Contacts of the helix formed by residues 57 - 67 (chain B) in PDB entry 1LK7
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 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B THR* 2.7 29.7 + - - +
55B PRO* 3.3 3.7 + - - +
56B THR* 1.3 79.6 - - - +
58B TYR* 1.3 60.5 + - - +
59B GLN* 3.5 1.9 + - - +
60B ALA* 3.0 19.3 + - - +
61B LYS* 2.9 29.7 + - - +
103B ALA* 3.9 10.8 - - - -
174B ASP* 4.1 4.9 - - - -
2006B CL 3.6 14.6 - - - -
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Residues in contact with TYR 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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57B SER* 1.3 72.2 - - - +
59B GLN* 1.3 61.2 + - - +
61B LYS* 4.3 11.4 - - + -
62B LEU* 2.8 50.2 + - + +
174B ASP* 3.2 51.2 + - + -
2006B CL 3.3 8.7 - - + +
142D PRO* 4.1 19.8 - - + +
170D PRO* 3.7 13.9 - - + -
172D ILE* 3.9 6.5 - - + -
176D GLY 4.9 2.7 + - - -
178D PHE* 3.6 37.0 - + - -
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 5.1 2.0 + - - -
28B THR* 3.3 13.5 - - - +
29B GLY* 2.9 39.5 + - - +
33B ALA* 4.3 4.9 - - - +
36B ILE* 5.1 1.0 - - - +
57B SER* 3.3 5.1 - - - +
58B TYR* 1.3 78.3 - - - +
60B ALA* 1.3 65.0 + - - +
62B LEU* 3.5 3.0 + - - +
63B LEU* 3.1 46.2 + - + +
2006B CL 3.4 4.9 - - + +
168D ASP* 4.6 6.2 - - + +
169D GLY* 3.7 30.6 - - - +
170D PRO* 5.1 0.9 - - - -
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Residues in contact with ALA 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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26B LEU* 3.4 16.9 - - + +
27B GLY 3.4 25.4 - - - +
36B ILE* 4.1 12.4 - - + +
55B PRO* 4.1 6.7 - - + -
56B THR 4.2 0.9 - - - +
57B SER* 3.0 20.9 + - - +
59B GLN* 1.3 84.5 - - - +
61B LYS* 1.3 58.3 + - - +
63B LEU* 3.4 1.3 + - - +
64B ALA* 2.9 31.0 + - - +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 3.6 21.7 - - + +
57B SER 2.9 17.5 + - - +
58B TYR* 3.3 13.6 + - + +
60B ALA* 1.3 75.1 - - - +
62B LEU* 1.3 67.7 + - + +
64B ALA* 3.3 6.2 + - - +
65B ILE* 2.9 40.1 + - + +
71B ILE* 3.6 27.1 - - + +
73C SER* 2.8 34.4 + - - -
75C ASP* 3.7 15.0 + - - +
76C GLN* 3.7 5.1 - - - +
143D GLN* 6.0 0.4 - - - +
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Residues in contact with LEU 62 (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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58B TYR* 2.8 51.3 + - + +
59B GLN* 4.3 2.9 - - - +
61B LYS* 1.3 85.4 - - + +
63B LEU* 1.3 57.3 + - - +
65B ILE* 3.3 14.0 + - + +
66B GLU* 3.0 40.7 + - + +
75C ASP* 3.5 20.9 - - + +
145D TRP* 3.4 43.3 - - + +
146D LYS* 6.2 0.9 - - + -
161D LEU* 5.7 4.0 - - + -
170D PRO* 5.5 3.1 - - + -
178D PHE* 5.3 5.6 - - + -
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Residues in contact with LEU 63 (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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33B ALA* 3.7 44.9 - - + +
36B ILE* 3.9 17.5 - - + -
37B LYS* 3.9 13.2 - - + -
59B GLN* 3.1 29.0 + - - +
60B ALA* 3.9 2.9 - - - +
62B LEU* 1.3 71.9 - - - +
64B ALA* 1.3 67.2 + - - +
66B GLU* 3.3 20.3 + - - +
67B HIS* 3.2 49.9 + - + +
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Residues in contact with ALA 64 (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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26B LEU* 3.9 17.5 - - + -
36B ILE* 4.0 11.0 - - + +
60B ALA 2.9 18.4 + - - +
61B LYS* 3.6 4.9 - - - +
63B LEU* 1.3 77.2 - - - +
65B ILE* 1.3 60.9 + - - +
67B HIS 3.1 6.6 + - - -
69B ILE* 3.0 35.9 + - + +
71B ILE* 3.7 26.7 - - + -
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Residues in contact with ILE 65 (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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61B LYS* 2.9 31.4 + - + +
62B LEU* 3.7 13.2 - - + +
63B LEU 3.3 0.2 - - - -
64B ALA* 1.3 75.1 - - - +
66B GLU* 1.3 66.5 + - + +
68B ASP* 3.0 20.9 + - - +
69B ILE 4.8 4.3 - - - +
71B ILE* 4.1 10.1 - - + -
75C ASP* 3.9 36.3 - - - +
76C GLN* 3.6 40.2 - - + +
146D LYS* 4.5 14.4 - - - +
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Residues in contact with GLU 66 (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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62B LEU* 3.0 26.5 + - + +
63B LEU* 3.6 24.2 - - - +
64B ALA 3.3 0.2 - - - -
65B ILE* 1.3 78.9 - - + +
67B HIS* 1.3 68.2 + - + +
68B ASP* 3.4 5.6 + - - +
145D TRP* 5.8 4.0 - - - -
146D LYS* 5.6 7.4 - - - +
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Residues in contact with HIS 67 (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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36B ILE* 4.6 1.6 - - + +
37B LYS* 3.5 53.2 - - + +
40B GLY* 4.0 25.2 - - - +
41B GLU* 5.5 4.6 + - + +
43B LEU* 5.4 1.0 - - - +
44B LYS* 6.1 0.2 - - - +
63B LEU* 3.2 36.8 + - + +
64B ALA 3.1 3.4 + - - +
65B ILE 3.0 1.2 - - - -
66B GLU* 1.3 85.4 - - + +
68B ASP* 1.3 71.7 + - - +
69B ILE* 3.1 15.5 + - + +
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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