Contacts of the helix formed by residues 79 - 97 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN* 2.9 42.3 + - - +
78A LEU* 1.3 79.8 + - - +
80A ASN* 1.3 69.4 + - - +
81A LEU* 3.9 13.7 - - + -
82A HIS* 2.8 42.2 + - + +
83A PHE 3.4 3.8 + - - -
119A LEU* 3.5 7.0 - - - +
120A GLY* 5.2 0.4 - - - -
53B PHE* 4.0 28.9 - - + -
56B MET* 4.1 4.0 - - + -
64B TYR* 4.2 7.5 - - - -
67B LYS 4.8 0.2 + - - -
68B ASN* 3.4 34.8 - - - +
69B MET* 3.8 8.1 + - + +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 1.3 72.9 + - - +
81A LEU* 1.3 64.3 + - - +
83A PHE 3.1 1.9 + - - -
84A ASP* 2.9 34.5 + - - -
115A ARG* 3.0 28.7 + - - +
119A LEU* 3.6 25.6 - - + +
68B ASN* 6.0 1.8 - - - +
116B LYS* 4.2 6.7 - - - +
117B ASP* 3.1 34.4 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 4.2 26.4 + - + -
79A GLN* 3.0 19.3 + - + -
80A ASN* 1.3 81.7 - - - +
82A HIS* 1.3 69.6 + - + +
84A ASP* 3.6 10.6 + - - +
85A ALA* 3.1 23.2 + - - +
53B PHE* 5.4 0.7 - - + -
57B LEU* 3.7 32.3 - - + -
110B VAL* 4.4 9.6 - - + +
113B HIS* 4.0 36.8 - - + +
114B THR* 3.9 16.8 - - + -
116B LYS* 6.3 0.7 - - - +
117B ASP* 4.3 6.0 + - - +
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG 3.3 20.4 + - - -
34A VAL* 3.7 9.8 - - + +
36A HIS* 4.9 1.3 - - - -
37A PHE* 3.5 25.0 - + - -
78A LEU* 3.9 14.8 - - + -
79A GLN* 2.8 46.0 + - + +
81A LEU* 1.3 82.8 - - + +
83A PHE* 1.3 65.2 + - - +
85A ALA* 3.2 4.7 + - - +
86A ILE* 3.1 25.5 + - - +
144A HEM 3.5 18.1 - - + +
56B MET* 3.6 25.7 - - - +
57B LEU* 4.0 16.5 - - + +
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN 3.4 2.0 + - - -
80A ASN 3.1 3.4 + - - +
82A HIS* 1.3 79.3 - - - +
84A ASP* 1.3 63.9 + - - +
86A ILE* 3.1 3.8 + - - +
87A ILE* 3.0 37.7 + - + +
111A ILE 3.6 12.1 - - - -
112A GLU* 3.4 22.9 - - - -
114A THR* 3.5 22.4 - - - -
115A ARG* 3.3 63.0 - - + +
118A MET* 3.7 21.5 - - + -
119A LEU* 4.1 11.7 - - + -
144A HEM 3.5 32.2 - - + +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.1 2.7 - - - +
80A ASN* 2.9 21.2 + - - +
81A LEU* 3.8 9.3 - - - +
83A PHE* 1.3 77.1 - - - +
85A ALA* 1.3 57.2 + - - +
87A ILE* 3.3 6.7 + - - +
88A GLU* 2.8 46.2 + - + +
115A ARG* 2.9 31.9 + - - -
113B HIS* 6.5 0.2 - - + -
116B LYS* 2.8 37.8 + - - -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.0 5.2 - - - +
33A ARG* 3.3 43.5 - - + +
34A VAL* 3.9 17.5 - - + -
81A LEU 3.1 16.5 + - - +
82A HIS 3.5 5.2 - - - +
83A PHE 3.2 0.2 - - - -
84A ASP* 1.3 76.9 - - - +
86A ILE* 1.3 64.6 + - - +
88A GLU* 3.4 1.6 + - - +
89A ASN* 2.9 31.4 + - - -
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.5 24.0 - - + -
25A TYR* 6.0 0.2 - - - +
28A VAL* 4.0 31.4 - - + -
34A VAL* 4.4 9.9 - - + -
38A PHE* 5.0 4.5 - - + -
50A GLU* 5.6 0.2 - - - +
82A HIS 3.1 5.0 + - - +
83A PHE* 3.6 7.4 - - - +
85A ALA* 1.3 78.3 - - - +
87A ILE* 1.3 62.5 + - + +
89A ASN* 3.3 1.5 + - - +
90A LEU* 2.9 29.8 + - + +
111A ILE* 5.8 0.9 - - + -
144A HEM 3.3 72.9 - - + -
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Residues in contact with ILE 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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83A PHE* 3.0 38.6 + - + +
84A ASP* 3.8 8.3 - - - +
86A ILE* 1.3 78.2 - - + +
88A GLU* 1.4 61.3 + - + +
90A LEU* 3.2 8.0 + - + +
91A ALA* 2.8 33.8 + - + +
108A ALA* 4.4 30.3 - - + +
111A ILE* 3.7 35.2 - - + -
112A GLU* 4.7 5.6 - - - +
115A ARG* 5.0 1.6 - - - +
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Residues in contact with GLU 88 (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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33A ARG* 2.9 37.2 + - - +
84A ASP* 2.8 34.6 + - - +
85A ALA 3.8 3.6 - - - +
87A ILE* 1.4 75.2 - - + +
89A ASN* 1.3 60.6 + - - +
91A ALA* 3.4 5.7 + - - +
92A ALA* 2.9 30.0 + - - +
113B HIS* 5.6 1.9 + - - -
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.8 4.7 - - + -
27A LYS* 3.3 32.5 - - + +
28A VAL* 4.0 25.6 - - + +
31A ASP* 2.9 33.5 + - - +
33A ARG* 4.3 2.3 + - - +
34A VAL* 4.6 1.4 - - - +
85A ALA* 2.9 29.6 + - - +
86A ILE 3.8 2.9 - - - +
88A GLU* 1.3 75.6 - - - +
90A LEU* 1.3 61.8 + - - +
92A ALA* 3.4 4.4 + - - +
93A THR* 2.8 32.4 + - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 5.5 4.7 - - + +
21A VAL* 6.4 0.9 - - + -
24A PHE* 3.5 30.6 - - + -
54A LEU* 4.6 20.6 - - + -
58A LEU* 6.1 1.8 - - + -
86A ILE* 2.9 20.5 + - + +
87A ILE* 3.7 8.7 - - + +
89A ASN* 1.3 73.4 - - - +
91A ALA* 1.3 67.7 + - - +
93A THR* 3.2 6.8 + - + -
94A LEU* 3.0 46.1 + - + +
107A ALA* 5.7 0.9 - - + -
108A ALA* 6.2 0.9 - - - -
111A ILE* 3.4 35.2 - - + -
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Residues in contact with ALA 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 ILE* 2.8 26.6 + - + +
88A GLU* 3.8 6.7 - - - +
90A LEU* 1.3 75.3 - - - +
92A ALA* 1.3 56.9 + - - +
94A LEU* 3.3 2.7 + - - +
95A LYS* 2.9 28.8 + - - +
104A ILE* 3.8 31.6 - - + +
108A ALA* 6.1 2.5 - - + -
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Residues in contact with ALA 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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27A LYS* 4.0 19.6 + - + +
88A GLU 2.9 19.1 + - - +
89A ASN* 3.8 5.4 - - - +
91A ALA* 1.3 76.1 - - - +
93A THR* 1.3 57.9 + - - +
95A LYS* 3.3 8.5 + - - +
96A GLU* 2.9 30.7 + - - +
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Residues in contact with THR 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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20A ALA* 3.3 39.9 - - + +
23A LEU* 3.8 16.1 - - + +
24A PHE* 3.2 26.2 + - + +
27A LYS* 3.5 16.1 - - - +
89A ASN 2.8 18.3 + - - -
90A LEU* 3.4 11.7 - - + -
92A ALA* 1.3 75.5 - - - +
94A LEU* 1.3 67.3 + - + +
96A GLU* 3.2 2.9 + - - +
97A LEU* 3.0 30.3 + - + +
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Residues in contact with LEU 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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11A LEU* 4.1 34.3 - - + -
17A MET* 6.2 1.3 - - + -
20A ALA* 4.2 24.0 - - + -
58A LEU* 6.0 1.1 - - + -
90A LEU* 3.0 39.6 + - + +
91A ALA 3.8 1.1 - - - +
93A THR* 1.3 77.5 - - - +
95A LYS* 1.4 62.9 + - - +
97A LEU* 3.3 6.3 + - + -
98A GLY 3.2 4.7 + - - -
99A VAL* 3.0 33.5 + - + +
104A ILE* 3.7 28.5 - - + -
107A ALA* 4.3 20.2 - - + -
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Residues in contact with LYS 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 ALA 2.9 15.1 + - - +
92A ALA* 3.5 12.3 - - - +
93A THR 3.2 0.2 - - - -
94A LEU* 1.4 76.1 - - - +
96A GLU* 1.3 56.5 + - - +
98A GLY* 2.8 24.1 + - - -
99A VAL 4.0 10.8 - - - +
100A THR* 5.6 0.7 - - - +
101A ASP* 3.4 32.1 + - - +
104A ILE* 3.7 13.8 - - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 21.9 - - + +
27A LYS* 2.7 34.6 + - - -
92A ALA 2.9 15.5 + - - +
93A THR 3.2 4.7 + - - +
95A LYS* 1.3 78.4 - - - +
97A LEU* 1.3 60.5 + - + +
98A GLY 3.2 1.3 + - - -
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Residues in contact with LEU 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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16A ALA* 4.4 9.0 - - + +
19A ALA* 4.4 14.4 - - + +
20A ALA* 3.7 40.8 - - + +
23A LEU* 4.0 16.2 - - + -
93A THR* 3.0 24.0 + - + +
94A LEU* 3.7 11.0 - - + +
95A LYS 3.1 0.2 - - - -
96A GLU* 1.3 78.8 - - + +
98A GLY* 1.3 59.0 + - - +
99A VAL* 3.5 7.4 - - + +
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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