Contacts of the helix formed by residues 44 - 62 (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 ASN 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP 3.5 2.6 + - - -
43C VAL* 1.3 73.2 - - - +
45C LEU* 1.3 63.6 + - - +
46C GLU* 2.9 27.2 + - - +
47C VAL* 3.2 12.4 + - + -
48C ALA* 2.7 33.4 + - - +
224C GLN* 3.0 42.5 + - - +
227C LEU* 3.2 33.8 - - + +
258C SER* 3.1 22.8 + - - +
41F ALA* 6.1 0.4 - - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 5.1 1.6 - - - -
39C MET* 3.5 29.3 - - - +
43C VAL 3.6 0.4 + - - -
44C ASN* 1.3 79.6 - - - +
46C GLU* 1.3 82.1 + - + +
48C ALA* 3.7 1.9 - - - +
49C ARG* 3.0 34.6 + - - +
224C GLN* 3.0 14.7 + - - +
37F MET* 4.0 49.6 - - + +
40F LEU* 4.7 12.6 - - + -
41F ALA* 3.8 22.2 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASN* 2.9 9.7 + - - +
45C LEU* 1.3 89.0 - - + +
47C VAL* 1.3 57.3 + - - +
49C ARG* 3.2 21.4 + - - +
50C ASP* 2.8 42.2 + - - +
227C LEU* 3.9 23.8 - - + +
261C HIS* 5.8 0.2 - - - -
37F MET* 6.4 1.1 - - + -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 4.0 6.1 - - + -
44C ASN* 3.2 27.5 + - + +
46C GLU* 1.3 75.5 - - - +
48C ALA* 1.3 53.5 + - - +
50C ASP* 3.3 6.7 + - - +
51C PHE* 2.8 34.9 + - + +
227C LEU* 4.0 17.3 - - + -
257C LEU* 3.9 23.8 - - + -
258C SER* 3.9 15.7 - - - -
261C HIS* 3.7 41.4 + - + +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 4.0 16.0 - - + +
38C LEU* 4.3 9.2 - - + -
39C MET* 4.1 19.3 - - + -
43C VAL* 3.8 15.7 - - + +
44C ASN 2.7 21.5 + - - +
45C LEU 3.7 5.2 - - - +
47C VAL* 1.3 73.2 - - - +
49C ARG* 1.3 57.5 + - - +
51C PHE* 4.0 4.4 - - - +
52C VAL* 3.1 35.5 + - - +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 3.8 19.7 - - - +
45C LEU* 3.0 30.4 + - - +
46C GLU* 3.2 22.5 + - - +
48C ALA* 1.3 73.8 - - - +
50C ASP* 1.3 70.4 + - - +
52C VAL* 3.3 1.7 + - - -
53C GLU* 3.0 44.2 + - + +
33F GLU* 5.6 4.0 + - - -
37F MET* 3.6 30.7 - - - +
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 2.8 25.6 + - - +
47C VAL 3.7 4.3 - - - +
49C ARG* 1.3 79.3 - - - +
51C PHE* 1.3 61.0 + - - +
53C GLU* 3.5 10.4 + - - +
54C ARG* 3.2 20.8 + - - +
261C HIS* 3.9 30.3 + - + +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 5.1 0.4 - - + -
38C LEU* 3.4 32.8 - - + -
47C VAL* 2.8 23.7 + - + +
48C ALA* 4.0 4.9 - - - +
50C ASP* 1.3 73.1 - - - +
52C VAL* 1.3 59.9 + - + +
54C ARG* 3.2 17.5 + - - +
55C VAL* 3.0 44.4 + - + +
78C VAL* 3.7 23.3 - - + -
81C ALA* 3.6 31.2 - - + -
82C LEU* 3.5 29.2 - - + -
85C ALA* 4.6 10.3 - - + -
257C LEU* 4.6 15.3 - - + -
261C HIS* 5.4 3.5 + - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.5 42.8 - - + +
34C ILE* 4.2 9.2 - - + -
35C ARG* 3.9 36.1 - - + +
38C LEU* 4.1 12.6 - - + -
48C ALA 3.1 21.4 + - - +
49C ARG 3.3 3.3 + - - +
51C PHE* 1.3 76.2 - - + +
53C GLU* 1.3 68.9 + - - +
55C VAL* 3.5 7.6 + - + +
56C ARG* 3.3 22.5 + - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 6.4 0.4 - - - +
31C LEU* 6.6 0.2 - - - -
35C ARG* 5.2 4.3 + - - -
49C ARG* 3.0 38.7 + - + +
50C ASP* 3.6 10.8 - - - +
51C PHE 3.2 0.2 - - - -
52C VAL* 1.3 84.4 - - - +
54C ARG* 1.3 62.5 - - - +
56C ARG* 3.1 32.7 + - - +
57C GLU* 3.1 31.3 + - + +
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Residues in contact with ARG 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 5.9 2.2 - - - +
50C ASP 3.2 9.8 + - - +
51C PHE* 3.2 18.5 + - - +
53C GLU* 1.3 80.1 - - - +
55C VAL* 1.3 60.7 + - - +
57C GLU* 3.4 7.9 + - - +
58C GLU* 2.9 57.9 + - + +
81C ALA* 3.4 33.7 + - - +
84C GLU* 3.4 28.3 - - - +
85C ALA* 3.5 22.4 - - - +
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.2 17.7 - - + -
34C ILE* 5.1 1.1 - - + -
51C PHE* 3.0 49.1 + - + +
52C VAL* 3.7 12.6 - - + +
53C GLU 3.2 0.6 - - - -
54C ARG* 1.3 75.2 - - - +
56C ARG* 1.3 52.5 + - - +
58C GLU* 3.1 4.3 + - - -
59C ALA* 2.7 33.7 + - + +
74C ILE* 4.9 3.1 - - + +
77C THR* 3.2 27.3 - - + +
78C VAL* 3.8 24.5 - - + -
81C ALA* 4.2 11.2 - - + -
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Residues in contact with ARG 56 (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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83A LYS* 5.7 4.0 - - - +
285A GLU* 3.1 43.2 + - - +
27C LEU* 4.4 22.3 - - + +
28C LYS* 5.7 2.2 - - - -
31C LEU* 3.5 33.0 - - + -
52C VAL 3.3 14.6 + - - +
53C GLU* 3.1 32.4 + - - +
55C VAL* 1.3 74.4 - - - +
57C GLU* 1.3 87.8 + - - +
58C GLU 3.1 1.6 - - - -
59C ALA* 3.8 7.8 - - - +
60C LEU* 3.0 50.1 + - - +
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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
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76A ALA* 4.5 11.2 - - - +
79A TYR* 4.2 22.1 - - + +
80A GLU* 3.5 38.6 - - + +
83A LYS* 4.0 33.1 + - - +
53C GLU* 3.1 26.5 + - + +
54C ARG* 3.6 7.4 - - - +
56C ARG* 1.3 95.3 + - - +
58C GLU* 1.3 60.4 + - - +
60C LEU* 3.7 11.0 + - - +
61C GLY* 3.5 13.9 + - - -
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Residues in contact with GLU 58 (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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72A GLU* 5.8 0.3 - - - +
76A ALA* 4.9 11.2 - - + +
80A GLU* 5.0 10.1 - - - +
54C ARG* 2.9 50.9 + - + +
55C VAL 3.3 7.4 - - - +
57C GLU* 1.3 76.6 - - - +
59C ALA* 1.3 58.6 + - - +
60C LEU 3.2 0.2 - - - -
61C GLY* 3.1 5.7 + - - +
62C LYS* 3.0 36.6 + - + +
77C THR* 3.9 12.0 - - + +
81C ALA* 3.6 24.3 + - - +
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Residues in contact with ALA 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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27C LEU* 5.1 2.5 - - + -
31C LEU* 6.1 0.7 - - + -
55C VAL* 2.7 22.1 + - + +
56C ARG* 3.3 12.3 + - + +
58C GLU* 1.3 72.3 - - - +
60C LEU* 1.3 57.4 + - - +
62C LYS* 3.0 19.0 + - - +
63C GLN 3.3 0.2 + - - -
64C VAL* 3.1 41.6 + - + +
73C VAL* 5.1 0.9 - - + -
74C ILE* 5.0 9.6 - - + -
77C THR* 3.9 19.9 - - + +
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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
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4A GLN* 5.6 3.6 - - - +
5A LEU* 5.0 1.2 - - - +
75A LEU* 3.8 9.9 - - - +
79A TYR* 4.3 38.6 + - + +
24C GLU* 5.5 3.6 - - - +
27C LEU* 4.7 10.8 - - + -
56C ARG* 3.0 45.7 + - + +
57C GLU* 3.8 8.1 - - - +
58C GLU 3.2 0.2 - - - -
59C ALA* 1.3 73.1 - - - +
61C GLY* 1.3 61.0 + - - +
63C GLN* 3.0 19.4 + - - +
64C VAL* 3.9 11.2 - - + +
65C LEU* 3.8 36.8 - - + -
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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
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13A ILE* 5.1 0.2 - - - +
71A ALA 5.1 0.2 - - - +
72A GLU* 3.8 26.8 - - - +
75A LEU* 3.6 30.8 - - - +
76A ALA* 4.5 4.5 - - - -
79A TYR* 5.0 0.8 - - - -
57C GLU 3.5 7.5 + - - -
58C GLU* 3.1 10.5 + - - -
60C LEU* 1.3 75.4 - - - +
62C LYS* 1.3 55.4 + - - +
63C GLN* 2.9 17.0 + - - -
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Residues in contact with LYS 62 (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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17A ARG* 4.6 8.2 + - - +
72A GLU* 3.4 38.5 + - + +
58C GLU* 3.0 31.5 + - - +
59C ALA 3.0 7.3 + - - +
61C GLY* 1.3 71.9 - - - +
63C GLN* 1.3 72.8 + - - +
64C VAL* 3.3 2.0 + - - -
67C SER* 5.6 0.3 - - - -
73C VAL* 3.6 24.0 + - + +
76C ALA* 4.3 4.6 - - - +
77C THR* 3.2 36.7 + - - +
80C GLU* 3.4 23.8 + - - -
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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