Contacts of the helix formed by residues 76 - 91 (chain A) in PDB entry 1Q0R
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 GLY 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 1.3 75.2 - - - +
77A PHE* 1.3 66.8 + - - -
78A GLY 3.2 3.1 - - - -
79A GLU* 2.9 17.0 + - - +
80A LEU* 3.2 21.9 + - - +
222A LEU* 3.9 12.6 - - - -
223A THR* 4.9 6.7 - - - -
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Residues in contact with PHE 77 (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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76A GLY* 1.3 71.0 - - - -
78A GLY* 1.3 60.8 + - - +
80A LEU* 3.7 6.6 - - + +
81A ALA* 2.9 31.2 + - - +
103A MET* 3.6 40.6 - - + -
106A THR* 3.6 24.9 - - + -
107A ILE* 3.7 28.6 - - + +
110A VAL* 4.1 9.0 - - + +
222A LEU* 4.1 18.6 - - + -
223A THR 3.4 23.6 + - - +
224A LEU* 3.8 23.8 - - + -
225A PRO* 3.8 26.2 - - + -
600A AKT 5.1 0.9 - - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY* 3.2 1.4 - - - -
77A PHE* 1.3 78.3 - - - +
79A GLU* 1.3 59.0 + - - +
81A ALA* 3.9 2.1 - - - +
82A ALA* 3.0 29.3 + - - +
110A VAL* 4.5 11.4 - - - +
114A ASP* 5.9 0.9 - - - -
115A HIS* 5.0 2.6 - - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 4.0 21.5 - - - +
74A PRO 4.8 2.1 - - - +
75A TYR* 3.7 28.8 - - + +
76A GLY* 2.9 26.2 + - - +
78A GLY* 1.3 76.6 + - - +
80A LEU* 1.3 59.7 + - - +
82A ALA* 3.8 4.8 - - - +
83A ASP* 2.9 37.1 + - - +
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Residues in contact with LEU 80 (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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57A TYR* 4.2 4.3 + - - -
59A HIS* 4.1 22.2 - - + -
60A ARG* 4.3 15.3 - - + +
75A TYR* 4.0 18.4 - - + -
76A GLY 3.2 14.9 + - - +
77A PHE* 3.3 13.6 + - + +
79A GLU* 1.3 76.7 - - - +
81A ALA* 1.3 61.6 + - - +
83A ASP* 3.5 8.2 - - + +
84A ALA* 3.3 16.8 + - - +
103A MET* 4.1 14.1 - - + -
107A ILE* 3.8 28.2 - - + +
219A HIS* 4.4 8.3 - - - +
222A LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE 2.9 17.3 + - - +
78A GLY 3.9 2.5 - - - +
80A LEU* 1.3 74.7 - - - +
82A ALA* 1.3 64.9 + - - +
84A ALA* 3.2 5.9 + - - +
85A VAL* 3.2 23.7 + - - +
107A ILE* 3.8 14.7 - - + +
110A VAL* 3.7 23.6 - - + -
111A ILE* 3.7 21.1 - - + +
115A HIS* 4.4 8.1 - - + +
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Residues in contact with ALA 82 (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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8A SER* 4.4 1.6 - - - +
78A GLY 3.0 18.8 + - - +
79A GLU* 3.8 6.1 - - - +
81A ALA* 1.3 77.3 - - - +
83A ASP* 1.3 59.9 + - - +
85A VAL* 3.2 5.6 + - - +
86A ALA* 2.8 27.7 + - - +
115A HIS* 4.1 20.8 - - + +
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Residues in contact with ASP 83 (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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8A SER* 2.7 30.1 + - - -
11A VAL* 4.4 1.6 - - - -
13A LEU* 3.5 21.2 - - + +
57A TYR* 4.8 5.8 - - + -
59A HIS* 6.3 1.1 - - + -
60A ARG* 2.7 51.4 + - - +
79A GLU 2.9 22.6 + - - +
80A LEU* 3.5 11.1 - - + +
81A ALA 3.2 0.2 - - - -
82A ALA* 1.3 75.6 - - - +
84A ALA* 1.3 64.6 + - - +
86A ALA* 3.1 3.6 + - - +
87A VAL* 3.0 26.3 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.6 21.2 - - + +
29A VAL* 4.6 2.2 - - + -
57A TYR* 3.3 28.6 + - + +
80A LEU 3.3 6.2 + - - +
81A ALA 3.2 10.4 + - - +
83A ASP* 1.3 78.3 - - - +
85A VAL* 1.3 61.8 + - - +
87A VAL* 3.2 14.7 + - - +
88A LEU* 3.3 8.9 + - - +
107A ILE* 4.9 1.6 - - + -
111A ILE* 3.6 24.5 - - + -
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Residues in contact with VAL 85 (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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81A ALA 3.2 11.7 + - - +
82A ALA* 3.6 8.3 - - - +
83A ASP 3.2 0.2 - - - -
84A ALA* 1.3 76.7 - - - +
86A ALA* 1.3 57.5 + - - +
88A LEU* 3.1 13.5 + - + +
89A ASP* 2.9 29.0 + - - +
111A ILE* 4.5 11.9 - - + -
115A HIS* 3.6 42.0 - - + -
118A ARG* 3.2 41.3 - - + +
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Residues in contact with ALA 86 (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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6A VAL* 4.1 6.4 - - - +
7A PRO 3.7 10.4 - - - +
8A SER* 3.3 37.9 - - - +
13A LEU* 4.7 1.3 - - + -
82A ALA 2.8 10.8 + - - +
83A ASP 3.1 6.3 + - - +
85A VAL* 1.3 72.9 - - - +
87A VAL* 1.3 60.5 + - - +
89A ASP* 3.3 14.7 + - - +
90A GLY* 2.9 25.6 + - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.1 13.2 - - + -
13A LEU* 3.9 11.7 - - + -
15A SER* 3.8 22.7 - - - +
27A LEU* 3.8 12.8 - - + -
55A ILE* 3.8 17.9 - - + -
57A TYR* 3.7 33.9 - - + -
83A ASP 3.0 18.3 + - - +
84A ALA 3.2 8.7 + - - +
86A ALA* 1.3 74.3 - - - +
88A LEU* 1.3 65.8 + - - +
90A GLY* 3.1 9.2 + - - -
91A TRP* 3.1 24.5 + - + +
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Residues in contact with LEU 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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25A ALA* 5.4 0.2 - - + -
27A LEU* 3.9 28.0 - - + -
55A ILE* 5.2 6.1 - - + -
84A ALA 3.3 9.8 + - - +
85A VAL* 3.1 16.6 + - + +
87A VAL* 1.3 76.3 - - - +
89A ASP* 1.3 63.3 + - - +
91A TRP* 3.2 5.0 + - - -
92A GLY 3.1 3.8 + - - -
93A VAL* 2.9 51.2 + - + +
94A ASP 5.0 0.4 - - - +
96A ALA* 3.6 28.3 - - + +
98A VAL* 5.0 5.2 - - + -
111A ILE* 6.5 0.9 - - + -
118A ARG* 3.8 39.3 - - + +
119A LEU* 6.0 0.2 - - + -
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Residues in contact with ASP 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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85A VAL* 2.9 18.5 + - - +
86A ALA* 3.4 15.6 - - - +
88A LEU* 1.3 75.4 - - - +
90A GLY* 1.3 58.8 + - - +
92A GLY* 3.0 18.5 + - - +
93A VAL 4.9 0.9 - - - +
118A ARG* 2.9 34.0 + - - +
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Residues in contact with GLY 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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4A ARG* 2.9 24.9 + - - -
6A VAL* 3.7 19.1 - - - +
7A PRO* 5.4 4.7 - - - -
86A ALA 2.9 14.6 + - - -
87A VAL 3.1 4.9 + - - -
89A ASP* 1.3 76.2 - - - +
91A TRP* 1.3 61.2 + - - +
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Residues in contact with TRP 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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2A SER* 3.5 19.5 - - - -
4A ARG* 3.5 57.8 + - + +
6A VAL* 4.6 2.2 - - + +
15A SER* 3.0 29.2 + - - -
16A ASP* 4.0 16.8 - - - -
17A ASP* 3.4 35.9 - - + -
21A PRO* 6.3 0.4 - - + -
53A HIS* 4.0 17.4 - + + -
55A ILE* 3.6 33.1 - - + +
87A VAL* 3.1 27.6 + - + +
88A LEU* 3.2 3.1 + - - +
90A GLY* 1.3 78.0 - - - +
92A GLY* 1.3 63.1 + - - +
93A VAL* 3.2 9.8 + - + +
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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