Contacts of the helix formed by residues 87 - 101 (chain F) in PDB entry 2ORE
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 CYS 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83F PRO 5.9 0.7 - - - +
84F GLU 4.5 4.3 - - - -
85F THR 2.9 8.6 + - - -
86F ASN* 1.3 77.0 - - - +
88F ALA* 1.3 68.9 + - - +
89F GLU* 2.9 11.9 + - + +
90F VAL* 3.0 44.6 + - - -
91F TYR* 3.0 9.7 + - - +
135F PHE* 3.5 10.8 - - - -
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Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E GLN 4.7 9.4 - - - +
87F CYS* 1.3 70.4 - - - +
89F GLU* 1.3 65.8 + - - +
91F TYR* 3.9 4.0 - - - -
92F TYR* 3.0 43.4 + - + -
135F PHE* 3.0 32.1 - - + -
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F CYS* 2.9 16.7 + - + +
88F ALA* 1.3 78.2 - - - +
90F VAL* 1.3 65.2 + - + +
92F TYR* 4.3 2.3 - - - +
93F GLN* 3.5 16.4 + - - +
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLU 3.3 22.4 - - - +
85F THR* 3.4 41.7 - - + +
87F CYS* 3.0 15.7 + - - +
89F GLU* 1.3 80.7 - - + +
91F TYR* 1.3 67.6 + - - +
93F GLN* 3.1 14.7 - - - +
94F PHE* 2.9 37.3 + - + -
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Residues in contact with TYR 91 (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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87F CYS 3.0 11.7 + - - +
88F ALA* 3.4 8.5 - - - +
90F VAL* 1.3 75.9 - - - +
92F TYR* 1.3 76.3 + + - +
93F GLN 2.8 0.9 + - - -
94F PHE* 2.7 27.9 + - - +
95F ARG* 2.8 18.2 + - + -
113F TYR* 3.5 27.8 + + - +
114F LEU* 3.8 19.8 + - + +
117F TYR* 3.9 6.3 - - + -
118F GLY* 3.3 34.2 - - - -
131F PHE* 3.9 13.2 - - - -
133F VAL 3.2 20.5 + - - -
134F PRO* 3.4 7.8 + - + -
135F PHE* 3.5 47.1 - + + -
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Residues in contact with TYR 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ARG* 3.8 5.4 + - - +
235E GLU* 4.6 1.3 - - - -
238E GLN* 3.1 53.4 - - + +
242E LEU* 6.1 0.5 - - - +
88F ALA* 3.0 46.6 + - + +
89F GLU 4.5 1.8 - - - +
91F TYR* 1.3 84.7 - + - +
93F GLN* 1.3 61.2 + - - +
95F ARG* 3.4 41.1 + - - +
96F GLU* 3.0 23.0 + - - +
134F PRO* 3.6 10.6 - - + +
135F PHE* 3.1 33.9 + - + +
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Residues in contact with GLN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLU 3.5 12.6 + - - +
90F VAL* 3.1 18.0 + - - +
91F TYR 2.8 1.0 + - - -
92F TYR* 1.3 78.1 - - - +
94F PHE* 1.3 80.5 + - + +
96F GLU* 3.0 9.3 + - - +
97F GLU* 2.9 33.0 + - + +
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Residues in contact with PHE 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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80F LEU* 3.3 36.1 - - + -
85F THR* 4.0 14.6 - - + -
90F VAL* 2.9 29.1 + - + -
91F TYR 2.7 13.1 + - - +
93F GLN* 1.3 96.6 - - + +
95F ARG* 1.3 60.1 + - - +
97F GLU* 3.9 9.0 - - - -
98F PHE* 3.2 22.5 + - - +
106F ARG* 4.5 11.7 - - - -
110F LEU* 3.7 25.2 - - + +
113F TYR* 3.4 39.0 - + + -
114F LEU* 4.5 2.3 - - + +
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Residues in contact with ARG 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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235E GLU* 3.0 39.6 + - - -
238E GLN* 3.9 4.0 + - - +
91F TYR* 2.8 19.5 + - + +
92F TYR* 3.4 35.4 + - - +
93F GLN 3.1 0.4 - - - -
94F PHE* 1.3 76.1 - - - +
96F GLU* 1.3 60.3 + - - +
98F PHE* 3.4 3.8 - - - +
99F ASN* 3.0 35.2 + - - +
114F LEU* 3.9 15.0 - - + +
131F PHE* 3.6 31.4 + - + -
132F ASN* 3.3 16.9 - - - +
133F VAL 3.2 25.9 + - - -
134F PRO 4.1 0.2 - - - -
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Residues in contact with GLU 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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92F TYR 3.0 16.5 + - - +
93F GLN* 3.0 7.1 + - - +
95F ARG* 1.3 74.4 - - - +
97F GLU* 1.3 66.9 + - - +
98F PHE 3.0 1.3 - - - -
99F ASN* 3.1 7.2 + - + +
100F LYS* 2.9 61.4 + - + +
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Residues in contact with GLU 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 GLN* 2.9 20.1 + - + +
94F PHE* 4.0 16.7 - - - +
96F GLU* 1.3 76.3 - - - +
98F PHE* 1.3 52.8 + - - +
100F LYS* 3.6 5.1 - - - +
101F SER* 2.7 43.2 + - - -
106F ARG* 2.5 51.3 + - - +
110F LEU* 4.0 6.3 - - + -
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Residues in contact with PHE 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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58F ASP* 3.3 27.6 - - - -
94F PHE 3.2 17.4 + - - +
95F ARG 3.4 3.8 - - - +
96F GLU 3.0 0.2 - - - -
97F GLU* 1.3 75.9 - - - +
99F ASN* 1.3 72.9 + - - +
100F LYS 2.9 5.1 + - - -
101F SER* 3.2 8.6 + - - +
107F ARG* 2.6 84.6 + - + -
110F LEU* 3.8 19.7 - - + +
111F PHE* 4.1 22.4 - + + -
114F LEU* 3.8 19.1 - - + -
125F TYR* 5.2 2.2 - + - -
131F PHE* 4.0 20.4 - + + -
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Residues in contact with ASN 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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95F ARG* 3.0 30.5 + - - +
96F GLU* 3.1 7.5 + - + +
98F PHE* 1.3 84.0 - - - +
100F LYS* 1.3 61.5 + - + +
101F SER 4.8 0.3 - - - +
107F ARG* 4.3 5.4 + - - +
129F GLY 4.5 0.9 - - - +
130F GLU* 3.1 30.2 + - + +
131F PHE* 2.7 50.9 + - - +
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Residues in contact with LYS 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 GLU* 2.9 53.6 + - + +
97F GLU* 3.9 4.3 - - - +
99F ASN* 1.3 82.7 - - + +
101F SER* 1.3 67.4 + - - +
102F GLN* 3.5 17.7 - - - +
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Residues in contact with SER 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 GLU* 2.7 26.0 + - - -
98F PHE* 3.2 1.9 + - - -
99F ASN 4.8 0.7 - - - +
100F LYS* 1.3 76.9 - - - +
102F GLN* 1.3 64.7 + - - +
103F ASP* 3.1 24.1 + - - +
106F ARG* 4.2 15.0 - - - +
107F ARG* 3.5 34.7 + - - +
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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
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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