Contacts of the helix formed by residues 67 - 80 (chain N) in PDB entry 5XS0
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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51N TYR 4.5 2.6 + - - -
53N SER* 3.6 18.2 + - - +
65N TYR* 3.6 29.0 + - + -
66N ILE* 1.3 77.8 - - - +
68N GLY* 1.3 66.6 + - - +
69N HIS* 3.4 27.0 - - + +
70N ARG* 3.0 33.4 + - + +
71N VAL* 3.2 9.9 + - - +
167O LEU 4.6 5.0 - - - +
169O LYS* 4.3 23.2 + - - +
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Residues in contact with GLY 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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66N ILE 3.7 2.3 + - - -
67N GLU* 1.3 72.5 - - - +
69N HIS* 1.3 62.8 + - - +
71N VAL* 3.0 10.0 + - - +
72N ILE* 2.9 32.2 + - - +
148N THR* 4.5 21.2 - - - +
152N LYS* 4.7 5.6 - - - +
167O LEU* 5.1 3.1 - - - -
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Residues in contact with HIS 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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67N GLU* 3.8 34.8 + - + +
68N GLY* 1.3 74.8 + - - +
70N ARG* 1.3 88.8 + - + +
72N ILE* 4.3 1.8 - - - -
73N ASN* 2.9 41.5 + - - -
160O ASN* 5.9 0.2 - - - -
164O ASN* 3.1 40.3 + - - +
165O CYS* 5.9 0.9 - - - -
167O LEU* 3.8 40.5 + - + +
168O ASP* 3.8 30.3 + - + -
169O LYS 5.3 0.2 - - - -
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Residues in contact with ARG 70 (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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195M ASP* 5.0 1.1 - - - +
50N GLU 3.7 15.1 + - - -
51N TYR* 3.7 45.7 + - + +
53N SER* 4.0 6.9 + - - -
66N ILE* 3.8 13.5 - - + -
67N GLU* 3.0 34.7 + - + +
69N HIS* 1.3 101.3 + - + +
71N VAL* 1.3 56.3 + - - +
73N ASN* 3.4 5.0 + - - +
74N LEU* 2.9 35.3 + - - +
168O ASP* 3.9 13.1 + - - -
170O ASP* 3.9 19.4 + - - -
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Residues in contact with VAL 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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66N ILE* 3.6 28.5 - - + -
67N GLU 3.5 12.8 - - - +
68N GLY 3.0 5.9 + - - +
70N ARG* 1.3 72.1 - - - +
72N ILE* 1.3 66.0 - - + +
74N LEU* 3.3 8.8 + - + +
75N ALA* 2.9 23.9 + - - +
151N LEU* 5.8 1.3 - - + -
152N LYS* 4.0 31.9 - - + -
155N LEU* 3.7 31.6 - - + -
162N LEU* 4.4 16.3 - - + +
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Residues in contact with ILE 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 GLY* 2.9 19.9 + - - +
69N HIS* 3.7 2.7 - - - +
71N VAL* 1.3 77.7 - - + +
73N ASN* 1.3 57.3 + - - +
75N ALA* 3.3 3.3 + - - +
76N ASN* 2.9 46.9 + - - +
84N TRP* 4.3 9.4 - - + -
151N LEU* 4.5 20.2 - - + -
155N LEU* 5.5 0.2 - - - -
156O ARG* 4.7 6.1 - - + +
157O SER* 3.5 39.3 - - - +
164O ASN* 3.2 33.7 - - - +
167O LEU* 5.4 4.9 - - + -
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Residues in contact with ASN 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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195M ASP* 3.7 22.2 + - + +
69N HIS* 2.9 30.7 + - - +
70N ARG* 3.9 4.4 - - - +
72N ILE* 1.3 72.1 - - - +
74N LEU* 1.3 66.2 + - - +
76N ASN* 3.3 10.7 + - - +
77N GLU* 2.9 31.0 + - + +
159O GLY* 4.4 1.0 - - - -
160O ASN* 3.4 38.6 + - - +
164O ASN* 2.9 18.6 + - - +
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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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192M LYS* 3.6 32.9 - - + -
195M ASP* 3.9 5.1 + - - +
47N LEU* 4.1 18.8 - - + -
51N TYR* 3.8 28.5 - - + +
66N ILE* 4.8 6.7 - - + -
70N ARG 2.9 28.5 + - - +
71N VAL* 3.5 11.2 - - + +
73N ASN* 1.3 76.6 - - - +
75N ALA* 1.3 56.0 + - - +
77N GLU* 3.3 5.0 + - - +
78N MET* 2.9 34.1 + - + +
161N ALA* 3.6 23.1 - - + +
162N LEU* 3.8 15.7 - - + -
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Residues in contact with ALA 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 VAL 2.9 17.1 + - - +
72N ILE 3.7 1.3 - - - +
74N LEU* 1.3 76.6 - - - +
76N ASN* 1.3 58.7 + - - +
78N MET* 4.4 0.2 - - - -
79N PHE* 2.9 39.0 + - + -
84N TRP* 3.6 36.5 - - + -
155N LEU* 4.0 17.9 - - + -
162N LEU* 3.7 12.5 - - + +
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Residues in contact with ASN 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 ILE* 2.9 30.2 + - - +
73N ASN* 3.3 9.8 + - - +
75N ALA* 1.3 75.9 - - - +
77N GLU* 1.3 62.7 + - + +
80N GLY* 2.8 28.9 + - - -
81N TYR* 3.5 19.9 + - + +
84N TRP* 3.0 18.2 + - - +
40O GLN* 3.4 11.6 + - - +
157O SER 3.1 24.6 + - - +
158O PHE* 3.6 20.1 + - - +
159O GLY* 3.7 6.2 - - - +
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Residues in contact with GLU 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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192M LYS* 6.0 0.7 - - - -
195M ASP* 3.4 41.8 - - + +
196M LEU* 4.0 15.1 - - - +
197M GLU* 4.6 12.6 + - + +
201M GLU* 4.8 3.6 + - - +
204M ARG* 2.9 21.8 + - - -
73N ASN* 2.9 21.1 + - + +
74N LEU 3.8 3.1 - - - +
76N ASN* 1.3 82.6 - - + +
78N MET* 1.3 59.8 + - + +
40O GLN* 4.6 8.2 + - - +
44O ARG* 2.7 51.7 + - - +
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Residues in contact with MET 78 (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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192M LYS* 5.5 5.6 - - - -
197M GLU* 4.2 15.5 - - + +
200M VAL* 3.8 6.2 - - + +
204M ARG* 2.6 17.3 + - - -
39N ILE* 3.6 46.6 - - + +
42N ALA* 3.9 27.1 - - + +
43N LEU* 3.5 39.5 - - + -
74N LEU* 2.9 23.5 + - + +
75N ALA* 3.9 3.4 - - - +
77N GLU* 1.3 78.8 - - + +
79N PHE* 1.3 70.5 + - + +
161N ALA* 4.6 7.0 - - + -
162N LEU* 4.7 7.0 - - + -
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Residues in contact with PHE 79 (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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81M TYR* 4.1 14.8 - + - -
204M ARG* 3.5 17.9 + - - +
31N TYR* 3.6 15.5 - - - +
35N GLU* 5.7 0.2 - - - -
39N ILE* 4.4 12.8 - - + -
43N LEU* 4.6 4.3 - - + -
75N ALA* 2.9 20.9 + - + +
78N MET* 1.3 88.2 - - + +
80N GLY* 1.3 59.3 + - - +
82N ASN* 4.9 0.9 - - - +
83N GLY* 3.2 34.4 - - - +
84N TRP* 3.8 16.4 - + + +
115N LEU* 3.5 35.7 - - + -
116N LYS* 4.5 5.2 + - - +
155N LEU* 4.8 1.8 - - + -
158N PHE* 4.3 15.0 - + + -
162N LEU* 3.6 32.3 - - + -
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Residues in contact with GLY 80 (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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204M ARG* 3.3 9.3 - - - +
76N ASN 2.8 20.8 + - - -
79N PHE* 1.3 79.8 - - - +
81N TYR* 1.3 67.5 + - - -
82N ASN* 3.0 5.3 + - - -
83N GLY 3.1 9.1 + - - -
84N TRP* 3.3 14.9 - - - -
36O TYR* 4.4 7.0 - - - -
40O GLN* 3.4 13.7 - - - -
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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