Contacts of the helix formed by residues 58 - 77 (chain C) in PDB entry 2E52
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 THR 58 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 4.2 13.9 - - + -
57C SER* 1.3 73.9 - - - +
59C GLN* 1.3 58.6 + - + +
61C LYS* 3.2 7.3 + - - +
62C LEU* 2.9 38.8 + - + +
10H G 3.6 21.9 + - - -
11H G 2.6 29.1 + - - +
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Residues in contact with GLN 59 (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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12C ILE* 3.8 26.9 - - + +
13C GLU* 3.0 44.4 + - - +
16C THR* 4.6 7.2 + - - +
52C ALA 4.8 2.8 - - - +
53C ILE* 3.9 30.8 - - + +
54C LYS 5.0 1.4 + - - -
57C SER* 3.2 10.5 + - - +
58C THR* 1.3 79.0 - - + +
60C GLU* 1.3 56.3 + - - +
62C LEU* 3.4 5.9 + - + +
63C PHE* 2.9 29.6 + - - +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.0 13.6 - - + +
53C ILE* 3.5 13.4 - - + +
54C LYS 3.8 1.6 - - - +
55C PRO* 3.3 4.6 - - - +
56C SER* 2.7 28.0 + - - -
57C SER* 3.1 21.4 + - - +
58C THR 3.2 0.2 - - - -
59C GLN* 1.3 76.9 - - - +
61C LYS* 1.3 58.5 + - + +
63C PHE* 3.3 5.9 + - - +
64C SER* 2.9 27.4 + - - -
113C ARG* 2.8 36.9 + - - -
5F A 4.4 10.0 - - + +
6F G 3.3 34.0 + - - +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.7 16.7 - - + -
56C SER* 2.8 29.3 + - - +
57C SER 3.3 5.3 + - - +
58C THR* 3.2 8.6 + - - +
60C GLU* 1.3 75.7 + - + +
62C LEU* 1.3 58.9 + - - +
64C SER* 3.5 7.6 + - - -
65C LYS* 2.9 28.2 + - - +
88C ARG* 4.0 22.1 + - - +
4F A 4.1 17.5 - - - -
5F A 4.3 13.9 + - + +
9H T 2.7 30.3 + - - -
10H G 3.4 23.9 + - - +
11H G 4.0 22.0 - - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 4.2 27.8 - - + +
15C LEU* 4.3 28.7 - - + +
20C PHE* 3.5 23.8 - - + -
23C ALA* 3.6 28.3 - - + -
24C THR* 4.6 2.5 - - - +
27C LEU* 3.4 25.3 - - + +
58C THR* 2.9 29.4 + - + +
59C GLN* 3.7 7.4 - - + +
61C LYS* 1.3 74.6 - - - +
63C PHE* 1.3 60.9 + - - +
65C LYS* 3.3 2.0 + - + -
66C ALA* 2.8 25.5 + - - +
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Residues in contact with PHE 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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5C LEU* 4.3 9.0 - - + -
8C LEU* 4.2 8.1 - - + -
9C LEU* 4.0 23.3 - - + -
12C ILE* 3.9 13.6 - - + +
45C SER 4.3 1.6 - - - -
46C ILE* 3.2 48.8 - - + +
48C ILE 3.4 24.0 - - - -
49C LEU* 3.3 32.5 - - + -
50C PRO* 3.7 17.3 - - + -
53C ILE* 4.0 6.5 - - + -
59C GLN 2.9 18.0 + - - +
60C GLU 3.3 4.9 + - - +
62C LEU* 1.3 76.3 - - - +
64C SER* 1.3 58.9 + - - +
66C ALA* 3.3 5.7 + - - +
67C GLY* 3.0 22.5 + - - -
111C SER* 4.3 3.1 - - - -
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 5.9 0.7 - - - -
60C GLU 2.9 15.7 + - - -
61C LYS* 3.6 6.3 - - - -
62C LEU 3.2 0.2 - - - -
63C PHE* 1.3 77.2 - - - +
65C LYS* 1.3 60.4 + - - +
67C GLY* 3.0 16.1 + - - +
68C ASP* 3.0 22.2 + - - +
88C ARG* 5.1 1.8 + - - -
109C ALA* 5.1 3.8 + - - +
111C SER* 5.7 3.4 - - - -
5F A 3.3 47.0 + - - -
6F G 4.3 6.7 + - - -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.5 11.7 - - + -
24C THR* 3.7 42.4 - - + +
27C LEU* 4.4 3.8 - - + -
61C LYS 2.9 18.1 + - - +
62C LEU* 3.3 8.3 + - - +
64C SER* 1.3 72.5 + - - +
66C ALA* 1.3 60.1 - - - +
68C ASP* 3.1 22.4 + - + +
69C ILE* 2.8 40.5 + - + +
84C PRO* 4.4 11.6 - - - +
85C LEU 2.7 32.9 + - - -
86C GLU* 4.3 8.0 + - - +
88C ARG* 4.8 13.4 - - - +
12H C 5.7 2.9 - - - -
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Residues in contact with ALA 66 (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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8C LEU* 3.9 28.5 - - + -
12C ILE* 4.9 0.2 - - + -
27C LEU* 4.0 5.8 - - + +
31C ILE* 3.8 13.2 - - + +
46C ILE* 4.0 9.6 - - + -
62C LEU 2.8 14.3 + - - +
63C PHE* 3.4 12.3 - - - +
65C LYS* 1.3 76.0 - - - +
67C GLY* 1.3 51.5 + - - +
69C ILE* 3.3 6.1 + - - +
70C VAL* 2.8 41.4 + - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.6 21.6 - - - +
63C PHE 3.0 9.0 + - - -
64C SER* 3.0 10.5 + - - -
66C ALA* 1.3 75.1 - - - +
68C ASP* 1.3 55.8 + - - +
70C VAL* 3.5 0.5 + - - +
71C LEU* 2.9 30.3 + - - +
109C ALA* 3.8 9.4 - - - -
111C SER* 5.7 2.0 - - - -
169C TRP* 3.6 13.6 - - - -
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.0 16.3 + - - +
65C LYS* 3.1 31.2 + - + +
67C GLY* 1.3 74.4 - - - +
69C ILE* 1.3 58.4 + - - +
71C LEU* 3.4 0.7 + - - -
72C ALA* 3.0 26.3 + - - +
84C PRO* 4.1 10.5 - - + +
88C ARG* 5.5 2.1 + - - -
93C ASP* 3.1 45.8 - - - +
94C VAL* 3.3 23.9 - - + +
109C ALA* 3.5 9.5 - - - +
5F A 5.8 0.7 - - - +
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Residues in contact with ILE 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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24C THR* 4.1 3.4 - - + +
27C LEU* 3.6 30.7 - - + -
28C ILE* 3.7 29.4 - - + -
31C ILE* 3.7 23.6 - - + -
32C TYR* 3.6 23.8 - - + -
65C LYS* 2.8 40.5 + - + +
66C ALA* 3.7 4.9 - - - +
68C ASP* 1.3 68.5 - - - +
70C VAL* 1.3 61.9 + - - +
72C ALA* 3.3 4.2 + - - +
73C LYS* 2.9 27.0 + - - +
84C PRO* 4.1 17.9 - - + -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 3.9 19.1 - - + -
39C VAL* 4.6 4.6 - - + +
42C LEU* 3.8 31.4 - - + -
43C VAL* 3.6 40.2 - - + +
46C ILE* 4.2 17.9 - - + -
66C ALA 2.8 27.1 + - - +
67C GLY* 3.7 5.6 - - - +
69C ILE* 1.3 71.2 - - - +
71C LEU* 1.3 58.8 + - - +
73C LYS* 3.3 3.1 + - - +
74C ALA* 2.8 27.5 + - - +
169C TRP* 4.5 2.5 - - + -
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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
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67C GLY 2.9 18.9 + - - +
68C ASP 3.7 4.5 - - - +
70C VAL* 1.3 78.6 - - - +
72C ALA* 1.3 57.4 + - - +
74C ALA* 3.2 4.7 + - - +
75C PHE* 2.9 58.4 + - + -
94C VAL* 4.1 9.4 - - + -
107C ALA* 3.9 16.2 - - + -
108C ASP 3.8 21.8 - - - +
109C ALA* 3.9 16.6 - - + +
142C THR* 3.9 21.5 - - + +
167C PHE* 5.7 0.2 - - + -
169C TRP* 4.2 8.3 - - + -
172C LEU* 3.6 26.0 - - + -
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Residues in contact with ALA 72 (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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32C TYR* 3.7 19.5 - - - +
68C ASP 3.0 17.2 + - - +
69C ILE 3.3 2.9 + - - +
71C LEU* 1.3 76.0 - - - +
73C LYS* 1.3 58.3 + - - +
75C PHE 3.3 1.4 + - - -
76C GLN* 3.0 32.9 + - - +
82C SER* 3.4 23.4 - - - +
83C LYS* 3.8 22.2 - - - +
84C PRO* 3.8 1.8 - - + -
94C VAL* 4.1 4.6 - - + +
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Residues in contact with LYS 73 (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 ILE* 4.2 10.3 - - + +
32C TYR* 3.2 46.0 + - + +
34C LEU 4.5 5.8 + - - -
39C VAL* 3.8 35.4 - - + -
69C ILE 2.9 17.6 + - - +
70C VAL* 3.6 5.2 - - - +
72C ALA* 1.3 77.0 - - - +
74C ALA* 1.3 63.3 + - - +
76C GLN* 3.2 27.8 + - + +
77C LEU* 3.0 38.2 + - + +
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Residues in contact with ALA 74 (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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39C VAL* 4.6 3.1 - - + +
43C VAL* 4.1 6.7 - - + -
70C VAL 2.8 21.0 + - - +
71C LEU 3.6 2.9 - - - +
73C LYS* 1.3 73.8 - - - +
75C PHE* 1.3 61.1 + - - +
77C LEU* 3.1 12.6 + - - +
78C LEU* 3.1 23.8 + - - +
172C LEU* 3.6 32.3 - - + -
176C LEU* 3.9 20.7 - - + +
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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
----------------------------------------------------------
71C LEU* 2.9 50.5 + - + -
72C ALA 3.3 1.5 + - - +
74C ALA* 1.3 76.1 - - - +
76C GLN* 1.3 63.1 + - - +
78C LEU* 3.1 27.7 + - + +
79C ASN 3.4 0.3 + - - -
80C LEU* 3.1 25.8 + - + +
82C SER* 3.6 27.1 - - - +
94C VAL* 4.1 5.2 - - + -
96C ALA* 4.1 13.7 - - + -
105C LEU* 4.0 19.7 - - + -
107C ALA* 3.8 18.8 - - + -
140C VAL* 4.5 11.0 - - + -
142C THR* 5.1 0.2 - - - -
167C PHE* 5.2 4.3 - + - -
172C LEU* 5.5 2.0 - - + -
192C TRP* 3.5 34.5 - + - -
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Residues in contact with GLN 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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32C TYR* 3.4 33.3 + - - -
72C ALA 3.0 18.6 + - - +
73C LYS* 3.3 30.6 + - + +
75C PHE* 1.3 75.0 - - - +
77C LEU* 1.3 60.3 + - + +
79C ASN* 2.8 22.2 + - - +
80C LEU 3.3 13.9 + - - +
81C ASN* 5.2 0.4 - - - -
82C SER* 3.0 32.8 + - - +
83C LYS* 5.1 2.4 - - - +
99C LYS* 5.3 1.9 + - - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 4.1 44.1 + - + +
39C VAL* 3.7 40.4 - - + -
40C ILE* 5.8 0.4 - - + -
73C LYS* 3.0 31.3 + - + +
74C ALA* 3.1 8.9 + - - +
76C GLN* 1.3 77.3 - - + +
78C LEU* 1.3 60.5 + - - +
79C ASN 3.1 1.5 + - - -
176C LEU* 3.6 20.8 - - + +
180C LEU 4.5 1.4 - - - +
181C GLU* 3.9 18.0 - - - +
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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
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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