Contacts of the helix formed by residues 79 - 97 (chain B) in PDB entry 3AQ9
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 GLN 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 2.9 42.7 + - - +
78B LEU* 1.3 78.7 + - - +
80B ASN* 1.3 68.6 + - - +
81B LEU* 3.6 14.8 - - + -
82B HIS* 2.9 37.1 + - + +
83B PHE 3.4 7.1 + - - -
119B LEU* 3.6 7.5 - - - +
120B GLY* 5.1 0.8 - - - -
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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
----------------------------------------------------------
79B GLN* 1.3 74.9 + - - +
81B LEU* 1.3 63.9 + - - +
82B HIS 3.1 0.2 + - - -
83B PHE 3.1 1.8 + - - +
84B ASP* 2.9 36.0 + - - -
115B ARG* 3.0 33.8 + - - +
119B LEU* 3.4 23.5 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 4.2 33.9 + - + -
79B GLN* 3.1 23.6 + - + -
80B ASN* 1.3 79.5 - - - +
82B HIS* 1.3 78.5 + - + +
84B ASP* 3.5 9.5 + - - +
85B ALA* 3.1 26.2 + - - +
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Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 3.2 20.5 + - - -
34B VAL* 3.7 12.0 - - + +
36B HIS* 5.0 2.0 - - - -
37B PHE* 3.5 29.8 - + - -
77B ASN 5.2 0.4 + - - -
78B LEU* 3.9 15.4 - - + -
79B GLN* 2.9 51.1 + - + +
81B LEU* 1.3 89.5 - - + +
83B PHE* 1.4 66.4 + - - +
85B ALA* 3.2 4.2 + - - +
86B ILE* 3.1 25.1 + - - +
144B HEM 3.5 17.2 - - + +
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN 3.4 2.0 + - - -
80B ASN 3.1 7.9 + - - +
82B HIS* 1.4 81.7 - - - +
84B ASP* 1.3 61.9 + - - +
86B ILE* 3.2 3.5 + - - +
87B ILE* 3.0 44.9 + - + +
111B ILE* 3.6 24.5 - - + -
112B GLU* 3.5 19.5 - - - -
114B THR* 3.6 11.4 - - - -
115B ARG* 3.3 56.3 - - + +
118B MET* 3.8 21.3 - - + -
119B LEU* 4.1 11.0 - - + -
144B HEM 3.4 28.4 - - + +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 5.2 2.0 - - - +
80B ASN* 2.9 27.2 + - - +
81B LEU* 3.8 8.6 - - - +
83B PHE* 1.3 77.7 - - - +
85B ALA* 1.3 58.3 + - - +
87B ILE* 3.3 5.5 + - - +
88B GLU* 2.8 46.6 + - + +
115B ARG* 3.0 31.2 + - - -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 4.0 5.2 - - - +
33B ARG* 3.4 42.1 - - + +
34B VAL* 4.0 17.9 - - + -
81B LEU 3.1 13.1 + - - +
82B HIS 3.6 8.5 - - - +
83B PHE 3.2 0.2 - - - -
84B ASP* 1.3 79.1 - - - +
86B ILE* 1.3 60.9 - - - +
88B GLU* 3.8 1.1 - - - +
89B ASN* 2.9 30.0 + - - -
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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
----------------------------------------------------------
24B PHE* 3.4 24.1 - - + -
25B TYR* 5.8 0.2 - - + -
28B VAL* 4.0 31.6 - - + -
34B VAL* 4.5 9.6 - - + -
38B PHE* 4.9 3.8 - - + -
50B GLU* 5.7 0.7 - - - +
82B HIS 3.1 4.2 + - - +
83B PHE* 3.2 8.0 + - - +
85B ALA* 1.3 76.2 - - - +
87B ILE* 1.3 62.6 + - + +
89B ASN* 3.3 1.8 + - - +
90B LEU* 2.9 29.1 + - + +
111B ILE* 6.1 0.4 - - + -
144B HEM 3.3 72.0 - - + -
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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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83B PHE* 3.0 42.8 + - + +
84B ASP* 3.8 5.4 - - - +
86B ILE* 1.3 83.1 - - + +
88B GLU* 1.4 59.9 + - + +
90B LEU* 3.3 8.8 + - + +
91B ALA* 2.8 33.5 + - + +
108B ALA* 4.1 30.1 - - + +
111B ILE* 3.6 38.1 - - + -
112B GLU* 5.1 3.1 - - - +
115B ARG* 5.2 1.3 - - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 2.9 35.3 + - - +
84B ASP* 2.8 33.7 + - + +
85B ALA 3.8 3.8 - - - +
87B ILE* 1.4 74.5 - - + +
89B ASN* 1.3 58.9 + - - +
91B ALA* 3.9 4.6 - - - +
92B ALA* 3.0 29.5 + - - +
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.7 15.7 - - + -
27B LYS* 3.3 33.1 - - + +
28B VAL* 4.0 10.7 - - + +
31B ASP* 2.8 36.8 + - - +
33B ARG* 4.2 2.5 + - - +
34B VAL* 4.6 1.4 - - - +
85B ALA* 2.9 25.4 + - - +
86B ILE 3.8 2.7 - - - +
88B GLU* 1.3 73.7 - - - +
90B LEU* 1.4 64.5 + - - +
92B ALA* 3.4 5.5 + - - +
93B THR* 2.8 28.9 + - - -
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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
----------------------------------------------------------
17B MET* 6.3 1.6 - - - -
20B ALA* 5.1 7.2 - - + -
21B VAL* 6.1 0.7 - - - -
24B PHE* 3.4 30.6 - - + -
54B LEU* 4.4 23.1 - - + -
58B LEU* 6.0 2.0 - - + -
86B ILE* 2.9 18.8 + - + +
87B ILE* 3.7 10.1 - - + +
89B ASN* 1.4 78.1 - - - +
91B ALA* 1.3 56.3 + - - +
93B THR* 3.2 6.1 + - - -
94B LEU* 2.9 52.8 + - + +
107B ALA* 5.7 1.3 - - + -
108B ALA* 6.3 0.4 - - - -
111B ILE* 3.5 32.8 - - + -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 2.8 25.9 + - + +
88B GLU* 3.9 5.6 - - - +
90B LEU* 1.3 71.8 - - - +
92B ALA* 1.3 57.9 + - - +
94B LEU* 3.4 4.9 + - - -
95B LYS* 2.8 40.2 + - - +
104B ILE* 3.6 32.5 - - + +
108B ALA* 6.1 1.3 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.0 17.5 - - + -
88B GLU 3.0 19.5 + - - +
89B ASN* 3.7 6.1 - - - +
90B LEU 3.2 0.2 - - - -
91B ALA* 1.3 76.1 - - - +
93B THR* 1.3 57.0 + - - +
95B LYS* 3.3 10.1 + - - +
96B GLU* 3.0 35.2 + - - +
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Residues in contact with THR 93 (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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20B ALA* 3.5 38.6 - - + +
23B LEU* 3.7 17.4 - - + +
24B PHE* 3.3 25.1 + - + +
27B LYS* 3.6 15.4 - - - +
89B ASN 2.8 15.0 + - - -
90B LEU* 3.3 9.6 - - - -
92B ALA* 1.3 71.4 - - - +
94B LEU* 1.3 67.1 + - - +
96B GLU* 3.3 7.9 + - - +
97B LEU* 3.0 22.5 + - + +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.7 23.6 - - + +
16B ALA* 5.8 1.1 - - + +
17B MET* 6.0 1.6 - - + -
20B ALA* 4.2 22.7 - - + -
90B LEU* 2.9 38.2 + - + +
91B ALA* 3.7 4.3 - - - +
93B THR* 1.3 74.5 - - - +
95B LYS* 1.3 65.4 + - - +
97B LEU* 3.1 12.4 + - + +
98B GLY 3.2 0.2 + - - -
99B VAL* 3.0 40.5 + - + +
104B ILE* 3.7 29.8 - - + -
107B ALA* 4.6 19.7 - - + -
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Residues in contact with LYS 95 (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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91B ALA* 2.8 37.8 + - - +
92B ALA* 3.6 9.6 - - - +
93B THR 3.3 0.2 - - - -
94B LEU* 1.3 71.8 - - - +
96B GLU* 1.3 58.3 + - + +
98B GLY* 2.9 21.0 + - - -
99B VAL 4.0 6.9 - - - +
101B ASP* 3.0 31.1 + - - +
104B ILE* 3.5 19.0 - - + +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.0 14.0 - - + +
27B LYS* 2.9 40.7 + - - -
92B ALA* 3.0 14.3 + - - +
93B THR* 3.4 10.9 - - - +
95B LYS* 1.3 77.3 - - + +
97B LEU* 1.3 59.9 + - + +
98B GLY 3.1 1.5 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 5.9 0.9 - - - +
16B ALA* 3.8 15.0 - - + +
19B ALA* 4.2 11.2 - - + -
20B ALA* 3.6 41.7 - - + +
23B LEU* 3.9 20.6 - - + -
93B THR* 3.0 18.8 + - + +
94B LEU* 3.1 14.7 + - + +
96B GLU* 1.3 76.2 - - - +
98B GLY* 1.3 60.5 + - - +
99B VAL* 3.4 9.2 + - + +
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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