.9 7.2 - - - +
77B GLY 3.3 0.2 - - - -
78B LEU* 1.3 74.8 - - - +
80B PHE* 1.3 63.6 + - - +
82B GLU* 3.4 6.8 + - + +
83B LYS* 3.1 54.6 + - + +
113B SER* 3.5 31.2 - - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO* 4.1 35.7 - - + -
76B GLN* 3.0 15.7 + - + +
77B GLY* 3.0 10.5 + - - +
79B ILE* 1.3 78.7 - - - +
81B TYR* 1.3 89.0 + + - +
83B LYS* 3.4 5.6 + - - +
84B LEU* 3.2 58.8 + - + +
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Residues in contact with TYR 81 (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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181A GLU* 4.0 7.8 + - - -
50B PRO* 4.8 8.5 + - - +
51B HIS* 5.6 1.6 + - - -
77B GLY* 3.0 26.6 + - - +
78B LEU 4.1 1.8 - - - +
80B PHE* 1.3 97.4 - + - +
82B GLU* 1.4 59.7 + - - +
84B LEU* 3.2 13.0 + - + -
85B LEU* 2.9 35.4 + - + +
109B LEU* 4.0 12.6 - - + -
146B ILE* 3.8 21.3 - - + -
149B SER* 3.3 39.7 + - - -
150B LEU* 3.5 35.7 - - + -
153B PHE* 3.8 30.1 - + + -
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Residues in contact with GLU 82 (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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78B LEU 3.0 18.5 + - - +
79B ILE* 4.0 9.0 - - + +
80B PHE 3.4 0.2 - - - -
81B TYR* 1.4 74.0 - - - +
83B LYS* 1.3 59.4 + - + +
86B GLY* 3.1 24.3 + - - -
106B HIS* 3.2 19.2 + - + +
109B LEU* 4.0 11.6 - - + +
110B LEU* 3.4 32.8 - - + +
113B SER* 6.0 0.7 - - - +
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Residues in contact with LYS 83 (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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79B ILE* 3.1 42.0 + - + +
80B PHE* 3.6 7.4 - - - +
81B TYR 3.2 0.2 - - - -
82B GLU* 1.3 75.2 - - + +
84B LEU* 1.3 69.4 + - + +
86B GLY* 3.5 2.2 + - - -
87B SER* 3.2 22.7 + - - -
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Residues in contact with LEU 84 (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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80B PHE* 3.2 62.2 + - + +
81B TYR* 3.2 19.1 + - + +
83B LYS* 1.3 82.8 - - + +
85B LEU* 1.3 61.8 + - - +
87B SER* 2.7 27.2 + - - +
89B ILE* 4.6 6.8 - - + +
90B PHE* 3.6 11.2 - - - -
146B ILE* 4.3 31.2 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 2.9 23.0 + - + +
83B LYS 3.4 0.2 - - - -
84B LEU* 1.3 77.3 - - - +
86B GLY* 1.3 56.1 + - - +
90B PHE* 3.3 42.3 - - + +
91B THR* 4.5 3.8 - - - +
102B VAL* 4.1 15.1 - - + +
105B LEU* 4.0 31.6 - - + -
106B HIS* 3.9 24.4 - - + +
109B LEU* 4.0 14.4 - - + -
146B ILE* 4.0 25.4 - - + -
147B LEU* 4.3 11.0 - - + -
150B LEU* 4.5 7.2 - - + -
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU 3.1 15.6 + - - -
83B LYS* 3.5 2.9 + - - -
84B LEU 3.2 0.2 - - - -
85B LEU* 1.3 75.8 - - - +
87B SER* 1.3 62.9 + - - +
91B THR* 3.7 16.4 + - - +
106B HIS* 4.4 10.5 - - - -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS 3.2 12.4 + - - -
84B LEU* 2.7 22.1 + - - -
86B GLY* 1.3 81.1 - - - +
88B ASP* 1.3 58.9 + - - +
89B ILE* 3.1 25.5 + - - +
90B PHE* 2.9 21.0 + - - -
91B THR* 3.0 11.4 + - - -
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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