Contacts of the helix formed by residues 70 - 88 (chain C) in PDB entry 4XYN
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 ASP 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 3.8 3.1 - - - -
26C HIS 4.3 9.0 - - - +
27C LYS* 4.3 21.6 - - + +
64C ASP* 3.4 11.4 - - - +
68C GLU 4.0 0.6 - - - -
69C CYS* 1.3 75.4 - - - +
71C PHE* 1.3 60.9 + - - +
72C GLN* 2.9 15.6 + - - +
73C GLU* 2.5 66.3 + - - +
74C PHE* 2.8 27.0 + - - +
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 3.9 3.1 - - - -
12C ILE* 3.4 43.1 - - + -
15C PHE* 3.5 42.7 - + + -
26C HIS 4.5 1.6 + - - -
70C ASP* 1.3 76.3 - - - +
72C GLN* 1.3 63.5 + - - +
74C PHE* 3.7 5.9 - + - +
75C MET* 2.9 62.3 + - + +
82D THR* 3.7 22.4 - - + -
83D THR* 4.3 7.9 - - + -
86D HIS* 3.5 42.2 - + + +
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Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASP* 2.9 12.8 + - - +
71C PHE* 1.3 77.8 - - - +
73C GLU* 1.3 63.7 + - + +
75C MET* 3.3 3.1 + - - +
76C ALA* 3.1 22.0 + - - +
83D THR* 3.9 34.1 - - + +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.2 27.3 - - - +
63C ASN* 3.1 12.9 + - + +
64C ASP* 2.9 28.6 + - - +
68C GLU 3.2 4.1 - - - +
69C CYS* 3.3 15.9 - - - -
70C ASP* 2.5 55.4 + - - +
72C GLN* 1.3 75.9 - - + +
74C PHE* 1.3 59.0 + - - +
76C ALA* 3.5 8.3 - - - +
77C PHE* 3.3 16.8 + - - +
502C CA 2.4 31.1 - - - -
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Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.5 28.5 - - + -
14C VAL* 4.2 16.2 - - + -
15C PHE* 3.7 27.8 - + + -
28C LEU* 4.2 14.4 - - + -
33C LEU* 5.5 1.3 - - + -
36C LEU* 4.0 27.1 - - + -
69C CYS* 3.1 12.9 - - - -
70C ASP 2.8 15.7 + - - +
71C PHE* 3.7 12.1 - + - +
72C GLN 3.3 0.2 - - - -
73C GLU* 1.3 72.2 - - - +
75C MET* 1.3 57.5 + - - +
76C ALA 3.1 1.8 - - - -
77C PHE* 2.8 23.9 + + - +
78C VAL* 2.7 57.0 + - + +
4D LEU* 4.4 7.9 - - + -
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.7 30.5 - - + -
71C PHE* 2.9 61.9 + - + +
72C GLN 3.3 5.6 + - - +
74C PHE* 1.3 83.7 - - - +
76C ALA* 1.3 56.8 + - - +
78C VAL* 3.3 11.1 + - + +
79C ALA* 2.8 27.2 + - - +
75D MET* 5.6 1.7 - - + +
78D VAL* 4.5 3.6 - - + +
79D ALA* 3.8 39.5 - - + +
82D THR* 3.8 13.2 - - + +
83D THR* 3.9 11.4 - - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 5.5 1.6 - - + +
63C ASN* 4.9 13.5 - - - +
72C GLN 3.1 11.9 + - - +
73C GLU* 3.5 13.0 - - - +
74C PHE 3.1 0.4 - - - -
75C MET* 1.3 77.1 - - - +
77C PHE* 1.3 63.2 + - - +
79C ALA* 3.2 8.6 + - - +
80C MET* 3.2 38.1 + - + +
79D ALA* 4.9 2.4 - - - +
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.4 5.8 - - + -
36C LEU* 5.2 3.4 - - + -
37C ILE* 3.6 37.5 - - + -
41C LEU* 3.9 14.4 - - + -
45C LEU* 4.0 10.3 - - + -
57C VAL* 4.5 12.1 - - + -
61C LEU* 3.5 44.5 - - + +
73C GLU 3.3 2.4 + - - +
74C PHE* 2.8 29.0 + + - +
76C ALA* 1.3 76.0 - - - +
78C VAL* 1.3 65.5 + - + -
80C MET* 3.2 12.0 + - - +
81C VAL* 3.1 49.3 + - + +
8D MET* 6.3 0.2 - - + -
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.1 31.4 - - + -
74C PHE* 2.7 55.1 + - + +
75C MET* 3.6 14.8 - - + +
76C ALA 3.3 0.2 - - - -
77C PHE* 1.3 74.1 - - + +
79C ALA* 1.3 61.8 + - - +
82C THR* 2.7 41.8 + - - +
4D LEU* 4.7 0.7 - - + -
8D MET* 4.3 21.1 - - + -
11D LEU* 4.9 1.6 - - + -
75D MET* 4.4 9.0 - - + -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C MET 2.8 14.6 + - - +
76C ALA* 3.5 11.9 - - - +
77C PHE 3.2 0.4 - - - -
78C VAL* 1.3 77.4 - - - +
80C MET* 1.3 51.6 + - - +
82C THR* 3.9 0.5 - - - -
83C THR* 2.7 43.3 + - - +
75D MET* 3.6 37.8 - - + +
76D ALA* 5.0 2.2 - - - +
79D ALA* 5.0 2.7 - - + -
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Residues in contact with MET 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C THR* 4.3 21.3 - - + +
61C LEU* 3.9 28.0 - - + -
63C ASN* 6.3 0.4 - - - +
76C ALA* 3.2 26.8 + - + +
77C PHE* 3.4 11.2 - - + +
79C ALA* 1.3 78.9 - - - +
81C VAL* 1.3 54.4 + - + +
83C THR* 3.2 7.0 + - - +
84C ALA* 2.7 36.2 + - - +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.5 7.0 - - + -
44C PHE* 4.4 13.9 - - + -
45C LEU* 4.4 24.7 - - + -
77C PHE* 3.1 48.4 + - + +
80C MET* 1.3 75.9 - - + +
82C THR* 1.3 58.7 + - - +
84C ALA* 3.2 8.7 + - + +
85C CYS* 2.9 28.1 + - - +
8D MET* 3.8 28.5 - - + -
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Residues in contact with THR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL* 2.7 29.1 + - - +
81C VAL* 1.3 75.9 - - - +
83C THR* 1.3 58.4 + - - +
85C CYS* 3.1 9.1 + - - +
86C HIS* 2.9 27.5 + - - +
8D MET* 3.2 50.4 - - + +
11D LEU* 4.3 3.2 - - + +
12D ILE* 4.0 5.3 - - + +
71D PHE* 3.7 24.0 - - + -
75D MET* 3.8 13.9 - - + +
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA* 2.7 28.7 + - - +
80C MET* 3.4 6.7 - - - +
82C THR* 1.3 72.4 - - - +
84C ALA* 1.3 64.5 + - - +
86C HIS* 3.3 14.6 + - - +
87C GLU* 3.5 15.0 + - + +
71D PHE* 3.9 13.7 - - + -
72D GLN* 4.1 33.2 - - + +
75D MET* 3.5 19.2 - - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C MET 2.7 16.5 + - - +
81C VAL* 3.2 12.3 + - + +
83C THR* 1.3 73.8 - - - +
85C CYS* 1.3 65.2 + - - +
87C GLU* 3.0 32.1 + - - +
88C PHE* 3.7 3.5 + - - +
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Residues in contact with CYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PHE* 4.0 36.3 - - + -
81C VAL 2.9 15.7 + - - +
82C THR* 3.5 10.8 - - - +
84C ALA* 1.3 72.9 - - - +
86C HIS* 1.3 62.2 + - - +
87C GLU 3.2 0.2 - - - -
88C PHE* 3.4 19.3 + - - +
89C PHE* 3.8 25.0 + - - -
9D VAL* 5.2 1.6 - - - -
12D ILE* 3.5 20.2 - - + -
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Residues in contact with HIS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR 2.9 11.7 + - - +
83C THR 3.4 10.5 - - - +
84C ALA 3.0 0.6 - - - -
85C CYS* 1.3 76.8 - - - +
87C GLU* 1.3 65.3 + - + +
89C PHE* 2.8 25.1 + - - +
90C GLU* 3.1 38.7 + - + +
12D ILE* 4.0 14.1 - - + +
15D PHE* 4.2 9.0 - + - -
16D HIS* 4.1 24.2 - + - -
26D HIS* 5.7 1.8 - - + -
71D PHE* 3.0 54.3 - + + +
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C THR* 3.5 15.2 + - + +
84C ALA* 3.0 19.1 + - - +
86C HIS* 1.3 82.0 - - + +
88C PHE* 1.3 54.7 + - - +
89C PHE 2.9 4.5 - - - -
90C GLU* 2.7 36.8 + - + +
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Residues in contact with PHE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA 3.7 3.9 + - - +
85C CYS* 3.4 15.8 + - - +
86C HIS 3.3 0.8 - - - -
87C GLU* 1.3 77.2 - - - +
89C PHE* 1.3 82.5 + + - +
90C GLU 3.4 0.6 + - - -
91C HIS 4.0 10.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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