Contacts of the helix formed by residues 58 - 67 (chain D) in PDB entry 1L9J
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D GLY 3.3 3.0 + - - -
57D TYR* 1.3 75.2 - - - +
59D GLU* 1.3 67.6 + - - -
60D GLY 3.3 3.1 - - - -
61D MET 3.2 4.5 + - - -
62D LYS* 3.0 20.7 + - - +
97D LYS 5.0 3.1 - - - -
99D LYS* 3.5 26.2 - - - +
2009D HEM 2.6 22.5 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D TYR 3.9 1.5 + - - +
58D GLY* 1.3 70.3 - - - +
60D GLY* 1.3 68.4 + - - +
62D LYS* 3.3 19.8 + - - +
63D GLU* 2.9 44.4 + - - +
97D LYS 4.9 1.0 + - - -
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLY 3.3 1.0 - - - -
59D GLU* 1.3 83.4 - - - +
61D MET* 1.3 55.7 + - - +
63D GLU* 3.0 9.3 + - - +
64D ALA* 2.9 28.1 + - - +
87D LEU* 4.3 12.1 - - - -
91D THR* 4.8 4.1 + - - -
96D ALA* 4.9 9.6 - - - -
97D LYS 3.8 25.4 + - - +
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Residues in contact with MET 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA* 3.7 12.8 - - - +
49D GLY 3.9 7.4 - - - +
57D TYR* 3.7 15.3 - - + -
58D GLY 3.2 3.6 + - - +
60D GLY* 1.3 72.2 - - - +
62D LYS* 1.3 63.0 + - - +
64D ALA* 3.5 2.1 + - - +
65D GLY 3.1 17.5 + - - -
71D TRP* 4.0 19.5 - - - -
79D TYR* 2.9 44.0 - - + +
87D LEU* 3.8 24.7 - - + +
97D LYS 4.8 0.2 + - - -
2009D HEM 3.3 62.6 + - + +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA 4.4 5.6 - - - +
49D GLY 4.6 10.0 - - - +
57D TYR* 3.5 36.1 - - + +
58D GLY 3.0 14.6 + - - +
59D GLU* 3.7 21.0 + - - +
61D MET* 1.3 74.3 - - - +
63D GLU* 1.3 65.3 + - + +
65D GLY* 3.2 3.5 + - - -
66D ALA* 3.0 20.3 + - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 2.9 42.7 + - - +
60D GLY* 3.3 9.6 - - - +
62D LYS* 1.3 77.4 - - + +
64D ALA* 1.3 55.9 + - - +
66D ALA* 2.8 34.2 + - - +
67D LYS* 3.0 16.9 + - - +
91D THR* 3.8 17.2 + - - +
93D ASP* 4.7 11.6 - - - +
96D ALA* 5.9 1.0 - - - +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA* 5.2 0.4 - - + -
60D GLY 2.9 17.3 + - - +
61D MET 4.0 3.8 - - - +
63D GLU* 1.3 72.9 - - - +
65D GLY* 1.3 63.7 + - - +
67D LYS* 3.3 12.4 + - - +
69D LEU* 3.3 15.9 + - + +
87D LEU* 4.3 15.5 - - + -
90D TYR* 3.1 45.1 - - + -
91D THR* 4.4 14.0 + - - +
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Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D THR* 3.1 25.5 - - - +
48D ALA* 3.3 35.6 - - - +
50D THR* 5.8 0.7 - - - -
61D MET 3.1 10.5 + - - -
62D LYS 3.6 1.1 - - - -
63D GLU 3.1 0.2 - - - -
64D ALA* 1.3 75.1 - - - +
66D ALA* 1.3 64.6 + - - +
68D GLY* 3.1 9.9 + - - -
69D LEU* 3.5 3.6 + - - -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS 3.0 11.3 + - - +
63D GLU* 2.8 17.4 + - - +
65D GLY* 1.3 74.8 - - - +
67D LYS* 1.3 51.4 + - + +
68D GLY* 2.7 16.8 + - - -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLU* 3.0 18.9 + - - +
64D ALA 3.3 11.3 + - - +
66D ALA* 1.3 74.5 - - + +
68D GLY* 1.3 61.4 + - - +
90D TYR* 3.3 17.7 + - + +
91D THR* 3.9 38.1 + - - +
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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