Contacts of the helix formed by residues 72 - 83 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279D LYS* 5.6 1.6 - - - +
66F VAL* 4.4 14.6 - - + +
67F ALA* 5.1 10.5 - - + +
70F PHE 3.6 8.0 - - - +
71F GLU* 1.3 88.3 - - + +
73F GLY* 1.3 67.2 + - - +
75F LEU* 4.5 2.7 - - + -
76F LEU* 3.0 41.1 + - + +
110F LEU* 4.7 4.9 - - + -
208F ILE* 5.4 5.4 - - + -
214F LYS* 5.7 7.9 - - + -
218F VAL* 3.6 32.8 - - + -
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Residues in contact with GLY 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLU* 2.9 9.6 + - - +
72F PRO* 1.3 86.9 - - - +
74F PRO* 1.3 69.8 - - - +
76F LEU* 3.0 8.8 + - - +
77F CYS* 3.0 11.1 + - - +
103F PHE* 4.3 0.9 - - - -
110F LEU* 4.7 14.6 - - - -
111F ARG 5.1 3.8 - - - -
112F VAL* 3.9 18.2 - - - +
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Residues in contact with PRO 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLU* 3.5 18.2 - - + +
73F GLY* 1.3 86.0 - - - +
75F LEU* 1.3 62.0 + - - +
77F CYS* 3.3 4.9 - - + +
78F CYS* 3.2 27.4 + - - -
111F ARG 5.8 0.7 - - - +
112F VAL* 4.1 4.2 - - + -
113F PRO* 4.8 9.4 - - + -
146F GLN* 3.4 30.5 - - + +
149F ALA* 4.2 19.7 - - + -
150F VAL* 3.8 18.4 - - + +
153F GLN* 4.8 7.6 - - - +
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 3.6 25.6 - - + -
59F LEU* 5.9 0.2 - - + -
62F LEU* 3.9 16.4 - - + -
63F LEU* 3.4 32.3 - - + -
66F VAL* 3.6 34.5 - - + -
71F GLU 5.0 0.4 + - - -
72F PRO* 4.2 3.9 + - + +
73F GLY 3.0 1.2 + - - -
74F PRO* 1.3 74.6 - - - +
76F LEU* 1.3 68.0 + - + +
77F CYS 3.0 3.1 + - - -
78F CYS* 3.3 2.7 + - - +
79F LEU* 3.2 26.3 + - + +
150F VAL* 3.5 27.3 - - + +
153F GLN* 4.0 13.5 - - - +
154F LEU* 6.4 0.4 - - + -
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LEU* 5.0 11.4 - - + -
72F PRO* 3.0 39.6 + - + +
73F GLY 3.0 2.7 + - - +
75F LEU* 1.3 78.0 - - + +
77F CYS* 1.3 60.6 + - - +
79F LEU* 4.0 10.4 - - + +
80F HIS* 3.2 30.4 + - + +
103F PHE* 3.9 13.5 - - + -
110F LEU* 3.9 13.2 - - + -
218F VAL* 4.1 14.8 - - + +
221F ALA* 3.8 34.1 - - + +
222F ILE* 3.7 27.4 - - + -
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Residues in contact with CYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F GLY 3.0 11.3 + - - +
74F PRO* 3.3 14.8 - - + +
75F LEU 3.0 0.2 - - - -
76F LEU* 1.3 74.6 - - - +
78F CYS* 1.3 66.9 + - - +
80F HIS* 3.1 4.9 + - - +
81F ALA* 2.9 22.7 + - - +
99F PHE* 3.8 18.1 - - - -
103F PHE* 3.8 17.9 - - + -
112F VAL* 4.4 11.9 - - + -
142F VAL* 3.5 33.0 - - - -
143F VAL* 5.2 3.4 - - - -
146F GLN* 4.2 10.5 - - + -
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Residues in contact with CYS 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 3.4 29.2 - - + -
74F PRO 3.2 15.6 + - - -
75F LEU 3.9 4.7 - - - +
77F CYS* 1.3 78.0 - - - +
79F LEU* 1.3 62.7 + - - +
81F ALA* 3.4 8.8 - - - +
82F ASP* 3.1 21.3 + - - +
143F VAL* 4.2 24.9 - - + +
146F GLN* 3.7 22.2 - - - -
147F GLN* 4.4 7.0 - - - -
150F VAL* 3.8 12.8 - - - -
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 4.6 9.2 - - + -
53F LYS* 3.9 21.8 - - + -
59F LEU* 4.1 23.6 - - + -
63F LEU* 4.3 20.9 - - + -
75F LEU* 3.2 21.4 + - + +
76F LEU* 4.0 11.2 - - + +
77F CYS 3.1 0.6 - - - -
78F CYS* 1.3 76.9 - - - +
80F HIS* 1.3 66.7 + - + +
82F ASP* 3.2 10.8 + - - +
83F MET 3.3 1.9 + - - -
222F ILE* 6.4 0.9 - - + -
225F TYR* 3.1 69.1 - - + -
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Residues in contact with HIS 80 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76F LEU* 3.2 19.6 + - + +
77F CYS 3.1 4.1 + - - +
79F LEU* 1.3 79.3 - - + +
81F ALA* 1.3 63.3 + - - +
83F MET* 2.9 39.6 + - - +
84F LEU* 3.2 10.8 - - + +
98F ASP* 6.1 3.3 - - + +
99F PHE* 4.5 19.9 + - + +
102F SER* 5.6 3.4 - - - -
103F PHE* 3.5 25.4 - + + -
221F ALA* 2.9 40.2 + - + +
224F LEU* 4.1 24.5 - - + +
225F TYR* 4.6 6.1 - - + -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77F CYS 2.9 11.3 + - - +
78F CYS 3.4 9.0 - - - +
80F HIS* 1.3 77.4 - - - +
82F ASP* 1.3 62.5 + - - +
84F LEU* 3.1 24.5 + - - +
85F GLY 4.0 5.0 + - - +
99F PHE* 4.9 7.4 - - + -
139F VAL* 3.8 17.4 - - + +
143F VAL* 3.3 35.0 - - + -
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Residues in contact with ASP 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 2.7 46.7 + - + +
78F CYS 3.1 10.1 + - - +
79F LEU* 3.2 11.0 + - - +
81F ALA* 1.3 79.4 - - - +
83F MET* 1.3 62.1 + - - +
84F LEU 3.0 3.5 + - - +
85F GLY 3.4 21.2 - - - +
225F TYR* 3.9 14.0 + - + -
228F HIS* 5.0 5.0 + - - -
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Residues in contact with MET 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F LEU 3.3 1.3 + - - +
80F HIS* 2.9 25.6 + - - +
82F ASP* 1.3 77.0 - - - +
84F LEU* 1.3 63.5 + - + +
224F LEU* 4.1 20.6 - - + +
225F TYR* 3.5 46.9 - - + -
227F ARG* 5.9 2.0 - - - +
228F HIS* 3.7 47.8 + - + -
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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