Contacts of the helix formed by residues 74 - 90 (chain C) in PDB entry 3OQN
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 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER 6.1 0.9 - - - +
74A ILE* 4.0 28.3 - - + -
279A ARG* 4.1 23.6 - - + +
72C SER 4.6 0.9 - - - +
73C SER* 1.3 80.2 - - - +
75C PHE* 1.3 63.2 + - - +
77C SER* 3.1 14.3 + - - -
78C GLU* 3.8 9.2 + - - +
250C GLU* 3.8 22.0 - - - +
278C THR* 3.8 30.9 - - + +
279C ARG* 4.8 15.0 - - + +
280C LEU* 4.7 17.3 - - + -
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Residues in contact with PHE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER* 3.9 4.0 - - - +
74C ILE* 1.3 77.3 - - - +
76C TYR* 1.3 97.1 + + + +
78C GLU* 3.0 18.5 + - - +
79C LEU* 3.1 26.8 + - + -
147C ALA* 4.4 8.7 - - + -
162C TYR* 5.3 1.1 - + - -
276C ASP* 4.0 26.0 - - + +
278C THR* 4.7 11.2 - - + +
293C GLN* 3.3 32.5 - - - -
295C THR* 2.7 41.4 - - + +
298C ILE* 5.2 0.4 - - + -
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 3.4 23.4 - - + +
69C PRO* 3.4 37.2 - - + -
70C ASP* 3.9 8.5 - - + +
73C SER* 2.9 28.4 + - - +
75C PHE* 1.3 98.4 - + + +
77C SER* 1.3 56.4 + - - +
79C LEU* 2.9 20.8 + - + +
80C ALA* 2.7 35.5 + - - +
101C GLN* 3.7 17.8 + - - -
124C MET* 4.4 13.6 + - + -
125C GLY 5.2 4.3 + - - -
126C GLY* 5.7 0.2 - - - -
147C ALA* 5.7 6.1 + - + -
190C GLU* 5.5 1.2 + - - -
222C TYR* 6.0 1.7 - - - -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.5 28.5 - - - +
72A SER* 4.1 13.2 + - - -
77A SER* 3.9 5.5 - - - -
71C ILE* 3.7 24.7 + - - -
73C SER 2.9 25.7 + - - -
74C ILE* 3.1 13.0 + - - +
75C PHE 3.2 0.2 - - - -
76C TYR* 1.3 77.2 - - - +
78C GLU* 1.3 70.7 + - - +
80C ALA* 3.2 6.1 - - - +
81C ARG* 3.2 15.6 + - - +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 4.1 9.6 - - - -
74C ILE 3.9 9.2 - - - +
75C PHE* 3.0 11.3 + - - +
77C SER* 1.3 78.8 + - - +
79C LEU* 1.3 58.3 + - - +
81C ARG* 2.6 33.5 + - - +
82C GLY 3.2 3.1 + - - -
295C THR* 3.6 19.1 - - + -
296C TYR* 3.7 29.9 + - - +
16D ALA* 5.1 5.2 - - - +
17D ARG* 3.7 23.3 + - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 3.1 27.5 + - + -
76C TYR* 2.9 24.8 + - + +
78C GLU* 1.3 77.4 - - - +
80C ALA* 1.3 64.5 + - - +
82C GLY* 3.0 13.6 + - - +
83C ILE* 3.0 18.6 + - + +
124C MET* 4.2 11.0 - - - -
146C ALA* 4.1 15.0 - - + -
147C ALA* 3.9 14.1 - - + -
295C THR* 3.3 32.1 - - + +
298C ILE* 3.9 13.2 - - + -
299C GLY* 3.4 34.0 - - - +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.2 8.3 - - + -
66C VAL* 6.0 0.2 - - - -
68C ILE* 4.2 10.3 - - + +
71C ILE* 4.1 20.6 - - + -
76C TYR 2.7 15.4 + - - +
77C SER 3.2 13.9 - - - +
79C LEU* 1.3 73.4 - - - +
81C ARG* 1.3 55.6 + - - +
83C ILE* 3.7 12.4 - - - +
84C GLU* 2.8 34.6 + - - +
96C LEU* 5.0 10.3 - - + -
124C MET* 5.5 0.2 - - + -
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 2.7 24.3 + - - +
71A ILE* 4.2 3.4 - - + -
72A SER* 4.4 5.2 - - - +
98A ASN* 3.3 34.8 + - - +
100A ASP* 2.6 42.0 + - - -
77C SER 3.2 7.9 + - - +
78C GLU* 2.6 25.9 + - - +
80C ALA* 1.3 69.6 - - - +
82C GLY* 1.3 58.2 + - - +
84C GLU* 4.4 0.9 - - - -
85C ASP* 2.4 73.2 + - - +
296C TYR* 3.6 19.7 - - + -
17D ARG* 3.7 28.2 - - - +
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU 3.2 3.8 + - - -
79C LEU 3.0 6.8 + - - -
81C ARG* 1.3 80.5 - - - +
83C ILE* 1.3 63.9 + - - +
85C ASP* 3.6 0.9 - - - +
86C ILE* 3.0 26.2 + - - +
296C TYR* 3.6 28.2 - - - -
300C ALA* 3.7 20.0 - - - -
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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
----------------------------------------------------------
66C VAL* 3.8 15.5 - - + -
79C LEU* 3.0 18.0 + - + +
80C ALA* 3.7 5.6 - - - +
82C GLY* 1.3 76.3 - - - +
84C GLU* 1.3 64.4 + - - +
87C ALA 3.2 15.6 + - - -
94C ILE* 3.8 9.2 - - + -
122C VAL* 3.9 21.5 - - + -
124C MET* 3.2 41.5 - - + -
146C ALA* 4.9 0.2 - - + -
299C GLY* 3.6 26.7 - - - +
303C MET* 3.3 37.9 - - + +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 5.5 1.6 - - + -
96A LEU* 2.8 24.5 - - + +
97A SER* 3.5 25.3 - - - -
98A ASN* 3.2 27.6 + - + +
80C ALA 2.8 23.5 + - - +
81C ARG* 3.9 3.1 - - - +
83C ILE* 1.3 74.1 - - - +
85C ASP* 1.3 63.3 + - - +
87C ALA* 3.4 3.1 + - - +
88C THR* 3.1 49.5 + - - -
92C TYR 5.1 1.8 - - - +
94C ILE* 3.6 24.8 + - + +
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 4.9 0.2 - - - +
81C ARG* 2.4 64.1 + - - +
82C GLY 3.7 1.8 - - - +
84C GLU* 1.3 74.9 - - - +
86C ILE* 1.3 66.6 + - + +
88C THR* 3.6 8.9 + - - -
89C MET* 3.3 20.3 + - - +
296C TYR* 3.1 25.3 + - - +
17D ARG* 3.9 8.3 - - - +
20D THR* 5.4 3.4 - - + +
24D GLN* 5.0 2.6 + - - -
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Residues in contact with ILE 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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82C GLY 3.0 13.6 + - - +
85C ASP* 1.3 79.6 - - + +
87C ALA* 1.3 66.0 + - - +
89C MET* 3.1 26.1 - - + +
90C TYR* 3.0 38.6 + - + -
296C TYR* 4.5 1.1 - - - +
300C ALA* 3.4 38.1 - - + +
303C MET* 3.2 26.2 - - + +
304C ARG* 3.7 15.7 - - + +
307C THR* 4.6 0.2 - - - +
20D THR* 4.0 17.7 - - + +
47D ILE* 4.1 11.7 - - + -
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Residues in contact with ALA 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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83C ILE 3.2 8.6 + - - +
84C GLU 3.6 4.7 - - - +
85C ASP 3.3 0.2 - - - -
86C ILE* 1.3 79.2 - - - +
88C THR* 1.3 61.7 + - - +
90C TYR* 3.1 7.3 + - - -
91C LYS 3.0 5.5 + - - -
92C TYR* 2.8 46.9 + - + +
94C ILE* 3.9 7.0 - - + -
303C MET* 3.2 37.7 - - + -
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Residues in contact with THR 88 (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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105A LYS* 5.8 8.5 - - + -
109A LEU* 6.3 3.1 - - + -
84C GLU* 3.1 31.7 + - - +
85C ASP* 3.8 11.7 + - - -
86C ILE 3.2 0.2 - - - -
87C ALA* 1.3 72.9 - - - +
89C MET* 1.3 68.8 + - - +
91C LYS* 2.7 20.8 + - - +
92C TYR 3.9 8.7 + - - +
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Residues in contact with MET 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 ASP 3.3 6.6 + - - +
86C ILE* 3.1 30.7 + - + +
88C THR* 1.3 80.8 - - - +
90C TYR* 1.3 80.2 + - + +
91C LYS* 3.3 19.2 + - - -
20D THR* 3.8 5.8 - - + -
23D VAL* 5.4 2.0 - - - -
24D GLN* 3.3 40.2 - - + +
27D SER* 5.9 2.9 - - - -
47D ILE* 3.6 36.1 - - + -
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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
----------------------------------------------------------
86C ILE* 3.0 32.7 + - + +
87C ALA* 3.1 6.0 + - - +
88C THR 3.0 0.2 - - - -
89C MET* 1.3 106.0 - - + +
91C LYS* 1.3 74.1 + - - +
92C TYR* 2.9 24.2 - - + -
304C ARG* 2.6 56.4 + - - -
307C THR* 3.5 24.5 - - + +
45D LYS 4.7 8.1 + - - -
47D ILE* 5.0 2.3 - - + +
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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
------------------------------------------------------------
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