Contacts of the helix formed by residues 23 - 40 (chain C) in PDB entry 2CNW
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 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG 6.0 0.2 - - - +
22C ILE* 1.3 77.3 - - - +
24C GLU* 1.3 64.9 + - - +
25C GLU* 3.8 8.6 + - - +
26C ASP* 3.2 23.3 + - - +
27C LEU* 3.0 23.4 + - - +
65C LEU* 4.4 2.0 - - - +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.1 43.4 + - + +
23C THR* 1.3 72.6 - - - +
25C GLU* 1.3 60.9 + - - +
27C LEU* 3.4 31.4 - - + +
28C LYS* 3.6 9.7 + - - +
60C LEU* 5.5 4.2 - - - +
65C LEU* 3.8 27.5 - - + +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 3.1 8.4 + - - +
24C GLU* 1.3 78.3 - - - +
26C ASP* 1.3 63.0 + - - +
28C LYS* 3.4 17.7 - - + +
29C ALA* 3.3 21.1 + - + +
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Residues in contact with ASP 26 (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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15C ARG* 5.9 1.2 + - - -
16C LEU* 4.0 18.6 - - - +
22C ILE* 4.4 9.6 - - + +
23C THR* 3.2 25.9 + - - +
25C GLU* 1.3 73.8 - - - +
27C LEU* 1.3 62.1 + - - +
29C ALA* 3.3 8.7 + - - +
30C THR* 2.7 45.1 + - - -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 4.1 16.3 - - + +
23C THR 3.0 13.1 + - - +
24C GLU* 3.4 29.6 - - + +
26C ASP* 1.3 72.8 - - - +
28C LYS* 1.3 60.4 + - + +
30C THR* 2.9 22.7 + - - -
31C LEU* 2.9 25.8 + - + +
56C ARG* 4.4 35.0 - - + +
59C ALA* 5.1 3.1 - - + -
60C LEU* 4.7 9.9 - - + -
64C VAL* 4.0 29.8 - - + -
65C LEU* 4.5 11.7 - - + -
74C ILE* 5.3 5.6 - - + +
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Residues in contact with LYS 28 (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 GLU 3.6 10.7 + - - +
25C GLU* 3.4 22.8 + - + +
27C LEU* 1.3 81.0 - - + +
29C ALA* 1.3 57.6 + - + +
31C LEU* 3.7 18.9 - - + +
32C ARG* 3.2 22.2 + - - +
35C ARG* 4.3 4.9 + - - -
56C ARG* 5.7 2.5 - - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 5.1 4.4 + - - +
25C GLU* 3.3 17.1 + - + +
26C ASP* 3.8 11.9 - - - +
27C LEU 3.1 0.8 - - - -
28C LYS* 1.3 76.5 - - + +
30C THR* 1.3 63.1 + - - +
32C ARG* 3.0 52.9 + - - +
33C GLU* 3.8 5.2 + - - +
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Residues in contact with THR 30 (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 ALA* 4.7 16.7 + - + +
13C ILE* 6.1 2.2 - - + -
15C ARG* 6.1 0.7 - - - +
16C LEU* 3.9 30.3 - - + +
22C ILE* 5.1 1.0 - - - +
26C ASP* 2.7 32.1 + - - -
27C LEU* 2.9 7.2 + - - -
29C ALA* 1.3 75.4 - - - +
31C LEU* 1.3 64.5 + - - +
32C ARG 3.3 0.2 - - - -
33C GLU* 3.3 9.1 + - - +
34C ILE* 3.3 23.1 + - + +
74C ILE* 4.6 22.7 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.9 25.2 + - + +
28C LYS* 3.7 22.0 - - + +
30C THR* 1.3 76.2 - - - +
32C ARG* 1.3 57.5 + - - +
34C ILE* 3.2 23.2 + - + +
35C ARG* 2.8 31.9 + - - +
52C VAL* 3.5 25.3 - - + +
55C VAL* 4.2 13.7 - - + -
56C ARG* 3.5 47.8 - - + -
59C ALA* 6.1 1.1 - - + -
74C ILE* 4.8 9.6 - - + -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 4.0 25.1 - - - +
28C LYS 3.2 12.6 + - - +
29C ALA* 3.0 45.2 + - - +
31C LEU* 1.3 78.7 - - - +
33C GLU* 1.3 62.0 + - - +
35C ARG* 3.3 34.7 + - - +
36C ARG* 3.0 52.9 + - - +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 3.2 41.0 + - - +
9C LEU* 4.5 2.5 - - - +
11C GLU* 5.8 0.7 - - - +
12C ALA* 4.2 19.0 + - + +
15C ARG* 4.2 21.5 - - - +
29C ALA 3.8 3.0 + - - +
30C THR* 3.3 12.7 + - - +
31C LEU 3.2 0.4 - - - -
32C ARG* 1.3 87.8 + - - +
34C ILE* 1.3 59.4 + - - +
36C ARG* 3.4 22.8 + - - +
37C ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.1 22.2 - - + -
30C THR* 3.3 16.8 + - + +
31C LEU* 3.2 22.1 + - + +
33C GLU* 1.3 74.6 - - + +
35C ARG* 1.3 60.2 + - - +
37C ALA* 3.0 3.6 + - - +
38C LEU* 3.0 38.6 + - + +
51C PHE* 5.1 0.9 - - + -
52C VAL* 4.2 14.1 - - + -
55C VAL* 5.1 0.7 - - + -
74C ILE* 3.6 31.9 - - + -
75C LEU* 6.5 0.9 - - + -
78C VAL* 3.8 36.1 - - + -
292C LEU* 5.7 1.1 - - + -
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Residues in contact with ARG 35 (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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28C LYS 4.3 5.5 + - - -
31C LEU* 2.8 16.6 + - - +
32C ARG* 3.3 45.8 + - - +
34C ILE* 1.3 76.9 - - - +
36C ARG* 1.3 59.8 + - - +
38C LEU* 3.6 5.6 + - - +
39C MET* 3.2 39.4 + - + +
45C LEU 5.1 0.9 - - - +
48C ALA* 4.0 13.3 - - + +
49C ARG* 3.8 34.3 - - - +
52C VAL* 3.9 20.6 - - + +
53C GLU* 5.2 4.4 + - - -
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Residues in contact with ARG 36 (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 ARG* 4.1 15.7 - - - +
32C ARG* 3.0 40.1 + - + +
33C GLU* 3.8 21.6 + - - +
34C ILE 3.2 0.4 - - - -
35C ARG* 1.3 75.3 - - + +
37C ALA* 1.3 59.9 + - - +
39C MET* 3.3 15.2 + - + +
40C ASP* 2.8 30.0 + - - +
36F GLU* 4.5 15.0 + - - -
40F LEU* 5.9 3.0 - - - +
46F LEU* 3.3 41.7 + - + +
49F THR* 6.1 2.8 - - - +
50F GLU* 3.0 44.3 + - - +
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Residues in contact with ALA 37 (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 SER* 4.6 5.8 - - - +
8C ARG* 3.6 20.1 - - + +
9C LEU* 3.9 31.0 - - + -
33C GLU 3.0 18.3 + - - +
34C ILE 3.0 5.3 + - - +
36C ARG* 1.3 77.4 - - - +
38C LEU* 1.3 58.4 + - + +
40C ASP* 3.5 6.8 - - - +
41C ALA* 3.2 24.1 + - - +
291C ILE 4.9 2.6 - - - +
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Residues in contact with LEU 38 (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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34C ILE* 3.0 24.4 + - + +
35C ARG 3.8 4.3 - - - +
37C ALA* 1.3 75.5 - - + +
39C MET* 1.3 59.7 + - - +
41C ALA* 3.0 13.9 + - - -
43C VAL* 2.9 41.5 + - + +
48C ALA* 4.3 14.1 - - + +
51C PHE* 3.4 36.8 - - + -
52C VAL* 4.1 13.9 - - + -
82C LEU* 4.7 5.6 - - + -
257C LEU* 5.0 6.5 - - + -
291C ILE* 3.8 26.5 - - + -
292C LEU* 4.3 16.6 - - + -
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Residues in contact with MET 39 (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* 3.2 36.3 + - + +
36C ARG* 3.7 21.5 - - + +
38C LEU* 1.3 73.7 - - - +
40C ASP* 1.3 57.9 + - - +
41C ALA 3.0 4.3 - - - -
42C ASP* 2.8 22.7 + - - +
43C VAL 3.5 19.4 - - - +
45C LEU* 3.5 35.7 - - + +
48C ALA* 4.1 5.2 - - + -
224C GLN* 4.2 9.6 + - - +
40F LEU* 4.2 32.3 - - + -
46F LEU* 4.9 7.6 - - + -
234F GLN* 4.4 5.2 + - - +
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 3.1 25.8 + - - +
36C ARG 2.8 17.5 + - - +
37C ALA* 3.5 11.2 - - - +
38C LEU 3.3 0.2 - - - -
39C MET* 1.3 75.5 - - - +
41C ALA* 1.3 55.5 + - - +
42C ASP* 3.3 3.0 + - - +
252C ARG* 4.8 3.9 - - - +
46F LEU* 3.7 18.0 + - + +
234F GLN* 3.9 28.9 - - - +
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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