Contacts of the helix formed by residues 56 - 72 (chain C) in PDB entry 2IHU
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 HIS 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.2 3.1 - - - -
54C THR* 2.8 18.9 + - - -
55C ARG* 1.3 79.6 - - + +
57C GLU* 1.3 66.6 + - - +
58C PHE* 3.1 37.0 + - + +
59C THR* 3.3 12.4 + - - +
87C ASN* 3.3 44.5 + - + -
469C ASN* 4.3 10.3 + - - +
471C SER* 6.5 0.4 - - - -
472C ASP* 3.4 10.0 + - - +
1502C K 3.6 21.1 - - - -
56D HIS* 4.4 19.4 + + - -
58D PHE* 6.0 2.8 - - - +
87D ASN* 5.5 2.2 - - - -
438D PHE* 5.2 0.9 - + - -
468D SER* 3.7 19.1 - - - +
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.7 22.2 - - + +
54C THR* 4.4 1.1 - - - -
56C HIS* 1.3 74.1 + - - +
58C PHE* 1.3 66.3 + - - +
60C ALA* 3.1 10.3 + - - +
61C GLY* 3.0 20.1 + - - -
78C TRP 4.5 2.5 - - - +
79C ALA* 3.8 14.9 - - + +
80C THR* 4.9 0.2 - - - +
84C GLY* 3.6 15.4 - - - +
87C ASN* 3.2 26.0 + - + -
88C LEU* 3.5 33.4 - - + +
438D PHE* 4.1 4.1 - - - -
600D TP9 2.5 36.2 + - - -
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Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 3.1 24.8 + - + +
57C GLU* 1.3 77.9 - - - +
59C THR* 1.3 61.0 + - - +
61C GLY* 3.2 2.3 + - - -
62C VAL* 3.0 50.8 + - + +
87C ASN 3.9 10.6 + - - +
90C THR* 3.6 28.5 - - + -
91C GLY* 3.9 7.1 - - - +
94C THR* 4.1 4.5 - - - -
437C SER* 3.5 30.7 - - - -
438C PHE 3.9 7.2 - - - -
439C GLY* 3.4 26.9 - - - -
440C TYR* 3.9 10.8 - - + -
443C PRO* 4.4 1.1 - - + -
469C ASN* 3.6 22.4 - - + -
56D HIS* 6.0 2.9 - - - +
87D ASN* 5.4 3.1 - - - +
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Residues in contact with THR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 3.8 11.4 - - + -
56C HIS* 3.3 8.0 + - - +
58C PHE* 1.3 76.4 - - - +
60C ALA* 1.3 56.2 + - - +
63C ALA* 3.0 29.5 + - + +
443C PRO* 3.3 29.7 - - + +
446C ILE* 4.1 10.3 - - + -
469C ASN* 3.1 22.7 + - - -
472C ASP* 2.6 46.3 + - + +
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 3.5 21.9 - - + +
32C GLY* 3.5 37.5 - - - +
54C THR* 3.6 14.1 + - + +
56C HIS 3.5 2.0 + - - -
57C GLU* 3.1 12.6 + - - +
59C THR* 1.3 80.2 - - - +
61C GLY* 1.3 61.6 + - - +
63C ALA* 3.5 0.6 + - - -
64C ALA* 3.1 21.1 + - - +
77C CYS* 4.0 4.3 - - + -
88C LEU* 4.6 2.7 - - + -
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU 3.0 13.8 + - - -
58C PHE 3.7 2.2 - - - -
60C ALA* 1.3 76.8 - - - +
62C VAL* 1.3 56.2 + - - +
64C ALA* 3.4 3.6 + - - +
65C ASP* 3.0 27.6 + - - +
77C CYS* 3.9 19.7 - - - -
88C LEU* 4.0 3.9 - - - +
91C GLY* 4.1 20.6 - - - +
102C VAL* 4.7 3.5 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.0 48.8 + - + +
61C GLY* 1.3 71.8 - - - +
63C ALA* 1.3 60.0 + - - +
65C ASP* 3.1 7.0 + - - +
66C VAL* 2.9 29.6 + - + +
91C GLY* 4.3 1.6 - - - -
94C THR* 4.0 19.5 - - + +
440C TYR* 3.6 31.4 - - + -
443C PRO* 3.6 26.7 - - + -
444C ALA 3.9 8.1 - - - +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 3.7 32.8 - - + -
54C THR* 5.8 0.4 - - + -
59C THR* 3.0 21.4 + - + +
60C ALA 3.8 0.7 - - - +
62C VAL* 1.3 76.4 - - - +
64C ALA* 1.3 57.6 + - - +
66C VAL* 3.9 0.4 - - - -
67C LEU* 2.9 31.7 + - - +
443C PRO* 3.5 22.3 - - + +
446C ILE* 4.3 10.3 - - + -
447C GLY* 4.1 6.2 - - - +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 4.0 11.1 - - + -
60C ALA 3.1 18.4 + - - +
61C GLY 3.7 4.3 - - - +
63C ALA* 1.3 72.1 - - - +
65C ASP* 1.3 65.7 + - - +
67C LEU* 4.6 0.4 - - - -
68C ALA* 3.0 25.8 + - - +
75C GLN* 3.5 7.7 - - + +
76C ALA 3.8 36.1 - - - +
77C CYS* 4.1 4.7 - - + -
102C VAL* 3.8 11.0 - - + -
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLY 3.0 15.2 + - - +
62C VAL* 3.1 11.0 + - - +
64C ALA* 1.3 76.5 - - - +
66C VAL* 1.3 65.1 + - - +
69C ARG* 3.1 56.8 + - - -
91C GLY 5.0 0.2 - - - +
94C THR* 3.9 22.1 - - + +
95C SER* 3.5 16.1 + - - -
98C ASP* 4.7 0.3 - - - +
100C SER* 2.5 36.2 + - - +
102C VAL* 3.5 7.5 - - + +
440C TYR* 4.2 2.9 + - - -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 2.9 22.2 + - + +
63C ALA 4.1 2.7 - - - +
65C ASP* 1.3 77.1 - - - +
67C LEU* 1.3 66.0 + - - +
69C ARG* 3.2 11.1 + - + +
70C ILE* 3.1 26.5 + - + +
430C LEU* 3.7 22.2 - - + -
440C TYR* 3.5 26.0 - - + +
444C ALA* 3.5 38.6 - - + +
447C GLY* 4.4 1.8 - - - -
448C ALA 3.8 10.8 - - - +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 4.8 11.2 - - + -
31C PHE* 3.8 25.8 - - + -
63C ALA 2.9 18.2 + - - +
64C ALA 3.9 1.1 - - - +
66C VAL* 1.3 76.1 - - - +
68C ALA* 1.3 52.2 + - - +
70C ILE* 3.4 0.7 + - - +
71C THR* 2.7 48.7 + - + +
75C GLN* 3.6 34.3 - - + +
447C GLY* 4.0 10.8 - - - +
450C MET* 4.4 9.9 - - + +
451C ALA* 3.8 37.2 - - + +
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Residues in contact with ALA 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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64C ALA 3.0 18.9 + - - +
65C ASP 3.6 4.9 - - - +
67C LEU* 1.3 76.3 - - - +
69C ARG* 1.3 57.2 + - - +
72C GLY* 2.8 30.3 + - - -
73C ARG 3.4 23.5 + - - +
75C GLN* 3.4 5.5 - - + +
100C SER* 4.3 1.8 - - - -
101C PRO* 3.7 37.7 - - + +
102C VAL* 4.5 0.2 - - + -
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Residues in contact with ARG 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 ASP* 3.1 47.2 + - - +
66C VAL* 3.6 19.4 - - + +
68C ALA* 1.3 80.2 - - - +
70C ILE* 1.3 63.2 + - + +
72C GLY* 3.7 6.1 + - - -
98C ASP* 3.2 37.6 + - - +
99C ARG 3.5 12.7 + - - +
100C SER* 3.9 4.2 - - - -
101C PRO* 5.5 1.3 - - - -
225C ALA* 5.9 1.0 - - - +
229C ARG* 5.8 6.5 - - + +
252C ILE* 4.3 16.0 - - - +
427C PHE* 3.4 56.4 - - + -
430C LEU* 5.0 10.0 - - - +
431C THR 5.9 1.6 - - - -
440C TYR* 4.1 7.4 + - - -
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Residues in contact with ILE 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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66C VAL* 3.1 26.5 + - + +
69C ARG* 1.3 78.9 - - + +
71C THR* 1.3 63.0 + - + +
427C PHE* 4.2 25.3 - - + -
430C LEU* 4.1 11.9 - - + -
448C ALA* 3.7 31.2 - - + +
451C ALA* 3.7 24.9 - - + +
452C ARG* 3.6 37.9 - - + +
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 2.7 44.5 + - + +
70C ILE* 1.3 75.8 - - + +
72C GLY* 1.3 62.8 + - - +
73C ARG* 3.2 58.4 + - - +
75C GLN* 3.4 12.1 + - - +
451C ALA* 4.7 9.0 - - + +
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA 2.8 19.1 + - - -
69C ARG 3.7 5.5 + - - -
70C ILE 3.4 2.2 - - - -
71C THR* 1.3 74.3 - - - +
73C ARG* 1.3 60.8 + - - +
74C PRO* 4.7 0.2 - - - +
101C PRO* 5.0 4.5 - - - -
157C MET* 4.2 18.2 - - - +
191C PRO 5.1 1.2 - - - +
192C ALA 4.5 10.4 - - - +
193C LYS* 5.6 0.3 - - - -
194C PRO* 6.0 0.9 - - - +
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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