Contacts of the helix formed by residues 93 - 113 (chain C) in PDB entry 2QAR
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 ASP 93 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER 4.0 1.2 + - - -
92C LEU* 1.3 73.0 - - - +
94C CYS* 1.3 58.9 + - - +
95C VAL* 3.8 23.1 + - - +
96C ARG* 2.7 50.4 + - - +
97C ARG* 2.9 23.9 + - - -
127C TRP* 6.2 0.2 - - - -
157C GLY 4.2 5.5 - - - +
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Residues in contact with CYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ASP* 1.3 74.1 + - - +
95C VAL* 1.3 63.1 + - + +
97C ARG* 3.6 25.6 - - - +
98C CYS* 3.2 21.7 + - - +
159C TRP* 4.8 3.7 - - - -
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ASP* 3.1 9.8 + - - +
94C CYS* 1.3 78.9 - - + +
96C ARG* 1.3 61.2 + - - +
98C CYS* 3.5 14.7 + - - +
99C ALA 3.6 4.2 + - - -
153C THR* 3.8 17.4 - - + +
157C GLY* 3.4 36.1 - - - +
158C THR* 3.7 17.7 - - - +
159C TRP* 3.8 37.3 - - + +
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.8 21.3 - - + +
93C ASP* 2.7 42.0 + - - +
95C VAL* 1.3 72.8 - - - +
97C ARG* 1.3 65.0 + - - +
98C CYS 3.3 0.2 - - - -
99C ALA* 3.4 7.8 + - - -
100C LEU 3.3 15.8 + - - -
127C TRP* 3.4 60.9 - - - +
153C THR 4.0 14.6 - - - +
154C PHE* 3.1 35.8 + - + +
155C ARG 3.6 10.5 + - - -
156C THR 3.9 4.0 + - - -
157C GLY* 3.6 25.2 - - - +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.1 54.7 + - + +
90C ASP* 3.2 39.8 + - - +
92C LEU* 2.8 27.0 + - + +
93C ASP 2.9 16.7 + - - +
94C CYS* 3.6 28.5 - - - +
95C VAL 3.3 0.2 - - - -
96C ARG* 1.3 76.9 - - - +
98C CYS* 1.3 62.5 + - - +
100C LEU* 3.2 4.7 + - - +
101C ILE* 3.1 29.1 + - + +
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Residues in contact with CYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.7 28.3 - - + +
7C MET* 3.6 11.4 - - - +
94C CYS 3.2 10.1 + - - +
95C VAL 3.5 11.4 - - - +
96C ARG 3.3 0.4 - - - -
97C ARG* 1.3 80.0 - - - +
99C ALA* 1.3 56.4 - - - +
101C ILE* 3.3 7.3 + - - +
102C ASN* 2.8 28.9 + - - +
159C TRP* 3.8 20.6 - - + -
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C MET* 3.7 20.4 - - + +
95C VAL 3.6 2.4 + - - -
96C ARG 3.4 10.9 + - - +
97C ARG 3.2 0.4 - - - -
98C CYS* 1.3 79.4 - - - +
100C LEU* 1.3 56.2 + - - +
102C ASN* 3.2 4.9 - - - +
103C MET* 3.1 30.3 + - - +
150C VAL* 3.9 10.8 - - + +
153C THR* 4.2 14.6 - - + -
154C PHE* 3.6 27.4 - - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.2 15.5 - - + -
85C LEU* 4.8 9.9 - - + +
88C VAL* 5.1 4.0 - - + -
89C TYR* 3.6 40.6 - - + +
92C LEU* 4.7 5.8 - - + -
96C ARG 3.3 9.4 + - - +
97C ARG 3.2 9.0 + - - +
99C ALA* 1.3 75.3 - - - +
101C ILE* 1.3 65.0 + - - +
103C MET* 3.4 9.2 + - - +
104C VAL* 3.1 27.5 + - + +
112C VAL* 4.0 17.3 - - + -
119C LEU* 3.8 27.4 - - + -
122C LEU* 5.1 3.8 - - + -
154C PHE* 3.7 18.0 - - + -
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.4 12.1 - - + -
8C LEU* 5.3 0.4 - - + -
72C VAL* 4.4 16.2 - - + -
75C ALA* 3.9 10.1 - - + -
76C VAL* 3.8 24.2 - - + -
79C ILE* 3.9 22.9 - - + -
89C TYR* 3.8 11.2 - - + +
97C ARG* 3.1 20.9 + - + +
98C CYS* 3.5 10.5 - - - +
100C LEU* 1.3 73.9 - - - +
102C ASN* 1.3 66.1 + - - +
104C VAL* 2.9 14.5 + - - +
105C PHE* 2.9 38.2 + - + -
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Residues in contact with ASN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C MET* 3.4 30.8 - - + +
8C LEU* 4.3 19.7 - - + +
11C ASP* 2.9 25.2 + - - +
98C CYS 2.8 14.7 + - - +
99C ALA* 3.2 13.2 - - - +
101C ILE* 1.3 77.3 - - - +
103C MET* 1.3 61.4 + - - +
104C VAL 3.5 0.2 + - - -
105C PHE* 3.5 5.9 + - - +
106C GLN* 3.6 2.3 + - - +
146C ARG* 3.0 41.7 + - - -
150C VAL* 3.8 14.8 - - + +
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Residues in contact with MET 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA 3.1 10.8 + - - +
100C LEU* 3.5 17.5 - - - +
101C ILE 3.2 0.2 - - - -
102C ASN* 1.3 78.8 - - - +
104C VAL* 1.3 58.0 + - - +
106C GLN* 3.4 4.3 + - - +
107C MET* 3.1 59.2 + - + +
112C VAL* 3.7 16.2 - - + -
115C PHE* 4.3 19.5 - - + -
119C LEU* 6.5 0.4 - - + -
134C LEU* 4.0 24.9 - - + -
139C TRP* 4.4 14.4 - - + -
150C VAL* 3.9 14.8 - - + -
154C PHE* 3.7 29.6 - - - -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ALA* 4.1 26.5 - - + +
79C ILE* 4.0 21.5 - - + -
85C LEU* 4.8 1.8 - - + -
100C LEU* 3.1 15.6 + - + +
101C ILE* 2.9 11.0 + - - +
103C MET* 1.3 72.6 - - - +
105C PHE* 1.3 61.4 + - - +
106C GLN 3.1 1.3 - - - -
108C GLY* 2.8 28.6 + - - +
109C GLU* 3.7 28.5 - - + +
112C VAL* 3.8 22.0 - - + -
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.5 31.4 - - + -
12C GLU* 3.7 21.9 - - - +
30C ILE 3.7 19.3 - - - -
31C GLY 4.8 10.1 - - - +
68C PHE* 4.0 16.4 - + - -
71C ASP* 3.7 22.7 - - + -
72C VAL* 3.7 39.9 - - + -
75C ALA* 4.2 5.8 - - + -
101C ILE* 2.9 37.0 + - + -
102C ASN 3.6 6.1 - - - +
104C VAL* 1.3 76.1 - - - +
106C GLN* 1.3 61.7 + - - +
146C ARG* 4.0 0.4 - - - +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 4.1 7.2 - - - +
102C ASN* 3.6 3.0 + - - +
103C MET* 3.4 7.7 + - - +
104C VAL 3.1 0.6 - - - -
105C PHE* 1.3 81.4 - - - +
107C MET* 1.3 65.5 + - + +
108C GLY 3.5 0.8 + - - -
139C TRP* 3.0 43.2 + - + +
142C GLN* 6.2 0.6 - - - +
143C THR* 3.8 17.0 + - - -
146C ARG* 3.3 45.6 + - - +
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET* 3.1 38.6 + - + +
106C GLN* 1.3 82.5 - - + +
108C GLY* 1.3 61.6 + - - +
111C GLY* 3.7 14.2 + - - -
112C VAL* 3.7 21.5 - - + +
115C PHE* 3.6 31.6 - - - -
139C TRP* 3.6 46.4 - - + +
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C VAL* 2.8 26.5 + - - -
106C GLN 3.5 1.6 + - - -
107C MET* 1.3 77.9 - - - +
109C GLU* 1.3 66.2 + - - -
110C THR 3.2 2.7 - - - -
111C GLY 3.0 11.6 + - - -
112C VAL* 3.1 13.5 + - - +
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY* 3.2 42.4 - - - +
79C ILE* 5.0 0.2 - - - -
81C ARG* 5.1 1.0 - - - +
82C ASN* 2.7 33.0 + - - +
85C LEU* 3.5 17.1 - - + +
104C VAL* 3.7 25.0 - - + +
108C GLY* 1.3 71.1 - - - +
110C THR* 1.3 66.8 + - - +
112C VAL* 3.5 0.9 + - - +
113C ALA* 3.3 19.2 + - - +
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ASN* 5.1 3.1 + - - +
108C GLY 3.2 0.8 - - - -
109C GLU* 1.3 83.0 - - - +
111C GLY* 1.3 62.4 + - - +
113C ALA* 3.6 13.2 + - + +
114C GLY* 3.8 6.8 + - - -
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C MET* 3.7 23.4 + - - -
108C GLY 3.0 7.5 + - - -
110C THR* 1.3 77.1 - - - +
112C VAL* 1.3 63.1 + - - +
114C GLY* 3.4 11.1 + - - -
115C PHE* 3.6 13.2 - - - -
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.0 13.2 - - + -
100C LEU* 4.0 28.9 - - + -
103C MET* 3.6 47.1 - - + +
104C VAL* 3.8 10.3 - - + +
107C MET* 3.7 7.6 - - + -
108C GLY 3.1 12.9 + - - +
109C GLU 3.8 6.5 - - - +
111C GLY* 1.3 70.8 - - - +
113C ALA* 1.3 58.5 + - - +
114C GLY 3.0 4.7 - - - -
115C PHE* 3.0 34.7 + - + +
119C LEU* 3.7 7.7 - - + +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 4.3 8.3 - - - +
84C LYS* 4.2 31.7 + - + +
85C LEU* 3.7 23.8 - - + +
109C GLU 3.3 14.9 + - - +
110C THR* 3.9 9.2 - - + +
111C GLY 3.3 0.4 - - - -
112C VAL* 1.3 77.8 - - - +
114C GLY* 1.3 59.8 + - - +
115C PHE 3.2 0.6 + - - -
116C THR* 3.9 10.7 + - - -
119C LEU* 3.9 9.1 - - - +
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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