Contacts of the helix formed by residues 36 - 46 (chain A) in PDB entry 2CTK
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 GLY 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.1 26.4 + - - -
35A LYS* 1.3 81.0 - - - +
37A SER* 1.3 64.6 + - - +
39A ILE* 4.5 4.2 - - - +
40A ARG* 3.6 22.8 + - - +
43A MET* 5.7 1.6 - - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE 3.5 1.6 + - - -
33A GLY* 5.3 3.1 - - - -
34A GLN* 5.1 11.3 + - - +
35A LYS* 5.2 0.6 - - - +
36A GLY* 1.3 74.6 + - - +
38A GLY* 1.3 65.8 + - - +
39A ILE 3.0 1.8 - - - -
40A ARG* 2.4 37.5 + - - +
41A LYS* 3.2 4.6 + - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL 4.2 10.1 - - - -
32A ILE 3.7 4.6 + - - -
33A GLY* 5.2 1.9 - - - -
37A SER* 1.3 82.4 + - - +
39A ILE* 1.3 60.7 + - - +
41A LYS* 3.5 21.2 - - - +
42A MET* 4.1 7.7 - - - +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.3 34.9 + - + +
32A ILE* 3.7 32.2 + - + +
36A GLY* 4.7 6.3 - - - +
37A SER 2.7 3.8 + - - -
38A GLY* 1.3 70.5 - - - +
40A ARG* 1.3 56.3 + - - +
41A LYS 3.0 1.8 - - - -
42A MET* 2.7 33.8 + - - +
43A MET* 3.1 24.8 + - + +
50A ILE* 3.9 39.3 - - + +
52A VAL* 4.3 13.9 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 3.6 15.7 + - - +
37A SER* 2.4 29.6 + - - +
39A ILE* 1.3 73.3 - - - +
41A LYS* 1.3 59.2 + - - +
43A MET* 4.0 21.4 - - - +
44A ASP* 3.1 47.2 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER 3.2 5.5 + - - +
38A GLY* 3.5 13.2 - - - +
39A ILE 3.0 0.8 + - - -
40A ARG* 1.3 77.4 - - - +
42A MET* 1.3 69.3 + - - +
44A ASP* 4.0 3.9 - - - +
45A GLU* 2.9 36.7 + - + +
46A PHE* 6.0 3.6 - - - -
81A ARG* 4.9 15.8 - - - +
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Residues in contact with MET 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 5.3 1.8 - - - -
38A GLY 4.1 8.3 - - - +
39A ILE* 2.7 29.7 + - - +
41A LYS* 1.3 80.5 - - - +
43A MET* 1.3 56.8 + - - +
44A ASP 2.8 4.5 - - - -
45A GLU* 2.6 22.3 + - - -
46A PHE* 2.6 46.6 + - + -
47A GLU 3.5 0.3 + - - -
48A VAL* 4.8 1.1 - - + -
50A ILE* 3.7 28.0 - - + -
74A ALA* 4.7 7.9 - - - +
77A GLY 4.9 2.2 - - - -
78A LEU* 3.6 44.0 - - + +
81A ARG* 6.1 2.9 - - + -
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Residues in contact with MET 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 5.7 1.6 - - - +
39A ILE* 3.1 25.4 + - + +
40A ARG* 4.1 27.4 - - - +
42A MET* 1.3 77.7 - - - +
44A ASP* 1.3 62.2 + - - +
47A GLU* 3.1 21.9 - - - -
48A VAL* 3.0 29.0 + - - +
49A ASN* 3.6 13.9 - - - +
50A ILE* 3.5 35.7 - - + +
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.1 40.8 + - - +
41A LYS* 4.0 4.0 - - - +
42A MET 2.7 4.4 + - - -
43A MET* 1.3 80.6 - - - +
45A GLU* 1.3 63.0 + - - +
47A GLU* 3.9 11.1 - - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 2.9 26.7 + - + +
42A MET* 2.6 10.2 + - - +
44A ASP* 1.3 72.3 - - - +
46A PHE* 1.3 75.6 + - + +
47A GLU* 3.0 18.6 + - - +
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 6.0 3.4 - - - -
42A MET* 2.6 45.1 + - + +
45A GLU* 1.3 86.6 - - + +
47A GLU* 1.3 73.2 + - - +
48A VAL* 3.5 18.6 - - + -
70A ASN* 3.6 17.5 - - - +
73A ARG* 3.1 50.9 - - + +
74A ALA* 3.5 26.9 - - + -
77A GLY* 4.6 11.2 - - - -
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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