Contacts of the helix formed by residues 61 - 68 (chain A) in PDB entry 4KN1
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A HIS 5.4 4.2 + - - +
38A LYS* 3.8 25.6 - - + -
44A GLU* 4.2 8.3 - - - +
47A LEU* 3.8 4.0 - - - +
60A CYS* 1.3 78.1 - - - +
62A ALA* 1.3 64.9 + - - +
63A SER* 3.5 10.5 + - - -
64A THR* 3.1 28.4 + - - +
65A SER* 3.1 19.2 + - - -
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Residues in contact with ALA 62 (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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44A GLU* 3.8 14.3 + - - +
46A LYS* 3.8 34.4 - - + +
47A LEU* 4.0 5.8 - - - +
48A HIS* 5.0 0.2 - - - +
61A THR* 1.3 73.0 - - - +
63A SER* 1.3 63.8 + - - +
65A SER* 2.7 25.1 + - - -
66A GLN* 3.0 12.2 + - - +
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Residues in contact with SER 63 (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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61A THR* 3.6 9.8 - - - -
62A ALA* 1.3 80.3 - - - +
64A THR* 1.3 62.7 + - - +
66A GLN* 3.3 6.5 + - - +
67A GLU* 3.1 23.2 + - - +
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Residues in contact with THR 64 (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 HIS* 4.3 22.4 + - + +
60A CYS* 4.3 13.0 - - + -
61A THR* 3.1 28.7 + - - +
63A SER* 1.3 77.1 + - - +
65A SER* 1.3 63.2 + - - +
66A GLN 3.3 0.2 + - - -
67A GLU* 3.3 2.7 + - - +
68A LEU* 3.1 24.6 + - + +
75A LEU* 4.0 30.4 - - + +
102A GLU* 4.3 18.6 - - + +
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Residues in contact with SER 65 (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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47A LEU* 3.5 11.7 - - - -
48A HIS* 2.8 30.9 + - - -
51A CYS* 3.8 20.0 - - - -
60A CYS* 4.5 3.1 - - - -
61A THR 3.1 11.4 + - - -
62A ALA 2.7 20.4 + - - -
64A THR* 1.3 77.1 - - - +
66A GLN* 1.3 54.9 + - - +
68A LEU* 3.4 15.7 - - - +
69A HIS* 2.7 33.1 + - - -
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Residues in contact with GLN 66 (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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48A HIS* 3.0 46.9 + - + -
62A ALA 3.0 12.4 + - - +
63A SER* 3.6 11.4 - - - +
64A THR 3.2 0.2 - - - -
65A SER* 1.3 80.3 + - - +
67A GLU* 1.3 63.4 + - - +
68A LEU 3.5 0.2 + - - -
69A HIS* 3.5 14.4 + - - +
70A LYS* 3.9 22.5 - - - +
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Residues in contact with GLU 67 (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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63A SER 3.1 13.1 + - - +
64A THR* 3.3 0.4 + - - -
66A GLN* 1.3 82.0 - - + +
68A LEU* 1.3 56.7 + - - +
69A HIS 3.1 0.7 - - - -
70A LYS* 3.1 38.1 + - - +
73A SER* 2.9 28.1 - - - -
74A ARG* 2.8 39.9 + - + +
75A LEU* 3.4 28.0 - - + +
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Residues in contact with LEU 68 (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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51A CYS* 3.8 17.0 - - - -
64A THR* 3.1 19.1 + - + +
65A SER* 3.4 12.6 - - - +
67A GLU* 1.3 75.7 - - - +
69A HIS* 1.3 79.4 + - + +
70A LYS 3.2 2.3 - - - +
73A SER* 4.2 6.4 + - - -
75A LEU* 3.6 21.7 - - + +
80A TRP* 3.4 23.2 - - - -
95A ILE* 3.9 16.8 - - + +
98A THR* 3.8 28.7 - - + +
99A CYS* 3.8 13.5 - - - -
102A GLU* 4.4 11.9 - - + -
103A CYS* 5.0 1.6 - - - -
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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