Contacts of the helix formed by residues 91 - 103 (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 GLU 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F LYS* 1.3 115.3 - - + +
92F ALA* 1.3 55.5 + - - +
93F LYS 3.1 3.6 - - - -
94F LYS* 2.7 48.4 + - + +
95F ALA* 3.5 4.7 + - - +
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Residues in contact with ALA 92 (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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84F LEU* 4.7 6.6 - - + +
89F PRO* 3.9 32.1 - - + +
90F LYS 2.9 5.2 + - - +
91F GLU* 1.3 76.1 - - - +
93F LYS* 1.3 61.3 + - - +
95F ALA* 3.3 15.5 + - - +
96F PHE 3.3 9.5 + - - -
135F GLN* 3.5 17.2 + - - +
136F ARG* 5.8 1.6 - - - +
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Residues in contact with LYS 93 (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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90F LYS 4.5 2.1 + - - +
91F GLU 3.1 1.2 - - - -
92F ALA* 1.3 76.2 - - - +
94F LYS* 1.3 64.8 + - - +
95F ALA 3.2 0.4 + - - -
96F PHE* 3.9 3.2 - - + +
97F LEU* 3.5 18.0 + - - +
135F GLN* 4.2 21.3 - - - +
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Residues in contact with LYS 94 (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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91F GLU* 2.7 38.1 + - + +
93F LYS* 1.3 75.4 + - - +
95F ALA* 1.3 57.5 + - - +
97F LEU* 3.4 38.4 - - - +
98F ASP* 3.6 9.0 - - - +
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Residues in contact with ALA 95 (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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84F LEU* 4.4 23.3 - - + -
91F GLU 3.5 3.7 + - - +
92F ALA* 3.3 10.2 + - - +
93F LYS 3.2 0.2 - - - -
94F LYS* 1.3 76.7 - - - +
96F PHE* 1.3 57.7 + - - +
97F LEU 2.8 11.1 + - - -
98F ASP* 3.1 19.8 + - - +
99F PHE* 3.3 13.4 + - - +
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Residues in contact with PHE 96 (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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84F LEU* 4.8 6.2 - - + +
92F ALA 3.3 4.5 + - - +
93F LYS* 4.1 6.1 - - + +
94F LYS 3.6 0.2 - - - -
95F ALA* 1.3 77.4 - - - +
97F LEU* 1.3 61.1 + - - +
99F PHE* 4.1 15.3 - + - -
100F TYR* 3.1 37.8 + + + +
104F LEU* 4.2 15.9 - - + -
122F LEU* 5.9 4.3 - - + -
135F GLN* 3.3 55.9 - - + +
138F PHE* 4.5 19.5 - + + -
139F VAL* 3.6 28.7 - - + -
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Residues in contact with LEU 97 (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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93F LYS 3.5 11.5 + - - +
94F LYS* 3.4 38.8 - - - +
95F ALA 2.8 0.6 + - - -
96F PHE* 1.3 81.4 - - - +
98F ASP* 1.3 75.6 - - - +
100F TYR* 3.2 4.5 + - - +
101F HIS* 2.9 60.3 + - + +
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Residues in contact with ASP 98 (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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80F HIS* 6.1 4.0 - - + +
94F LYS 3.6 14.5 - - - +
95F ALA* 3.1 8.9 + - - +
97F LEU* 1.3 84.4 - - - +
99F PHE* 1.3 58.0 + - - +
100F TYR 2.8 4.3 - - - -
101F HIS* 2.6 32.2 + - - +
102F SER* 2.8 20.2 + - - +
224F LEU* 5.6 9.7 - - + +
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Residues in contact with PHE 99 (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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77F CYS* 3.8 29.2 - - - -
80F HIS* 4.5 15.0 + - + +
81F ALA* 4.9 5.6 - - + -
84F LEU* 5.8 10.5 - - + -
95F ALA 3.3 13.2 + - - +
96F PHE* 4.0 23.6 - + - +
98F ASP* 1.3 78.6 - - - +
100F TYR* 1.3 60.1 + - - +
103F PHE* 3.1 53.8 + + - +
104F LEU* 3.9 21.1 + - + +
139F VAL* 3.7 36.6 - - + -
142F VAL* 4.1 22.2 - - + -
143F VAL* 5.5 0.4 - - + -
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Residues in contact with TYR 100 (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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96F PHE* 3.1 34.5 + + + +
97F LEU* 3.4 4.7 - - - +
98F ASP 2.7 4.8 + - - -
99F PHE* 1.3 75.7 - - - +
101F HIS* 1.3 72.0 + + - +
102F SER 3.2 2.1 + - - -
104F LEU* 3.4 37.6 + - + -
105F GLU* 2.8 56.7 + - - -
122F LEU* 3.6 39.5 - - + +
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Residues in contact with HIS 101 (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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97F LEU* 2.9 49.3 + - + +
98F ASP* 2.6 14.8 + - - +
100F TYR* 1.3 84.5 - + - +
102F SER* 1.3 57.9 + - - +
105F GLU* 3.8 28.3 + - - +
108F ALA* 3.3 19.2 - - - +
109F VAL* 4.6 3.6 + - - +
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Residues in contact with SER 102 (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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80F HIS* 5.6 3.4 - - - -
98F ASP* 2.8 17.7 + - - +
101F HIS* 1.3 80.1 - - - +
103F PHE* 1.3 83.7 + - - +
108F ALA* 3.2 9.1 - - - +
109F VAL* 4.9 5.1 - - - +
110F LEU* 2.8 42.9 + - - +
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Residues in contact with PHE 103 (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 4.3 0.9 - - - -
76F LEU* 3.9 15.0 - - + -
77F CYS* 3.8 22.4 - - + -
80F HIS* 3.5 32.1 - + - -
99F PHE* 3.1 43.6 + + + +
102F SER* 1.3 91.4 - - - +
104F LEU* 1.3 66.4 + - + +
105F GLU 3.3 5.1 + - - +
108F ALA* 4.3 0.4 - - - -
110F LEU* 3.2 50.5 - - + +
111F ARG* 3.5 8.0 - - - +
112F VAL* 3.3 48.8 + - + +
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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