Contacts of the helix formed by residues 67 - 77 (chain N) in PDB entry 4XLR
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 GLU 67 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62N ALA 4.9 0.2 - - - +
63N LEU* 3.3 25.8 - - + +
64N ALA* 2.9 34.4 + - + +
66N GLU* 1.3 82.8 - - + +
68N VAL* 1.3 59.7 + - - +
69N PRO* 3.6 1.1 - - - -
70N VAL* 3.1 24.3 - - + +
71N ILE* 3.4 13.7 - - - +
103N TYR* 3.1 25.4 + - - +
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Residues in contact with VAL 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N LEU* 5.7 3.6 - - + -
64N ALA 4.1 4.5 - - - +
65N PRO* 3.3 22.0 - - + +
67N GLU* 1.3 77.4 - - - +
69N PRO* 1.4 71.8 - - + +
71N ILE* 3.0 9.3 + - - +
72N LEU* 3.0 51.3 + - + +
140N VAL* 4.3 13.7 - - + -
143N SER* 4.4 6.7 - - - +
144N LEU* 3.6 41.1 - - + -
154N LEU* 5.0 1.8 - - + -
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Residues in contact with PRO 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N PRO 4.6 2.0 - - - +
66N GLU* 3.2 20.9 - - - +
67N GLU 3.6 0.9 - - - -
68N VAL* 1.4 93.4 - - + +
70N VAL* 1.3 61.7 + - + +
72N LEU* 3.4 14.9 + - + +
73N ASP* 2.9 29.8 + - - +
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Residues in contact with VAL 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N GLU 5.7 1.1 - - - +
67N GLU* 3.1 30.1 - - + +
69N PRO* 1.3 81.1 - - + +
71N ILE* 1.3 55.8 + - - +
73N ASP* 3.5 7.3 + - - +
74N LEU* 2.9 34.6 + - + +
103N TYR* 3.5 29.4 - - + +
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Residues in contact with ILE 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N LEU* 3.5 21.5 - - + -
67N GLU 3.4 16.8 - - - +
68N VAL* 3.0 9.1 + - - +
70N VAL* 1.3 72.9 - - - +
72N LEU* 1.3 61.9 + - + +
73N ASP 3.1 1.6 - - - -
74N LEU* 2.8 21.7 + - + +
75N LEU* 3.0 12.2 + - + +
102N PRO* 3.6 25.6 - - + +
103N TYR* 3.5 32.1 - - + +
106N ALA* 3.7 15.1 - - + +
136N LEU* 3.8 17.7 - - + -
140N VAL* 4.9 7.4 - - + -
155N PHE* 4.9 11.4 - - + -
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Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N VAL* 3.0 39.3 + - + +
69N PRO* 3.7 14.1 - - + +
71N ILE* 1.3 77.0 - - + +
73N ASP* 1.3 57.6 + - - +
75N LEU* 3.2 9.5 + - - +
76N LYS* 2.9 28.8 + - - +
154N LEU* 4.1 26.0 - - + +
155N PHE* 3.5 36.3 - - + -
157N GLU* 3.9 23.3 - - - +
158N ALA* 4.0 6.3 - - + +
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Residues in contact with ASP 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N PRO 2.9 17.3 + - - +
70N VAL* 3.6 8.1 - - - +
72N LEU* 1.3 73.0 - - - +
74N LEU* 1.3 62.1 + - - +
75N LEU 3.0 5.3 + - - -
76N LYS* 4.5 4.7 - - - +
77N ASN* 3.3 27.2 + - - +
78N GLY* 3.1 19.9 + - - -
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Residues in contact with LEU 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N VAL* 2.9 21.3 + - + +
71N ILE* 2.8 14.6 + - + +
73N ASP* 1.3 80.9 - - - +
75N LEU* 1.3 55.5 + - - +
78N GLY* 3.2 24.0 - - - -
103N TYR* 3.4 55.4 - - + +
106N ALA* 3.0 26.7 - - + +
107N GLN* 3.7 18.5 - - + +
110N GLY* 3.7 2.6 - - - -
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Residues in contact with LEU 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71N ILE* 3.0 11.4 + - + +
72N LEU* 3.3 9.4 - - - +
73N ASP 3.0 1.6 - - - -
74N LEU* 1.3 78.3 - - - +
76N LYS* 1.3 69.6 + - - +
78N GLY 3.7 2.8 + - - +
106N ALA* 3.4 18.8 - - + +
109N ALA* 3.7 21.3 - - + -
110N GLY* 3.7 21.4 - - - +
133N ILE* 4.4 1.8 - - + -
136N LEU* 3.7 20.6 - - + -
155N PHE* 3.4 44.9 - - + -
158N ALA* 4.7 2.9 - - + -
159N TRP* 3.4 36.6 + - + +
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Residues in contact with LYS 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N LEU 2.9 18.4 + - - +
73N ASP* 4.5 2.0 - - - +
75N LEU* 1.3 76.5 - - - +
77N ASN* 1.3 86.6 + - - +
78N GLY 4.9 0.9 - - - +
79N ARG* 5.4 4.2 + - - -
110N GLY 5.6 0.2 - - - +
157N GLU* 5.5 2.0 - - - +
158N ALA* 3.2 35.1 - - + +
159N TRP* 3.6 17.8 + - + +
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Residues in contact with ASN 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ASP* 3.3 29.9 + - - +
76N LYS* 1.3 108.7 + - - +
78N GLY* 1.3 64.3 + - - +
79N ARG* 3.7 20.2 + - - +
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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