Contacts of the helix formed by residues 70 - 85 (chain C) in PDB entry 2H8C
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 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 5.3 0.6 - - - +
69C ARG* 1.3 76.0 + - - +
71C LEU* 1.3 66.8 + - - +
72C ASP* 3.3 17.8 - - - +
73C ASN* 2.8 37.1 + - - +
74C LEU* 4.0 7.6 + - - +
91D ASP* 5.7 3.8 + - - -
11Y G 2.7 50.0 + - - +
12Y T 3.6 10.7 + - - -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C CYS* 4.7 4.7 - - - -
63C MET* 3.8 31.2 - - + -
69C ARG 4.0 6.1 - - - +
70C ASN* 1.3 71.3 - - - +
72C ASP* 1.3 68.6 + - - +
74C LEU* 2.9 28.3 + - + +
75C GLN* 3.0 10.6 + - - +
99C VAL* 3.9 13.4 - - + +
101C LYS* 4.3 13.2 - - + +
94D VAL* 3.6 24.5 - - + +
95D VAL* 4.1 20.9 - - - +
97D TYR* 3.9 27.1 - - + -
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASN* 3.3 22.7 - - - +
71C LEU* 1.3 74.1 + - - +
73C ASN* 1.3 75.6 + - - +
75C GLN* 3.0 12.1 - - - +
76C LYS* 2.4 36.3 + - - +
72D ASP* 5.9 1.6 - - + +
75D GLN* 3.5 33.3 + - - +
76D LYS* 5.7 4.2 - - + +
79D PHE* 5.2 3.3 - - - -
97D TYR* 3.2 14.6 + - - +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 5.5 0.6 - - - +
14C ASN* 3.2 44.6 + - + +
70C ASN* 2.8 41.3 + - - +
71C LEU 3.0 0.8 + - - -
72C ASP* 1.3 88.8 + - - +
74C LEU* 1.3 62.2 + - + +
76C LYS* 3.3 8.8 - - - +
77C ALA* 3.0 28.9 + - - +
11Y G 3.0 20.1 + - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 3.4 47.1 - - + +
11C PRO* 4.0 21.8 - - + +
59C ILE* 5.1 0.4 - - - -
61C CYS* 3.5 28.7 - - + -
63C MET* 4.5 2.9 - - + -
69C ARG* 5.9 2.9 - - + -
70C ASN 4.0 7.9 - - - +
71C LEU* 2.9 24.3 + - + +
73C ASN* 1.3 76.6 - - + +
75C GLN* 1.3 66.5 + - - +
76C LYS 3.0 1.1 + - - -
77C ALA 4.6 0.2 - - - +
78C ALA* 2.8 30.9 + - - +
110C LEU* 4.2 17.3 - - + +
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Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.7 17.1 - - + +
71C LEU 3.0 8.1 + - - +
72C ASP* 3.0 29.1 - - - +
74C LEU* 1.3 73.7 - - - +
76C LYS* 1.3 72.5 + - - +
79C PHE* 3.1 43.7 + - + +
97C TYR* 3.3 33.8 + - + -
99C VAL* 3.9 16.4 - - + +
72D ASP* 3.2 35.2 + - - +
75D GLN* 4.3 0.2 - - - +
97D TYR* 4.0 0.9 - - - +
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Residues in contact with LYS 76 (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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14C ASN* 5.0 10.8 - - - +
18C TYR* 4.3 15.3 - - + +
72C ASP 2.4 22.5 + - - +
73C ASN* 3.3 16.6 - - - +
74C LEU 3.0 0.2 - - - -
75C GLN* 1.3 84.8 - - - +
77C ALA* 1.3 62.9 + - + +
79C PHE* 3.2 3.5 + - - +
80C ASP* 3.0 20.5 + - + +
72D ASP* 4.6 15.3 - - - +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 4.2 19.3 - - + -
12C PRO 5.4 2.2 - - - +
14C ASN* 6.6 0.2 - - - -
17C TYR* 3.7 40.8 + - + -
18C TYR* 4.5 2.0 - - + +
34C TYR* 4.7 1.8 - - + -
73C ASN 3.0 14.4 + - - +
74C LEU 4.3 0.7 - - - +
76C LYS* 1.3 74.2 - - - +
78C ALA* 1.3 67.8 + - - +
80C ASP* 3.6 4.3 - - - +
81C ALA* 2.7 28.1 + - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 5.5 0.2 - - - +
34C TYR* 5.1 4.7 - - - -
59C ILE* 4.4 16.8 - - + -
74C LEU 2.8 25.9 + - - +
75C GLN* 3.6 6.5 - - - +
77C ALA* 1.3 75.0 - - - +
79C PHE* 1.3 72.4 + - + +
81C ALA* 3.0 11.4 + - - +
82C LEU* 3.1 18.6 + - + +
110C LEU* 4.9 12.6 - - + +
112C LEU* 5.0 10.1 - - + -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 3.9 14.1 - - + -
59C ILE* 3.6 22.4 - - + -
75C GLN* 3.1 34.6 + - - +
76C LYS* 3.5 3.8 - - - +
78C ALA* 1.3 80.8 - - + +
80C ASP* 1.3 60.1 + - - +
82C LEU* 3.3 3.3 - - + +
83C THR* 2.4 33.7 + - - -
88C TRP* 3.8 23.1 - + + -
91C ASP* 4.3 14.4 - - + +
94C VAL* 3.9 29.6 - - + -
97C TYR* 3.7 40.8 - + + -
112C LEU* 5.7 0.4 - - + -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 2.8 31.2 + - + +
18C TYR* 4.5 9.8 + - - +
27C VAL* 5.7 0.2 - - - +
35C ARG* 2.9 35.7 + - - -
76C LYS 3.0 13.3 + - - +
77C ALA* 3.6 9.6 - - - +
79C PHE* 1.3 74.2 - - - +
81C ALA* 1.3 67.2 + - - +
83C THR* 2.9 7.7 + - - -
84C LYS* 2.9 21.1 + - - +
91C ASP* 4.9 3.1 + - - -
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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
----------------------------------------------------------
17C TYR* 4.1 4.5 - - - +
34C TYR* 4.0 11.7 - - + +
35C ARG* 4.3 10.7 - - - +
38C VAL* 3.6 34.1 - - + -
77C ALA 2.7 19.6 + - - +
78C ALA* 3.0 5.3 + - - +
80C ASP* 1.3 78.0 + - - +
82C LEU* 1.3 53.7 + - - +
84C LYS* 3.1 2.1 + - - +
85C ALA* 2.7 37.8 + - - +
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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
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6C ILE* 3.8 21.8 - - + -
38C VAL* 4.1 7.3 - - + +
42C ILE* 4.5 9.9 - - + -
57C ILE* 4.7 2.9 - - + -
78C ALA 3.1 11.1 + - - +
79C PHE* 3.3 11.2 - - + +
81C ALA* 1.3 75.7 - - - +
83C THR* 1.3 64.4 + - - +
85C ALA* 3.0 22.8 + - - +
87C PHE* 3.3 50.7 + - + +
88C TRP* 3.6 28.0 - - + -
112C LEU* 4.5 22.0 - - + -
114C ILE* 4.9 2.0 - - + -
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Residues in contact with THR 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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79C PHE 2.4 31.6 + - - -
80C ASP* 2.9 9.0 + - - -
82C LEU* 1.3 71.1 - - - +
84C LYS* 1.3 60.2 + - + +
86C GLY* 3.1 18.4 + - - -
88C TRP* 2.9 37.3 + - - +
89C LEU 4.0 15.5 - - - +
90C ASP* 4.5 1.8 - - - +
91C ASP* 3.5 22.7 + - - +
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Residues in contact with LYS 84 (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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35C ARG* 3.7 43.1 - - + +
39C ALA* 5.5 0.6 - - - +
80C ASP* 2.9 14.6 + - - +
81C ALA 3.8 2.0 - - - +
83C THR* 1.3 73.4 - - + +
85C ALA* 1.3 56.9 + - - +
86C GLY* 2.8 12.5 + - - -
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Residues in contact with ALA 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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35C ARG* 5.1 1.2 - - - +
38C VAL* 4.6 0.7 - - + -
39C ALA* 3.8 37.4 - - + +
42C ILE* 4.2 22.8 - - + +
48C ASP* 4.5 6.8 - - - +
81C ALA 2.7 22.6 + - - +
82C LEU* 3.0 12.8 + - - +
84C LYS* 1.3 70.1 - - - +
86C GLY* 1.3 61.5 + - - +
87C PHE* 2.8 8.7 + - + +
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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