Contacts of the helix formed by residues 71 - 86 (chain C) in PDB entry 4HSZ
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 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.6 5.8 - - - -
27C PHE 4.2 6.3 - - - +
28C LYS* 4.3 20.5 - - + +
65C ASN* 3.3 25.5 + - - -
67C ASP* 4.7 1.2 - - - +
69C GLU 3.9 1.0 - - - -
70C VAL* 1.3 76.4 - - - +
72C PHE* 1.3 60.0 + - - +
73C GLN* 3.2 11.5 + - - +
74C GLU* 2.8 45.8 + - - +
75C TYR* 2.9 26.0 + - - +
102C CA 4.2 0.7 - - - -
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Residues in contact with PHE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C MET 5.2 0.4 - - - -
13C VAL* 4.3 20.6 - - + -
16C PHE* 3.4 40.5 - + + -
17C HIS* 5.1 0.2 - - - -
27C PHE 4.5 2.0 + - - +
71C ASP* 1.3 72.2 - - - +
73C GLN* 1.3 62.1 + - - +
75C TYR* 3.1 21.4 + + - +
76C CYS* 2.8 51.7 + - - -
83D ALA* 3.6 34.3 - - + -
84D MET* 3.8 21.5 - - + -
87D ASN* 3.4 34.1 - - + +
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Residues in contact with GLN 73 (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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64C SER* 6.2 1.2 - - - -
71C ASP* 3.2 9.7 + - - +
72C PHE* 1.3 78.4 - - - +
74C GLU* 1.3 72.1 + - - +
76C CYS* 3.1 10.1 + - - +
77C VAL* 3.1 45.3 + - - +
84D MET* 4.6 23.5 - - + +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.5 20.6 - - - +
63C ASP* 3.9 0.4 - - - -
64C SER* 2.9 19.5 + - - +
65C ASN* 2.8 30.6 + - - +
69C GLU 3.0 9.0 - - - +
70C VAL* 3.2 10.0 - - + +
71C ASP* 2.8 36.7 + - - +
73C GLN* 1.3 82.5 - - - +
75C TYR* 1.3 55.8 + - - +
77C VAL* 3.4 8.9 + - + +
78C PHE* 3.0 27.7 + - - +
102C CA 2.3 30.2 - - - -
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C MET* 2.7 36.2 + - + -
15C THR* 4.0 8.0 - - - -
16C PHE* 3.3 41.6 + + + -
29C LEU* 4.6 9.0 - - + -
34C LEU* 6.0 1.6 - - + -
37C LEU* 4.2 24.2 - - + -
70C VAL* 3.9 9.2 - - + +
71C ASP 2.9 12.9 + - - +
72C PHE* 3.1 23.3 + + - +
74C GLU* 1.3 73.5 - - - +
76C CYS* 1.3 64.5 + - - +
78C PHE* 3.3 14.0 + + - +
79C LEU* 3.0 62.3 + - + +
5D LEU* 4.1 5.6 - - + +
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Residues in contact with CYS 76 (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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12C MET* 5.4 6.3 - - - -
72C PHE* 2.8 50.8 + - - +
73C GLN* 3.5 8.7 - - - +
75C TYR* 1.3 77.9 - - - +
77C VAL* 1.3 65.6 + - + +
79C LEU* 3.4 6.7 + - - +
80C SER* 2.9 28.4 + - - -
80D SER* 4.5 16.2 + - - -
83D ALA* 4.4 11.2 - - - -
84D MET* 4.0 16.2 - - + -
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 6.5 0.2 - - + -
64C SER* 5.7 6.7 - - - +
73C GLN* 3.1 39.7 + - - +
74C GLU* 3.5 9.0 - - + +
76C CYS* 1.3 74.1 - - + +
78C PHE* 1.3 65.0 + - - +
80C SER* 3.2 7.8 + - - -
81C CYS* 3.0 34.8 + - - -
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Residues in contact with PHE 78 (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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34C LEU* 5.4 2.7 - - + -
37C LEU* 5.8 1.3 - - + -
38C LEU* 3.8 41.7 - - + -
42C LEU* 4.1 6.5 - - + -
58C LEU* 5.2 9.6 - - + -
62C LEU* 3.7 45.3 - - + -
70C VAL* 6.1 0.9 - - + -
74C GLU 3.0 16.7 + - - +
75C TYR* 3.6 16.2 - + - +
76C CYS 3.2 0.4 - - - -
77C VAL* 1.3 77.2 - - - +
79C LEU* 1.3 72.0 + - + +
81C CYS* 3.2 11.5 + - + +
82C ILE* 3.2 50.5 + - + +
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Residues in contact with LEU 79 (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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12C MET* 3.5 42.2 - - + -
42C LEU* 4.7 1.6 - - + -
75C TYR* 3.0 51.9 + - + +
76C CYS* 3.8 5.6 - - - +
77C VAL 3.3 0.2 - - - -
78C PHE* 1.3 93.4 - - + +
80C SER* 1.3 61.2 + - - +
82C ILE* 3.3 10.8 + - + +
83C ALA* 3.1 23.0 + - - +
5D LEU* 4.4 11.4 - - + -
9D LEU* 4.0 33.2 - - + +
12D MET* 5.4 2.2 - - + +
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Residues in contact with SER 80 (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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76C CYS 2.9 18.3 + - - -
77C VAL* 3.2 7.1 + - - -
79C LEU* 1.3 74.9 - - - +
81C CYS* 1.3 62.3 + - - +
83C ALA* 3.5 6.1 + - - +
84C MET* 3.1 38.5 + - - +
12D MET* 5.9 4.4 - - - +
76D CYS* 4.3 19.6 - - - +
80D SER* 3.2 21.0 + - - -
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Residues in contact with CYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 6.6 0.4 - - - -
77C VAL* 3.0 29.1 + - - -
78C PHE* 3.4 15.0 - - + +
79C LEU 3.2 0.2 - - - -
80C SER* 1.3 74.5 - - - +
82C ILE* 1.3 61.8 + - + +
84C MET* 3.3 15.8 + - - +
85C MET* 2.9 30.2 + - - +
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Residues in contact with ILE 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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42C LEU* 4.1 16.4 - - + -
45C PHE* 3.6 43.1 - - + -
78C PHE* 3.2 51.6 + - + +
79C LEU* 3.3 14.8 + - + +
81C CYS* 1.3 77.5 - - + +
83C ALA* 1.3 58.7 + - - +
85C MET* 3.2 15.5 + - + +
86C CYS* 2.8 30.8 + - - -
9D LEU* 4.5 11.9 - - + -
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Residues in contact with ALA 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 LEU 3.1 16.2 + - - +
80C SER* 3.9 7.6 - - - +
82C ILE* 1.3 76.2 - - - +
84C MET* 1.3 58.1 + - - +
86C CYS* 3.2 7.0 + - - +
87C ASN* 3.0 25.8 + - - +
9D LEU* 4.9 8.2 - - + +
12D MET* 4.7 14.6 - - + -
13D VAL* 3.8 26.7 - - + +
72D PHE* 3.9 12.2 - - + -
76D CYS* 4.6 5.8 - - - -
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Residues in contact with MET 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 SER* 3.1 32.0 + - - +
81C CYS* 3.9 15.5 - - - +
83C ALA* 1.3 73.2 - - - +
85C MET* 1.3 65.7 + - - +
87C ASN* 3.1 14.9 + - - +
88C GLU* 3.8 6.8 + - - +
72D PHE* 3.7 26.0 - - + -
73D GLN* 4.2 36.8 - - + +
76D CYS* 4.4 8.5 - - - -
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Residues in contact with MET 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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45C PHE* 4.2 29.4 - - + -
81C CYS 2.9 17.9 + - - +
82C ILE* 3.4 18.8 - - + +
84C MET* 1.3 77.4 - - - +
86C CYS* 1.3 63.9 + - - +
87C ASN 3.4 0.5 + - - -
88C GLU* 3.6 10.3 + - - +
91C GLU* 3.5 26.5 - - + +
92C GLY* 3.6 28.4 + - - +
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Residues in contact with CYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.7 33.4 - - - -
82C ILE* 2.8 27.9 + - - +
83C ALA* 3.5 10.1 - - - +
84C MET 3.2 0.2 - - - -
85C MET* 1.3 79.1 - - - +
87C ASN* 1.3 55.7 + - - +
88C GLU 3.3 8.3 + - - +
91C GLU* 3.9 28.5 - - - +
9D LEU* 6.4 1.6 - - - -
13D VAL* 4.6 15.7 - - + +
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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
------------------------------------------------------------
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