Contacts of the helix formed by residues 33 - 40 (chain P) in PDB entry 6CNC
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 GLN 33 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31P PHE* 4.8 0.2 - - - -
32P THR* 1.3 74.8 - - - +
34P GLN* 1.3 64.8 + - - +
35P GLU 3.2 0.2 - - - -
36P LEU* 3.1 28.9 + - + +
37P GLN* 3.9 2.9 + - - +
48P LEU* 4.1 0.6 - - - +
49P MET* 2.4 45.2 - - - +
69P GLU* 2.9 28.7 - - + +
70P LEU 3.4 6.1 + - - -
72P PHE* 3.5 27.0 - - + -
364S LEU* 4.2 3.5 - - - +
372S MET* 2.7 46.6 - - + +
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Residues in contact with GLN 34 (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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32P THR* 3.1 12.6 + - - +
33P GLN* 1.3 78.7 - - - +
35P GLU* 1.3 68.2 + - - +
36P LEU 3.2 0.5 + - - -
37P GLN* 3.2 28.8 + - - +
38P LYS* 3.2 15.7 + - + +
69P GLU* 4.7 5.8 - - + +
371S THR* 6.0 3.8 - - - +
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Residues in contact with GLU 35 (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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27P ILE* 3.8 33.8 - - + +
30P LEU 5.1 2.0 - - - +
31P PHE* 3.4 27.8 - - + -
32P THR* 3.2 18.0 + - - +
33P GLN 3.2 1.0 - - - -
34P GLN* 1.3 80.6 - - - +
36P LEU* 1.3 64.3 + - - +
38P LYS* 3.2 32.5 - - - +
39P GLN* 3.1 21.8 + - - +
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Residues in contact with LEU 36 (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* 4.5 16.8 - - + -
21P GLN* 5.3 8.1 - - - +
31P PHE* 3.8 18.0 - - + -
33P GLN* 3.1 24.3 + - + +
35P GLU* 1.3 77.4 - - - +
37P GLN* 1.3 65.0 + - + +
39P GLN* 3.0 4.1 + - - -
40P MET* 2.7 58.2 + - + +
48P LEU* 3.6 47.1 - - + -
52P VAL* 4.2 20.4 - - + -
72P PHE* 6.2 1.8 - - + -
372S MET* 4.6 1.6 - - + -
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Residues in contact with GLN 37 (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 3.9 2.7 + - - +
34P GLN* 3.2 30.2 + - - +
36P LEU* 1.3 79.5 - - + +
38P LYS* 1.3 62.4 + - - +
39P GLN 3.5 0.9 + - - +
41P GLY* 3.7 30.2 + - - +
45P LEU* 5.5 0.6 - - - +
48P LEU* 5.6 0.4 - - + -
371S THR* 3.5 22.2 - - - +
372S MET* 3.3 35.6 - - + +
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Residues in contact with LYS 38 (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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27P ILE* 6.1 1.6 - - + -
34P GLN* 3.2 8.3 + - + +
35P GLU* 3.2 42.0 - - - +
36P LEU 3.1 0.6 - - - -
37P GLN* 1.3 78.2 - - - +
39P GLN* 1.3 60.1 + - + +
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Residues in contact with GLN 39 (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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21P GLN* 2.9 48.6 + - - +
25P LYS* 5.4 6.1 - - - +
27P ILE* 5.1 14.1 - - + +
31P PHE* 5.9 1.0 - - - -
35P GLU 3.1 11.0 + - - +
36P LEU* 3.0 4.3 + - - +
37P GLN 4.5 0.5 - - - +
38P LYS* 1.3 80.4 - - + +
40P MET* 1.3 78.2 + - + +
41P GLY 3.9 2.4 + - - -
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Residues in contact with MET 40 (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* 5.3 7.4 - - - +
17P THR* 3.8 36.8 - - + +
18P LEU* 5.7 2.0 - - - -
21P GLN* 4.5 11.4 + - - +
36P LEU* 2.7 40.0 + - + +
39P GLN* 1.3 96.1 - - + +
41P GLY* 1.3 58.8 + - - +
42P ILE* 3.4 17.3 - - + +
43P GLY 5.1 1.0 + - - +
48P LEU* 5.0 0.9 - - - +
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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
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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