Contacts of the helix formed by residues 49 - 61 (chain B) in PDB entry 1K9K
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LYS 3.8 2.2 + - - +
48B LEU* 1.3 75.6 - - - +
50B ASP* 1.3 65.1 + - - +
51B ALA* 4.2 9.7 - - + +
52B GLU* 3.1 32.3 + - + +
53B ILE* 3.1 20.1 + - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 2.9 35.4 + - - +
39B GLN* 4.5 4.9 + - - -
48B LEU 3.6 3.2 + - - +
49B GLN* 1.3 72.3 - - - +
51B ALA* 1.3 57.1 + - - +
53B ILE* 3.3 8.7 + - - +
54B ALA* 3.0 29.2 + - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN* 3.2 12.0 - - + +
50B ASP* 1.3 80.9 - - - +
52B GLU* 1.3 62.6 + - - +
54B ALA* 3.4 7.3 + - - +
55B ARG* 3.0 26.7 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 5.0 10.1 - - + -
49B GLN* 3.1 37.3 + - + +
51B ALA* 1.3 79.0 - - - +
53B ILE* 1.3 60.6 + - - +
55B ARG* 3.3 41.1 + - - +
56B LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 4.0 27.4 - - + -
38B ILE* 4.3 18.4 - - + -
39B GLN* 4.2 26.5 - - + +
45B GLY 3.9 20.2 - - - +
48B LEU* 3.9 30.1 - - + +
49B GLN 3.1 13.2 + - - +
50B ASP* 3.3 8.9 + - - +
52B GLU* 1.3 75.3 - - - +
54B ALA* 1.3 58.3 + - - +
56B LEU* 3.2 8.3 + - - +
57B MET* 2.9 46.6 + - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.9 1.7 + - - -
50B ASP 3.0 17.9 + - - +
51B ALA* 3.6 9.4 - - - +
53B ILE* 1.3 78.4 - - - +
55B ARG* 1.3 56.5 + - - +
57B MET* 3.9 15.5 - - + +
58B GLU* 2.9 29.5 + - - +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA 3.0 17.5 + - - +
52B GLU* 3.3 33.5 + - - +
54B ALA* 1.3 75.7 - - - +
56B LEU* 1.3 65.2 + - - +
58B GLU* 3.2 6.7 + - + +
59B ASP* 3.0 49.1 + - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.7 30.7 - - + -
42B LEU* 5.7 2.0 - - + -
48B LEU* 5.0 10.1 - - + -
52B GLU 2.9 13.9 + - - +
53B ILE* 3.2 11.9 + - - +
55B ARG* 1.3 80.0 - - - +
57B MET* 1.3 63.6 + - - +
59B ASP* 3.3 5.8 + - + +
60B LEU* 3.1 40.6 + - + +
76B PHE* 4.1 29.6 - - + -
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 3.3 57.2 + - + +
34B LEU* 3.4 32.1 - - + -
35B LYS* 3.6 27.4 - - + -
38B ILE* 4.3 5.6 - - + -
53B ILE* 2.9 36.2 + - + +
54B ALA* 3.9 13.7 - - + +
56B LEU* 1.3 75.4 - - - +
58B GLU* 1.3 63.7 + - - +
60B LEU* 3.3 5.1 + - - +
61B ASP* 3.2 22.3 + - - +
68B VAL* 4.3 3.7 - - + +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 3.5 19.8 + - - +
54B ALA 2.9 19.8 + - - +
55B ARG* 3.2 9.4 + - + +
57B MET* 1.3 77.2 - - - +
59B ASP* 1.3 63.9 + - - +
61B ASP* 3.2 13.4 + - - +
64B LYS* 2.7 58.8 + - - +
66B GLN* 4.7 8.7 + - - +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.0 50.3 + - - +
56B LEU* 3.3 5.8 + - + +
58B GLU* 1.3 77.9 - - - +
60B LEU* 1.3 57.5 + - + +
61B ASP 3.4 1.2 + - - -
62B ARG* 2.5 41.1 + - - +
64B LYS* 4.5 3.9 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.2 23.3 - - + -
38B ILE* 5.8 0.4 - - + -
56B LEU* 3.1 33.2 + - + +
57B MET 3.3 4.9 + - - +
59B ASP* 1.3 77.8 - - + +
61B ASP* 1.3 57.5 + - - +
62B ARG* 3.0 26.1 + - - +
68B VAL* 4.1 13.2 - - + -
72B GLU* 3.3 32.2 - - - +
75B THR* 4.5 2.8 - - + -
76B PHE* 3.7 57.0 - - + +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.8 5.3 + - - +
57B MET 3.2 11.2 + - - +
58B GLU* 3.6 13.4 - - - +
59B ASP 3.2 1.9 - - - -
60B LEU* 1.3 73.5 - - - +
62B ARG* 1.3 60.6 + - - +
63B ASN* 3.0 7.3 - - - +
64B LYS* 3.0 39.1 + - - +
65B ASP* 3.2 1.4 - - - +
66B GLN* 2.8 33.8 + - - +
67B GLU 3.2 10.5 - - - +
68B VAL* 4.3 5.1 - - + +
72B GLU* 3.8 4.7 - - - -
400B CA 2.3 30.2 - - - -
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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