Contacts of the strand formed by residues 117 - 125 (chain C) in PDB entry 2OVI
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 MET 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C LYS* 3.1 4.3 - - - +
114C PHE 2.7 40.5 + - - +
115C MET 4.4 3.1 - - - +
116C GLY* 1.3 81.2 - - - +
118C ASP* 1.3 65.6 + - - +
119C THR* 3.4 1.8 + - + +
139C ARG* 4.0 21.8 - - - +
143C ARG* 5.4 3.4 - - + +
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Residues in contact with ASP 118 (chain C).
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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111C GLU* 5.3 9.6 - - + +
112C ARG 3.5 5.6 - - - -
113C LYS* 3.0 34.4 - - - +
116C GLY 4.4 0.2 + - - -
117C MET* 1.3 71.4 - - - +
119C THR* 1.3 57.4 + - - +
139C ARG* 2.8 33.4 + - - +
145C LEU* 3.5 15.4 - - + +
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ILE 4.1 0.2 - - - +
111C GLU* 3.3 6.7 - - - +
112C ARG* 2.7 50.5 + - - +
114C PHE* 3.6 26.3 - - + +
117C MET* 3.4 11.0 - - + +
118C ASP* 1.3 73.5 - - - +
120C ALA* 1.3 61.0 + - - +
121C SER* 5.5 1.0 + - - -
136C PHE* 4.5 22.4 - - + -
139C ARG* 3.2 24.0 - - - +
145C LEU* 4.1 4.9 - - - -
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ILE 3.3 6.1 - - - -
111C GLU* 4.4 8.1 - - - +
119C THR* 1.3 74.4 - - - +
121C SER* 1.3 61.0 + - - +
136C PHE* 3.5 5.8 - - - +
137C LEU* 3.0 57.5 + - + +
145C LEU* 3.9 14.9 - - + +
150C VAL* 5.3 1.1 - - + -
153C PHE* 4.2 20.6 - - + -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA 3.7 0.5 - - - +
109C LEU* 3.4 4.0 - - - -
110C ILE* 2.8 70.6 + - - +
119C THR* 4.3 1.8 + - - -
120C ALA* 1.3 75.1 - - - +
122C ILE* 1.3 66.6 + - - +
123C LEU* 3.3 9.8 - - - +
135C ILE 3.1 12.8 - - - -
136C PHE* 3.7 30.0 - - - -
137C LEU* 5.6 0.2 - - - -
153C PHE* 3.7 4.4 - - - -
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Residues in contact with ILE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.9 21.3 - - + -
54C VAL* 3.7 30.1 - - + -
57C TRP* 4.3 17.5 - - + -
107C ILE* 3.9 12.3 - - + -
108C ALA 3.3 8.5 - - - +
109C LEU* 4.1 17.7 - - + -
121C SER* 1.3 77.9 - - - +
123C LEU* 1.3 63.8 + - - +
124C PHE* 3.8 21.4 - - + -
133C LEU 4.1 0.2 - - - +
134C LYS* 3.2 5.5 - - - +
135C ILE* 2.7 48.5 + - + +
137C LEU* 5.5 1.6 - - + -
153C PHE* 4.3 6.3 - - + -
156C LEU* 4.6 2.5 - - + -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 5.4 2.7 - - + -
29C LEU* 4.2 12.8 - - + -
33C VAL* 4.4 10.3 - - + -
107C ILE* 3.2 6.8 - - - +
108C ALA* 2.8 36.4 + - + +
110C ILE* 3.7 20.4 - - + -
121C SER* 3.3 28.7 - - - +
122C ILE* 1.3 78.0 - - - +
124C PHE* 1.3 63.2 + - - +
125C PHE* 3.6 32.9 - - + -
131C ALA* 4.6 2.5 - - + -
133C LEU 3.6 4.0 - - - +
134C LYS* 3.9 35.0 - - + +
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.8 36.1 - + - -
50C VAL* 4.0 15.7 - - + -
51C TRP* 4.0 16.4 - + - -
99C ILE* 6.3 1.3 - - + -
104C CYS* 4.0 7.9 - - + -
106C HIS 3.8 3.4 - - - -
107C ILE* 3.7 26.7 - - + +
122C ILE* 3.8 24.9 - - + -
123C LEU* 1.3 75.8 - - - +
125C PHE* 1.3 55.1 + - - +
131C ALA* 3.4 2.3 - - - -
132C MET* 2.6 44.0 + - + +
133C LEU* 3.0 36.8 + - + +
135C ILE* 3.9 24.0 - - + -
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 3.8 15.7 - - + -
30C LEU* 3.5 42.6 - - + -
33C VAL* 3.8 22.4 - - + -
104C CYS* 3.2 6.8 - - - -
105C THR* 2.9 25.5 + - - +
106C HIS* 2.7 32.7 + - + +
108C ALA* 3.7 16.6 - - + -
123C LEU* 3.6 31.6 - - + -
124C PHE* 1.3 73.0 - - - +
126C ASN* 1.3 66.7 + - - +
129C GLY* 3.6 11.7 - - - -
130C SER 3.3 20.2 - - - +
131C ALA* 3.8 6.5 - - - -
132C MET* 4.0 4.3 - - - -
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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