Contacts of the helix formed by residues 79 - 96 (chain C) in PDB entry 3QNQ
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 ILE 79 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C SER 4.2 4.0 - - - +
75C ALA 2.7 33.4 - - - +
76C THR* 2.9 11.1 + - - +
77C PHE 2.8 0.8 + - - -
78C ASN* 1.3 80.0 - - - +
80C MET* 1.3 69.5 + - - +
82C LEU* 3.2 30.1 + - + -
83C ILE* 3.4 16.5 + - + +
141C MET* 2.9 18.8 - - + -
108D LEU* 5.3 3.6 - - + +
109D VAL* 5.1 2.9 - - + -
112D LEU* 2.8 45.1 - - + -
117D PHE* 4.6 8.3 - - + -
136D ILE* 4.8 3.1 - - + -
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Residues in contact with MET 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 6.0 0.7 - - + -
32C THR* 4.0 14.2 - - + +
36C LEU* 3.6 42.0 - - + -
76C THR 3.1 5.7 + - - -
77C PHE* 3.5 13.6 + - - +
79C ILE* 1.3 74.4 - - - +
81C ALA* 1.3 57.0 + - - +
83C ILE* 2.8 28.6 + - - +
84C ALA* 2.8 13.1 + - + +
141C MET 3.3 1.2 + - - -
143C SER* 3.5 30.5 - - - +
146C LEU* 3.1 35.7 - - + -
264C LEU* 3.4 17.3 - - + -
267C MET* 4.6 8.5 - - - -
268C ASP* 5.0 2.0 - - - -
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Residues in contact with ALA 81 (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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80C MET* 1.3 79.9 - - - +
82C LEU* 1.3 61.0 + - - +
84C ALA* 3.9 9.9 - - - -
85C VAL* 3.0 29.3 + - - +
111C PHE* 3.7 17.5 - - + -
141C MET 3.2 7.7 + - - +
142C GLY 3.6 10.9 + - - +
145C GLY* 3.7 5.4 - - - -
146C LEU* 3.4 34.7 - - - +
149C ALA* 4.1 0.7 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 3.2 41.3 + - + -
80C MET 3.0 1.0 + - - -
81C ALA* 1.3 77.2 - - - +
83C ILE* 1.3 62.8 + - + +
85C VAL* 3.2 16.1 - - - +
86C PHE* 4.0 0.9 + - - +
108C LEU* 3.4 29.3 - - + +
111C PHE* 4.1 11.2 - - + -
112C LEU* 3.7 33.7 - - + -
141C MET* 3.6 18.1 + - + -
82D LEU* 4.3 15.0 - - + -
108D LEU* 4.6 10.1 - - + -
112D LEU* 3.7 13.0 - - + -
136D ILE* 5.6 2.0 - - + -
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Residues in contact with ILE 83 (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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31C LEU* 3.7 33.4 - - + +
32C THR* 3.8 17.0 - - + -
35C PHE* 3.5 34.3 - - + -
36C LEU* 6.5 0.9 - - + -
75C ALA 5.3 0.2 - - - +
76C THR 5.1 2.0 - - - +
79C ILE* 3.6 20.0 - - + +
80C MET* 2.8 9.9 + - - +
82C LEU* 1.3 76.3 - - + +
84C ALA* 1.3 55.5 + - - +
86C PHE* 2.8 30.1 + - - +
87C GLY 3.1 10.4 + - - -
105D ALA* 5.1 4.3 - - + +
108D LEU* 4.5 15.0 - - + -
109D VAL* 3.8 21.8 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLY 5.0 4.3 - - - -
29C LEU* 3.9 28.3 - - + -
32C THR* 3.9 10.5 - - + +
80C MET 2.8 15.4 + - - +
81C ALA* 3.2 13.2 + - - +
83C ILE* 1.3 73.1 - - - +
85C VAL* 1.3 57.0 + - - +
87C GLY 3.3 0.8 + - - +
88C ILE* 2.8 42.2 + - + +
146C LEU* 4.7 3.8 - - + -
149C ALA* 4.5 8.7 - - + -
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Residues in contact with VAL 85 (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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81C ALA 3.0 13.8 + - - +
82C LEU* 3.2 18.6 - - - +
84C ALA* 1.3 75.7 - - - +
86C PHE* 1.3 66.2 + - - +
88C ILE* 4.7 0.2 - - - -
89C ALA* 3.1 24.3 + - - +
107C SER* 3.5 27.0 - - - +
108C LEU* 4.2 6.7 - - + -
111C PHE* 3.6 27.4 - - + -
149C ALA* 3.2 40.4 - - + +
152C ILE* 4.5 1.3 - - + -
153C ALA* 3.6 13.1 - - + +
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Residues in contact with PHE 86 (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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31C LEU* 4.4 5.4 - - + -
82C LEU 4.4 4.9 - - - +
83C ILE* 2.8 12.8 + - - +
85C VAL* 1.3 80.3 - - + +
87C GLY* 1.3 61.3 + - - +
89C ALA* 2.9 3.3 + - - -
90C TYR* 2.7 50.5 + + + +
101C LEU* 4.5 6.7 - - + -
104C GLY* 3.3 20.4 - - - -
105C ALA* 3.2 29.6 - - + -
108C LEU* 4.5 14.6 - - + -
86D PHE* 2.8 59.5 - + + -
101D LEU* 3.7 20.9 - - + -
108D LEU* 6.4 1.1 - - + -
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Residues in contact with GLY 87 (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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28C GLY* 3.4 19.6 - - - -
31C LEU* 3.7 22.5 - - - +
83C ILE 3.1 7.2 + - - -
84C ALA 3.7 2.2 - - - -
86C PHE* 1.3 79.6 - - - +
88C ILE* 1.3 59.4 + - - +
90C TYR* 3.6 8.0 + - - +
91C ARG* 3.1 25.3 + - - +
101D LEU* 5.6 2.0 - - - -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 3.8 32.1 - - + +
25C ILE* 4.0 22.4 - - + +
28C GLY* 4.0 8.1 - - - -
29C LEU* 4.4 7.2 - - + +
84C ALA* 2.8 34.9 + - + +
87C GLY* 1.3 71.8 - - - +
89C ALA* 1.3 59.4 + - - +
91C ARG* 3.1 3.1 + - - +
92C LEU* 2.9 28.6 + - + +
146C LEU 5.4 0.2 - - - +
149C ALA 4.9 0.4 - - - -
150C MET* 3.7 37.5 - - + +
153C ALA* 4.0 16.4 - - + -
154C ILE* 4.5 11.0 - - + -
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Residues in contact with ALA 89 (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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85C VAL 3.1 18.0 + - - +
86C PHE 2.9 5.0 + - - +
88C ILE* 1.3 73.8 - - - +
90C TYR* 1.3 63.2 + - - +
92C LEU* 4.7 0.4 - - - -
93C GLY 3.2 10.0 + - - -
103C SER* 3.2 22.9 + - - +
104C GLY* 4.1 1.6 - - - -
107C SER* 3.2 22.0 - - - +
153C ALA* 3.7 8.7 - - + +
157C THR* 3.0 32.2 + - - +
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Residues in contact with TYR 90 (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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86C PHE* 2.7 41.9 + + + +
87C GLY* 3.7 5.6 - - - +
89C ALA* 1.3 73.4 - - - +
91C ARG* 1.3 60.0 + - + +
93C GLY* 3.3 1.2 + - - -
94C GLU* 3.0 49.5 + - - +
100C ALA* 3.2 52.4 - - + +
101C LEU* 3.6 6.5 - - - -
103C SER* 4.1 5.2 - - - -
104C GLY* 4.1 2.8 - - - -
90D TYR* 2.6 33.5 + + - -
101D LEU* 3.6 44.1 + - + +
182D ARG* 5.9 0.7 - - - -
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Residues in contact with ARG 91 (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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23C LEU* 3.7 37.7 - - - +
24C ALA* 3.9 24.0 - - + +
27C ASP* 3.8 5.6 + - + -
28C GLY* 4.9 0.4 - - - +
87C GLY 3.1 18.2 + - - +
88C ILE 3.1 3.3 + - - +
90C TYR* 1.3 75.7 - - + +
92C LEU* 1.3 55.6 + - - +
93C GLY 2.6 14.8 + - - -
94C GLU* 2.7 39.3 + - - +
95C TYR* 2.9 31.7 + - - +
600C ZDM 2.7 49.7 + - - +
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Residues in contact with LEU 92 (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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20C ARG* 4.4 9.9 - - + -
21C HIS* 3.9 21.3 - - + -
23C LEU* 6.5 0.2 - - - -
24C ALA* 3.6 22.6 - - + +
88C ILE* 2.9 17.0 + - + +
89C ALA* 4.7 0.2 - - - -
91C ARG* 1.3 72.6 - - - +
93C GLY* 1.3 58.6 + - - +
95C TYR* 3.7 9.4 - - + +
96C TYR* 3.4 39.5 + - + -
153C ALA 4.6 0.2 - - - +
154C ILE* 4.1 29.6 - - + +
157C THR* 3.7 28.9 - - + +
158C GLU* 4.0 17.3 - - - +
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Residues in contact with GLY 93 (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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89C ALA 3.2 7.8 + - - -
90C TYR 3.5 5.8 - - - -
91C ARG 2.6 3.0 + - - -
92C LEU* 1.3 77.5 - - - +
94C GLU* 1.3 63.6 + - - -
96C TYR 3.2 5.7 + - - -
98C VAL* 3.2 42.0 + - - +
100C ALA* 4.7 0.9 - - - -
103C SER* 3.7 18.4 - - - -
157C THR* 4.0 4.3 - - - -
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Residues in contact with GLU 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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90C TYR* 3.0 39.0 + - - +
91C ARG* 2.7 40.3 + - - +
93C GLY* 1.3 70.5 - - - +
95C TYR* 1.3 62.6 + - - +
97C LYS* 2.8 22.5 + - - +
98C VAL 4.9 2.5 - - - -
100C ALA* 4.1 13.3 - - + +
600C ZDM 4.8 6.2 + - - +
182D ARG* 5.9 0.9 + - - -
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Residues in contact with TYR 95 (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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18C GLU 4.2 10.9 + - - -
20C ARG* 3.2 57.9 + - + +
23C LEU* 3.9 23.6 - - + -
91C ARG* 2.9 22.0 + - - +
92C LEU* 3.7 16.4 - - + +
94C GLU* 1.3 76.9 - - - +
96C TYR* 1.3 78.0 + + - +
97C LYS* 2.9 10.7 + - - +
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Residues in contact with TYR 96 (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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20C ARG* 2.9 36.2 + - - -
92C LEU* 3.4 30.0 + - + +
93C GLY 3.2 5.7 + - - +
95C TYR* 1.3 96.7 - + - +
97C LYS* 1.3 70.7 + - - +
98C VAL* 3.2 10.0 + - + +
157C THR* 4.8 2.9 - - + -
158C GLU* 2.7 42.1 + - - -
161C ARG* 3.0 57.2 + - + -
165C GLN* 3.9 15.3 + - - +
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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
------------------------------------------------------------
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