Contacts of the helix formed by residues 44 - 58 (chain P) in PDB entry 6CNB
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 SER 44 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42P ILE 3.5 3.6 + - - -
43P GLY* 1.3 77.7 - - - +
45P LEU* 1.3 68.3 + - - +
46P THR* 4.3 5.9 + - - +
47P ASP* 3.1 26.9 + - - +
48P LEU* 3.1 19.4 + - - +
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Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P GLY 3.9 0.2 + - - -
44P SER* 1.3 75.8 - - - +
46P THR* 1.3 68.8 + - - +
48P LEU* 3.6 2.4 - - - +
49P MET* 3.3 31.7 + - + +
365S LYS 5.5 0.4 - - - -
366S LEU* 3.5 51.4 - - + +
367S ASN 5.9 1.6 - - - +
371S THR* 4.8 9.0 - - + -
372S MET* 3.6 42.1 - - + +
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Residues in contact with THR 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P SER* 4.5 7.0 - - - +
45P LEU* 1.3 87.2 - - - +
47P ASP* 1.3 61.3 + - + +
49P MET* 4.4 3.6 - - - -
50P SER* 2.5 42.2 + - - -
366S LEU* 6.1 1.1 - - - -
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Residues in contact with ASP 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLN 4.9 10.0 + - - -
14P ASN* 4.3 12.0 + - - -
43P GLY* 4.9 4.9 - - - -
44P SER* 3.1 28.0 + - - +
46P THR* 1.3 85.0 - - + +
48P LEU* 1.3 62.9 + - - +
50P SER* 4.0 4.5 - - - -
51P ILE* 3.3 20.8 + - - +
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Residues in contact with LEU 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASN* 4.4 8.1 - - - +
18P LEU* 5.1 3.4 - - + +
33P GLN* 3.3 31.2 - - + +
36P LEU* 3.9 32.5 - - + -
37P GLN* 4.8 8.7 - - + -
40P MET 4.9 1.6 - - - +
41P GLY 5.8 0.2 - - - +
43P GLY* 3.3 34.7 - - - +
44P SER 3.1 11.4 + - - +
45P LEU 3.6 2.7 - - - +
47P ASP* 1.3 78.4 - - - +
49P MET* 1.3 76.9 + - + +
51P ILE* 3.2 10.6 - - - +
52P VAL* 3.0 33.7 + - + +
372S MET* 3.8 15.5 - - + -
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Residues in contact with MET 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P GLN* 2.5 40.4 - - - +
45P LEU* 3.3 21.7 + - + +
46P THR* 3.2 5.9 + - - +
48P LEU* 1.3 82.5 - - + +
50P SER* 1.3 61.5 + - - +
52P VAL* 3.3 28.4 - - + +
53P GLN* 2.9 32.5 + - + +
72P PHE* 5.8 2.0 - - + -
364S LEU* 3.5 43.5 - - + -
372S MET* 4.2 9.2 - - + -
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Residues in contact with SER 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P THR* 2.5 28.9 + - - -
47P ASP* 4.0 5.4 - - - -
49P MET* 1.3 73.9 - - - +
51P ILE* 1.3 58.9 + - - +
53P GLN* 3.3 6.2 + - - +
54P GLU* 2.9 30.3 + - - +
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Residues in contact with ILE 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLN 3.1 28.9 - - - +
11P LEU* 3.2 26.9 - - + +
14P ASN* 3.4 25.1 - - + +
15P ALA* 3.3 16.4 - - - +
18P LEU* 5.1 5.4 - - + -
47P ASP* 3.3 14.3 + - - +
48P LEU 3.2 16.4 - - - +
50P SER* 1.3 75.9 - - - +
52P VAL* 1.3 65.6 + - - +
54P GLU* 4.3 8.3 - - - +
55P LEU* 2.8 45.3 + - + +
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Residues in contact with VAL 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P LEU* 4.6 17.0 - - + -
33P GLN* 6.4 0.7 - - + -
36P LEU* 4.9 9.6 - - + -
48P LEU* 3.0 27.5 + - + +
49P MET* 3.3 34.5 - - + +
51P ILE* 1.3 77.7 - - - +
53P GLN* 1.3 66.6 + - - +
55P LEU* 3.1 0.4 + - - -
56P LEU 3.0 19.4 + - - -
61P ILE* 3.1 36.1 - - + +
63P LEU* 6.2 0.4 - - + -
72P PHE* 4.5 15.3 - - + -
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Residues in contact with GLN 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P MET* 2.9 20.3 + - + +
50P SER* 3.6 6.5 - - - +
52P VAL* 1.3 76.5 - - + +
54P GLU* 1.3 58.1 + - - +
56P LEU* 3.4 10.7 + - - +
57P ASP* 2.9 26.6 + - + +
361S ALA* 3.9 13.7 - - - +
362S ILE 2.7 28.5 + - - +
363S GLN* 3.1 52.8 + - - +
364S LEU* 4.2 5.5 - - - +
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Residues in contact with GLU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 3.4 31.4 - - + +
50P SER* 2.9 20.5 + - - +
51P ILE* 4.0 7.8 - - - +
53P GLN* 1.3 75.7 - - - +
55P LEU* 1.3 53.4 + - - +
57P ASP* 2.9 11.5 + - + +
58P LYS* 2.3 75.4 + - + +
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Residues in contact with LEU 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 3.7 20.6 - - + -
14P ASN 4.8 0.7 - - - +
15P ALA* 3.6 34.8 - - + +
18P LEU* 4.7 7.0 - - + -
51P ILE* 2.8 43.4 + - + +
52P VAL* 3.7 0.4 - - - +
54P GLU* 1.3 73.2 - - - +
56P LEU* 1.3 51.7 + - - +
58P LYS* 3.9 4.3 - - + -
59P ASN 2.7 11.3 + - - -
60P LEU* 2.3 65.4 + - + -
61P ILE* 3.6 29.2 - - + -
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Residues in contact with LEU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P VAL 3.0 9.0 + - - +
53P GLN* 3.7 20.4 - - - +
55P LEU* 1.3 74.8 - - - +
57P ASP* 1.3 60.0 + - - +
59P ASN* 3.0 19.7 + - - +
61P ILE* 3.4 32.2 - - + +
62P LYS* 4.8 12.1 - - + +
63P LEU* 4.8 24.9 - - + +
83P LYS* 4.2 15.5 + - - +
361S ALA* 4.8 13.0 - - + -
362S ILE* 5.0 9.0 - - + +
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Residues in contact with ASP 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P GLN* 2.9 18.7 + - + +
54P GLU* 2.9 17.7 + - + +
56P LEU* 1.3 76.3 - - - +
58P LYS* 1.3 63.2 + - - +
59P ASN* 3.2 6.1 + - - +
360S THR* 5.3 13.0 + - - -
361S ALA* 5.3 11.5 - - + +
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Residues in contact with LYS 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 3.7 19.3 - - + +
54P GLU* 2.3 65.8 + - + +
55P LEU* 3.1 9.0 - - - +
57P ASP* 1.3 73.2 - - - +
59P ASN* 1.3 81.1 + - - +
60P LEU* 3.4 19.3 + - + +
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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
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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