Contacts of the helix formed by residues 72 - 83 (chain C) in PDB entry 1SHZ
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 PRO 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C LEU* 6.2 1.3 - - + -
66C VAL* 4.3 12.5 - - + -
67C ALA* 4.3 18.8 - - + +
70C PHE 3.6 9.6 - - - +
71C GLU* 1.3 88.4 - - + +
73C GLY* 1.3 68.8 + - - +
75C LEU* 3.7 2.4 + - + -
76C LEU* 3.0 43.7 + - + +
110C LEU* 4.4 9.4 - - + -
208C ILE* 5.4 3.8 - - + -
214C LYS* 5.3 8.5 - - + -
218C VAL* 3.7 29.2 - - + -
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Residues in contact with GLY 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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71C GLU* 2.9 8.8 + - - +
72C PRO* 1.3 84.5 - - - +
74C PRO* 1.3 67.5 - - - -
76C LEU* 3.7 0.7 - - - +
77C CYS* 2.9 20.8 + - - +
103C PHE* 4.3 1.0 - - - -
110C LEU* 4.4 16.5 - - - +
111C ARG 4.7 4.5 - - - -
112C VAL* 3.6 17.8 - - - +
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Residues in contact with PRO 74 (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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71C GLU* 3.6 15.9 - - + +
73C GLY* 1.3 85.1 - - - +
75C LEU* 1.3 62.5 + - - +
77C CYS* 3.4 3.8 + - + +
78C CYS* 3.0 27.2 + - - +
111C ARG 5.5 0.4 - - - +
112C VAL* 3.8 4.9 - - + -
113C PRO* 4.6 10.8 - - + -
146C GLN* 3.5 35.5 - - + +
149C ALA* 3.7 30.3 - - + -
150C VAL* 4.0 7.4 - - + +
153C GLN* 5.0 5.4 - - - +
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Residues in contact with LEU 75 (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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49C LEU* 3.6 34.8 - - + -
62C LEU* 4.2 14.4 - - + -
63C LEU* 3.9 33.4 - - + -
66C VAL* 3.6 36.8 - - + -
71C GLU 4.9 0.2 + - - -
72C PRO* 3.7 5.1 + - + +
73C GLY 3.3 1.0 - - - -
74C PRO* 1.3 79.8 - - - +
76C LEU* 1.3 64.1 + - + +
78C CYS* 3.3 5.5 + - - +
79C LEU* 3.1 27.1 + - + +
150C VAL* 4.1 14.8 - - + +
153C GLN* 4.2 15.7 - - - +
154C LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 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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63C LEU* 3.9 15.3 - - + -
72C PRO* 3.0 41.7 + - + +
73C GLY 3.7 1.3 - - - +
75C LEU* 1.3 74.3 - - + +
77C CYS* 1.3 64.4 + - - +
79C LEU* 3.0 13.0 + - + +
80C HIS* 2.8 28.0 + - + +
103C PHE* 3.8 15.3 - - + -
110C LEU* 3.9 23.1 - - + -
218C VAL* 4.0 13.0 - - + -
221C ALA* 4.0 16.8 - - + -
222C ILE* 3.6 29.8 - - + +
225C TYR* 6.4 0.9 - - + -
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Residues in contact with CYS 77 (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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73C GLY 2.9 16.6 + - - +
74C PRO* 3.5 6.1 - - + +
76C LEU* 1.3 77.2 - - - +
78C CYS* 1.3 55.2 + - - +
80C HIS* 3.2 0.9 + - - +
81C ALA* 2.7 39.5 + - - +
99C PHE* 3.9 18.2 - - - -
103C PHE* 3.8 18.7 - - + -
112C VAL* 3.9 21.5 - - + -
142C VAL* 3.8 30.5 - - - -
143C VAL* 5.4 1.8 - - - -
146C GLN* 4.4 8.1 - - + -
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Residues in contact with CYS 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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49C LEU* 3.5 22.7 - - + -
74C PRO 3.0 9.7 + - - +
75C LEU 3.5 9.4 - - - +
77C CYS* 1.3 77.3 - - - +
79C LEU* 1.3 59.2 + - - +
81C ALA* 3.5 5.5 - - - +
82C ASP* 3.0 33.6 + - - +
143C VAL* 4.1 20.5 - - + +
146C GLN* 4.3 9.6 - - - -
147C GLN* 4.0 16.4 - - - -
150C VAL* 3.7 25.4 - - + -
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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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49C LEU* 4.5 13.5 - - + -
53C LYS* 4.2 19.1 - - + -
59C LEU* 3.8 17.3 - - + -
63C LEU* 3.6 32.3 - - + -
75C LEU* 3.1 20.4 + - + +
76C LEU* 3.0 13.9 + - + +
78C CYS* 1.3 77.3 - - - +
80C HIS* 1.3 68.1 + - + +
82C ASP* 4.0 3.5 - - + +
83C MET* 3.1 22.7 + - - +
225C TYR* 3.6 48.1 - - + +
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Residues in contact with HIS 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 LEU* 2.8 21.2 + - + +
77C CYS 3.9 0.7 - - - +
79C LEU* 1.3 74.0 - - + +
81C ALA* 1.3 64.6 + - - +
83C MET* 3.0 32.8 - - + +
84C LEU* 3.1 12.1 - - - +
99C PHE* 4.3 10.4 - - + -
102C SER* 5.8 2.6 - - - -
103C PHE* 3.3 29.3 - + + -
221C ALA* 2.8 52.4 + - + +
224C LEU* 3.9 22.4 - - + +
225C TYR* 4.2 16.2 - - + -
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Residues in contact with ALA 81 (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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77C CYS* 2.7 19.1 + - - +
78C CYS 3.5 4.5 - - - +
80C HIS* 1.3 72.2 - - - +
82C ASP* 1.3 52.8 + - - +
83C MET 2.7 15.1 + - - -
84C LEU* 2.7 32.8 + - - +
99C PHE* 4.2 15.2 - - + -
139C VAL* 4.2 16.2 - - + +
143C VAL* 3.7 28.3 - - + -
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Residues in contact with ASP 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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50C GLU* 4.1 11.9 - - - +
53C LYS* 3.4 37.5 + - + +
78C CYS 3.0 16.5 + - - +
79C LEU* 4.0 3.8 - - + +
81C ALA* 1.3 76.0 - - - +
83C MET* 1.3 61.0 + - - +
84C LEU 3.0 13.0 + - - +
143C VAL* 5.4 0.4 - - + +
225C TYR* 5.7 1.0 + - - -
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Residues in contact with MET 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 14.8 + - - +
80C HIS* 3.0 40.8 - - + +
81C ALA 2.7 4.0 + - - -
82C ASP* 1.3 76.1 - - - +
84C LEU* 1.3 67.7 + - + +
85C GLY 3.7 1.6 + - - -
86C SER* 5.7 0.2 + - - -
95C ALA* 5.0 10.8 - - + +
224C LEU* 4.3 37.0 - - + -
225C TYR* 4.6 13.5 - - + -
228C HIS* 3.8 46.1 + - + -
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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