Contacts of the helix formed by residues 53 - 72 (chain C) in PDB entry 6O81
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 ASN 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.5 16.0 - - - +
52C SER* 1.3 81.7 + - - +
54C ALA* 1.3 73.4 + - - +
55C GLY* 3.2 12.2 + - - +
56C GLU* 3.5 19.7 + - + +
57C LEU 3.9 1.2 + - - -
93C TYR* 3.8 24.8 + - - -
126C TYR* 4.0 11.7 + - - +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TRP* 4.7 6.9 - - - +
53C ASN* 1.3 77.7 + - - +
55C GLY* 1.3 59.7 + - - +
56C GLU 3.3 0.2 - - - -
57C LEU* 3.4 7.0 + - - +
58C MET* 2.9 39.5 + - + +
89C ILE* 4.9 6.0 - - + +
93C TYR* 3.8 40.1 - - + -
126C TYR* 6.2 0.2 - - - -
129C LEU* 4.8 12.9 - - + +
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Residues in contact with GLY 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN* 3.2 13.3 - - - +
54C ALA* 1.3 76.9 - - - +
56C GLU* 1.3 59.0 + - - +
58C MET* 3.3 15.3 + - - +
59C GLU* 2.9 29.3 + - - +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ARG 4.5 6.3 - - - +
51C TRP* 4.0 12.3 - - + -
52C SER* 3.9 25.1 + - - -
53C ASN* 3.5 14.0 + - + +
54C ALA 3.3 0.6 - - - -
55C GLY* 1.3 74.1 - - - +
57C LEU* 1.3 59.7 + - - +
59C GLU* 3.3 7.4 + - - +
60C LEU* 2.9 32.3 + - + +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.4 21.8 - - + -
49C HIS* 6.0 1.1 - - + -
51C TRP* 3.5 59.3 - - + +
53C ASN 3.9 2.2 + - - -
54C ALA* 3.4 10.3 + - - +
56C GLU* 1.3 74.5 - - - +
58C MET* 1.3 61.1 + - - +
60C LEU* 3.7 13.4 - - + +
61C ILE* 2.9 50.3 + - + +
85C VAL* 6.0 0.9 - - + -
89C ILE* 3.7 31.2 - - + -
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Residues in contact with MET 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 2.9 27.3 + - + +
55C GLY* 3.4 16.8 - - - +
57C LEU* 1.3 76.2 - - - +
59C GLU* 1.3 56.8 + - - +
61C ILE 3.8 0.7 - - - -
62C ARG* 2.9 41.2 + - - +
86C LEU* 3.8 17.9 - - + +
89C ILE* 3.8 20.9 - - + +
90C ARG* 3.8 56.1 - - + +
93C TYR* 5.1 8.3 - - + -
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLY 2.9 16.9 + - - +
56C GLU* 3.3 6.9 + - - +
58C MET* 1.3 76.0 - - - +
60C LEU* 1.3 58.1 + - - +
62C ARG* 3.3 13.2 + - + +
63C ARG* 2.7 71.3 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 4.8 9.6 - - + +
46C ILE* 6.0 0.9 - - + -
49C HIS* 3.9 37.5 - - + +
56C GLU* 2.9 21.3 + - + +
57C LEU* 3.7 16.6 - - + +
58C MET 3.3 0.2 - - - -
59C GLU* 1.3 79.8 + - - +
61C ILE* 1.3 68.8 + - + +
63C ARG* 3.3 13.0 + - - +
64C GLU* 3.0 57.8 + - + +
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Residues in contact with ILE 61 (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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42C LEU* 3.8 18.2 - - + -
45C ILE* 3.8 31.9 - - + -
46C ILE* 4.5 10.5 - - + -
57C LEU* 2.9 37.6 + - + +
58C MET 3.9 2.9 - - - +
60C LEU* 1.3 78.8 - - + +
62C ARG* 1.3 57.0 + - - +
64C GLU* 3.5 6.8 + - + +
65C GLY* 2.9 26.9 + - - -
82C VAL* 3.7 26.3 - - + +
85C VAL* 5.0 8.1 - - + -
86C LEU* 3.8 20.6 - - + -
89C ILE* 5.1 1.1 - - + -
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C MET* 2.9 33.0 + - - +
59C GLU* 3.5 12.6 - - + +
61C ILE* 1.3 77.1 - - - +
63C ARG* 1.3 56.7 + - - +
65C GLY* 3.4 0.7 + - - -
66C ARG* 2.9 38.7 + - - +
86C LEU* 4.1 14.4 - - + +
90C ARG* 3.5 10.5 - - - +
347C ASP* 3.2 35.3 + - - -
348C ASP* 2.4 35.1 + - - +
350C VAL* 4.5 6.1 - - - +
351C LEU* 3.4 38.2 + - + +
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Residues in contact with ARG 63 (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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59C GLU* 2.7 59.9 + - - +
60C LEU* 3.3 15.7 + - - +
62C ARG* 1.3 75.6 - - - +
64C GLU* 1.3 61.1 + - + +
66C ARG* 3.3 11.9 + - + +
67C ARG* 3.0 40.3 + - + +
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.1 1.6 - - - +
15C ILE* 3.3 26.9 - - + +
42C LEU* 6.5 0.2 - - + -
45C ILE* 3.3 31.4 - - + +
49C HIS* 5.7 2.2 - - - -
60C LEU* 3.0 49.1 + - + +
61C ILE* 4.1 5.6 + - + +
63C ARG* 1.3 79.9 - - + +
65C GLY* 1.3 56.9 - - - +
67C ARG* 3.3 18.6 + - - +
68C MET* 2.9 44.9 + - + +
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Residues in contact with GLY 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE 2.9 17.3 + - - -
62C ARG 3.8 1.1 - - - -
64C GLU* 1.3 74.8 - - - +
66C ARG* 1.3 59.5 + - - +
68C MET* 3.7 10.0 - - - +
69C THR* 2.9 35.4 + - - +
79C GLY* 6.0 0.7 - - - -
82C VAL* 4.1 10.8 - - - -
351C LEU* 3.6 19.5 - - - -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 2.9 23.9 + - - +
63C ARG* 3.3 10.7 + - - +
65C GLY* 1.3 74.6 - - - +
67C ARG* 1.3 57.7 + - + +
69C THR* 3.2 9.6 + - - +
70C ALA* 2.9 29.2 + - - +
350C VAL* 4.2 22.1 + - - +
351C LEU* 3.0 38.3 + - + +
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Residues in contact with ARG 67 (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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329B ASP* 5.2 5.5 + - - -
15C ILE* 3.5 26.9 - - - +
16C GLU* 2.6 31.2 + - - -
19C VAL* 4.1 24.0 - - + +
63C ARG* 3.0 29.7 + - + +
64C GLU* 3.6 18.6 + - - +
65C GLY 3.3 0.2 - - - -
66C ARG* 1.3 77.9 - - + +
68C MET* 1.3 57.5 + - + +
70C ALA* 3.3 7.7 + - - +
71C ALA* 2.9 26.7 + - - +
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Residues in contact with MET 68 (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 PHE* 3.7 37.2 - - + -
19C VAL* 4.8 11.0 - - + -
22C LEU* 4.8 5.1 - - + +
38C THR* 4.9 4.5 - - + -
41C LEU* 4.6 12.3 - - + -
42C LEU* 5.3 6.5 - - + -
45C ILE* 5.8 2.9 - - + -
64C GLU* 2.9 41.0 + - + +
65C GLY* 3.3 5.1 + - - +
67C ARG* 1.3 77.0 - - + +
69C THR* 1.3 62.9 + - + +
71C ALA* 3.4 18.6 + - + +
72C GLN 3.6 7.3 + - - +
78C VAL* 4.4 30.2 - - + +
79C GLY* 6.2 0.2 - - - -
82C VAL* 3.8 24.5 - - + -
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Residues in contact with THR 69 (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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65C GLY 2.9 18.5 + - - +
66C ARG* 3.2 15.9 + - - +
68C MET* 1.3 74.2 - - + +
70C ALA* 1.3 62.8 + - - +
71C ALA 3.2 0.4 - - - -
72C GLN 3.3 24.6 - - - -
73C PRO* 3.3 14.3 - - - +
75C GLU 5.5 4.3 - - - +
76C THR* 5.8 4.0 - - - +
78C VAL* 5.6 0.4 - - + -
79C GLY* 4.2 18.6 - - - +
83C ARG* 5.9 0.9 - - - +
351C LEU* 3.9 18.0 - - + +
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Residues in contact with ALA 70 (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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325B ALA 4.6 4.0 - - - +
326B ASN* 6.1 0.3 - - - +
23C LYS* 4.0 12.4 + - - +
66C ARG 2.9 19.8 + - - +
67C ARG* 3.3 9.1 + - - +
69C THR* 1.3 75.3 + - - +
71C ALA* 1.3 64.8 + - - +
72C GLN* 4.6 0.2 - - - -
73C PRO* 5.0 3.3 - - - +
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Residues in contact with ALA 71 (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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325B ALA* 4.9 2.9 - - - +
19C VAL* 3.9 37.0 - - + +
22C LEU* 4.6 9.6 - - + -
23C LYS* 3.4 33.8 - - - +
67C ARG 2.9 12.1 + - - +
68C MET* 3.5 14.4 - - - +
69C THR 3.2 0.6 - - - -
70C ALA* 1.3 79.2 - - - +
72C GLN* 1.3 64.4 + - - +
73C PRO* 4.5 1.3 - - - +
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Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 4.6 11.6 + - - -
22C LEU* 3.4 28.4 + - + +
23C LYS 4.1 11.7 + - - -
24C ARG 5.7 1.0 + - - -
25C GLY* 5.8 0.4 + - - -
68C MET 3.6 4.3 + - - +
69C THR* 3.3 11.9 + - - +
70C ALA 3.4 0.2 - - - -
71C ALA* 1.3 82.7 + - + +
73C PRO* 1.3 81.7 - - - +
74C SER* 4.0 12.3 + - - +
75C GLU* 3.4 48.4 - - + +
287C LYS* 4.2 15.4 - - + +
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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