Contacts of the helix formed by residues 83 - 95 (chain F) in PDB entry 1O1F
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 THR 83 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785D GLU 6.5 0.4 - - - -
786D ILE* 6.4 0.2 - - - -
789D ALA* 4.7 3.6 - - + -
80F ASP 5.2 3.8 - - - +
81F GLN* 3.1 14.6 + - - +
82F GLY* 1.3 71.1 - - - +
84F PHE* 1.3 64.1 + - - +
85F GLU* 3.2 16.1 + - - +
86F ASP* 3.1 38.6 + - + +
87F PHE* 3.4 16.3 + - - -
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Residues in contact with PHE 84 (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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82F GLY 3.8 3.4 + - - -
83F THR* 1.3 70.9 + - - +
85F GLU* 1.3 95.2 + - - +
87F PHE* 3.6 10.9 - - - +
88F VAL* 3.2 35.2 + - + +
143F VAL* 5.4 0.2 - - + -
147F MET* 3.6 33.4 - - + -
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Residues in contact with GLU 85 (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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83F THR* 3.2 11.7 + - - +
84F PHE* 1.3 113.8 - - - +
86F ASP* 1.3 61.4 + - - +
88F VAL* 3.3 2.9 + - - +
89F GLU* 2.9 52.8 + - - +
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Residues in contact with ASP 86 (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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785D GLU* 5.8 1.9 - - - +
786D ILE* 3.6 45.8 - - + +
83F THR* 3.1 35.9 + - + +
85F GLU* 1.3 80.7 - - - +
87F PHE* 1.3 60.5 + - + +
89F GLU* 3.6 11.7 - - - +
90F GLY* 2.9 26.0 + - - -
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Residues in contact with PHE 87 (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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786D ILE* 3.7 5.4 - - - -
789D ALA* 2.5 38.8 - - + -
790D THR* 1.5 65.2 - - + +
793D ARG* 4.5 14.4 - - + -
82F GLY* 4.0 7.6 - - - -
83F THR 3.4 28.5 - - - -
84F PHE* 3.3 14.8 + - - +
85F GLU 3.3 0.4 - - - -
86F ASP* 1.3 80.2 - - + +
88F VAL* 1.3 63.2 + - - +
90F GLY* 3.4 7.0 + - - -
91F LEU* 3.4 21.7 + - + +
143F VAL* 4.2 15.9 - - + -
147F MET* 4.0 16.8 - - + -
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Residues in contact with VAL 88 (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 PHE* 3.2 24.5 + - + +
85F GLU* 4.0 2.9 - - - +
87F PHE* 1.3 76.4 - - - +
89F GLU* 1.3 60.1 + - + +
91F LEU* 3.4 6.5 + - - +
92F ARG* 2.9 32.5 + - + +
139F TYR* 4.1 18.3 - - + +
140F GLU* 5.3 12.1 - - + +
143F VAL* 4.0 27.6 - - + -
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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
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722D GLN* 4.4 15.8 + - - +
786D ILE* 5.5 4.6 - - + +
85F GLU* 2.9 45.8 + - - +
86F ASP* 3.6 13.7 - - - +
88F VAL* 1.3 76.9 - - + +
90F GLY* 1.3 64.9 + - - +
92F ARG* 3.2 7.9 + - + +
93F VAL* 3.0 32.4 + - + +
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Residues in contact with GLY 90 (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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786D ILE* 4.8 16.5 - - - +
86F ASP 2.9 18.3 + - - -
87F PHE 3.8 2.0 - - - -
88F VAL 3.3 0.4 - - - -
89F GLU* 1.3 78.3 - - - +
91F LEU* 1.3 63.1 - - - +
93F VAL* 3.2 13.6 + - - +
94F PHE* 3.3 11.1 + - - +
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Residues in contact with LEU 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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790D THR* 6.3 3.8 - - + -
87F PHE 3.4 10.6 + - - +
88F VAL 3.4 4.3 + - - +
89F GLU 3.4 0.2 - - - -
90F GLY* 1.3 77.0 - - - +
92F ARG* 1.3 58.3 + - - +
94F PHE* 3.1 33.5 + - + +
95F ASP* 2.9 24.9 - - - +
102F VAL* 4.5 6.3 - - + -
107F LEU* 4.7 10.5 - - + -
139F TYR* 3.1 34.3 + - + -
142F PHE* 4.5 12.1 - - + -
143F VAL* 3.8 28.9 - - + -
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Residues in contact with ARG 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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88F VAL* 2.9 24.2 + - + +
89F GLU* 3.2 11.6 + - + +
91F LEU* 1.3 77.7 - - - +
93F VAL* 1.3 60.3 + - + +
95F ASP 3.2 20.9 - - - +
97F GLU 4.8 8.7 - - - -
98F GLY* 3.9 9.5 - - - -
99F ASN* 3.7 20.2 - - - +
100F GLY* 3.7 22.4 - - - +
139F TYR* 3.0 24.7 + - - +
140F GLU* 3.8 24.0 + - - +
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Residues in contact with VAL 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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779D ARG* 4.7 17.0 - - - +
89F GLU* 3.0 18.0 + - + +
90F GLY* 3.2 9.8 + - - +
92F ARG* 1.3 80.5 - - + +
94F PHE* 1.3 60.0 + - - +
95F ASP 3.4 1.9 + - - -
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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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90F GLY 3.3 10.2 + - - +
91F LEU* 3.1 27.1 + - + +
93F VAL* 1.3 79.5 - - - +
95F ASP* 1.3 59.7 + - - +
102F VAL* 3.6 40.4 - - + -
106F GLU* 3.8 29.6 - - + +
107F LEU* 4.3 4.9 - - + -
110F VAL* 3.7 33.9 - - + -
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Residues in contact with ASP 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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91F LEU 2.9 8.5 + - - +
92F ARG 3.2 14.8 - - - +
93F VAL 3.4 1.9 - - - -
94F PHE* 1.3 82.7 - - + +
96F LYS* 1.3 78.5 + - - +
97F GLU 4.1 3.6 - - - +
99F ASN 3.7 6.4 - - - +
101F THR 3.1 30.0 + - - +
102F VAL* 3.4 14.9 - - - +
103F MET* 6.4 0.4 - - + -
106F GLU* 5.1 4.7 - - - +
139F TYR* 2.8 43.1 + - - -
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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