Contacts of the helix formed by residues 86 - 96 (chain F) in PDB entry 2OV2
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 SER 86 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F VAL* 5.8 0.4 - - - -
83F SER* 3.0 19.3 + - - +
84F LEU 3.5 0.6 - - - -
85F VAL* 1.3 79.2 - - - +
87F PRO* 1.3 66.7 - - - +
88F ALA* 3.1 8.0 + - - +
89F SER* 2.7 49.5 + - - -
90F PHE* 3.2 4.4 + - - +
137F ILE* 5.0 0.7 - - - -
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Residues in contact with PRO 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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85F VAL 3.8 7.6 - - - +
86F SER* 1.3 85.4 - - - +
88F ALA* 1.3 61.9 + - - +
90F PHE* 3.4 2.6 + - + +
91F GLU* 3.0 31.8 + - + +
129F LEU* 4.2 11.2 - - + -
134F LEU* 4.3 32.5 - - + -
135F ALA 3.4 24.5 - - - +
137F ILE* 3.9 24.0 - - + -
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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
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11F ASP* 4.2 3.8 - - - +
86F SER* 3.1 7.1 - - - +
87F PRO* 1.3 80.4 - - - +
89F SER* 1.3 61.1 + - - +
91F GLU* 3.3 8.2 + - - +
92F ASN* 3.1 28.8 + - - +
134F LEU* 5.9 0.8 - - - +
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Residues in contact with SER 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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11F ASP* 3.4 21.6 + - - +
12F GLY 5.6 0.2 - - - -
14F VAL* 3.7 26.0 - - - -
81F CYS 5.0 0.9 - - - +
82F PHE* 3.5 8.4 - - - +
83F SER 2.9 24.2 + - - -
86F SER* 2.7 32.0 + - - -
88F ALA* 1.3 77.3 - - - +
90F PHE* 1.3 61.4 + - - +
92F ASN* 3.3 11.1 + - - +
93F VAL* 3.3 9.7 + - - +
97F TRP* 5.0 2.1 - - - -
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Residues in contact with PHE 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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82F PHE* 3.5 45.3 - + + -
86F SER 3.2 2.0 + - - +
87F PRO* 3.4 9.4 - - + +
89F SER* 1.3 81.7 + - - +
91F GLU* 1.3 65.5 + - + +
93F VAL* 3.1 22.0 + - - +
94F ARG* 6.0 0.4 - - - -
137F ILE* 3.3 40.8 - - + -
141F GLN* 3.4 39.7 - - + -
142F GLY* 4.1 2.9 - - - -
145F MET* 3.4 47.1 - - + +
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Residues in contact with GLU 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 PRO* 3.0 20.4 + - + +
88F ALA* 3.7 8.3 - - - +
90F PHE* 1.3 80.5 - - + +
92F ASN* 1.3 58.5 + - - +
94F ARG* 3.2 20.7 + - - +
95F ALA* 2.9 27.1 + - + +
145F MET* 4.7 5.8 - - - -
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Residues in contact with ASN 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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11F ASP* 2.7 42.8 + - - +
88F ALA* 3.1 15.7 + - - +
89F SER 3.6 4.7 - - - +
90F PHE 3.2 0.8 - - - -
91F GLU* 1.3 73.8 - - - +
93F VAL* 1.3 60.6 + - - +
94F ARG 3.2 0.4 - - - -
95F ALA* 3.7 17.1 - - - +
96F LYS* 2.8 32.6 + - + +
97F TRP* 3.0 15.2 + - - +
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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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80F ILE* 4.1 13.9 - - + -
81F CYS 4.7 2.2 - - - +
82F PHE* 4.0 19.3 - - + -
89F SER 3.3 11.1 + - - +
90F PHE* 3.1 16.1 + - + +
92F ASN* 1.3 76.3 - - - +
94F ARG* 1.3 58.9 + - - +
97F TRP* 4.0 9.4 - - + -
98F TYR* 2.9 30.6 + - + +
112F LEU* 3.9 22.4 - - + -
145F MET* 3.9 14.6 - - + -
149F ILE* 3.7 31.6 - - + -
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Residues in contact with ARG 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 PHE* 6.0 1.2 - - - -
91F GLU* 3.2 22.8 + - - +
93F VAL* 1.3 82.3 - - - +
95F ALA* 1.3 63.6 - - - +
98F TYR* 4.6 8.9 - - + -
99F PRO* 3.3 19.2 - - - +
145F MET* 3.9 30.2 - - + +
148F GLU* 2.6 42.1 + - - +
149F ILE* 4.9 3.6 - - + -
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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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91F GLU* 2.9 17.6 + - + +
92F ASN* 3.7 17.3 - - - +
94F ARG* 1.3 79.9 - - - +
96F LYS* 1.3 59.3 + - - +
99F PRO* 3.8 10.2 - - - +
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Residues in contact with LYS 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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11F ASP* 5.2 2.5 - - - +
60F GLY 5.2 1.0 + - - -
62F GLU* 3.6 20.4 + - - +
65F ASP* 2.8 39.6 + - - -
68F ARG* 4.2 2.6 - - - +
92F ASN* 2.8 24.4 + - + +
94F ARG 3.4 0.4 - - - -
95F ALA* 1.3 80.3 - - - +
97F TRP* 1.3 93.5 + - + +
99F PRO* 3.4 5.7 - - - +
100F GLU* 2.9 44.1 + - - +
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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