Contacts of the strand formed by residues 129 - 141 (chain C) in PDB entry 1OPO
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 LYS 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ASP* 3.4 25.8 + - - -
192B ASP* 5.3 7.7 + - - +
194B LYS* 6.1 1.0 - - - +
127C PHE* 3.7 0.9 - - - +
128C ASN* 1.3 84.9 - - - +
130C TYR* 1.3 65.4 + - - +
195C THR* 4.1 15.5 - - + -
196C ARG 3.1 15.3 - - - +
197C PHE* 3.7 31.6 - - + -
198C ILE* 3.8 8.1 - - - +
239C LEU* 3.5 3.5 - - - +
240C SER* 2.9 37.6 + - - +
241C ASP* 3.8 16.2 - - + +
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Residues in contact with TYR 130 (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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109C VAL 4.3 2.3 + - - -
111C PRO* 3.7 30.4 - - + +
129C LYS* 1.3 76.4 - - - +
131C ARG* 1.3 64.7 + - - +
132C ILE* 4.1 31.2 - - + -
194C LYS 4.1 0.7 - - - +
195C THR* 3.6 3.5 - - - -
196C ARG* 2.8 57.3 + - + +
197C PHE 3.5 11.4 - - - -
198C ILE* 3.7 17.9 - - + -
209C VAL* 2.7 29.0 + - + -
210C ASP* 3.8 0.3 - - - -
211C PHE* 3.3 23.7 + + + +
237C ILE* 4.2 5.8 - - + -
238C VAL 3.1 9.2 - - - +
239C LEU* 3.9 18.6 - - + -
240C SER* 4.8 0.7 - - - -
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Residues in contact with ARG 131 (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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130C TYR* 1.3 78.3 - - - +
132C ILE* 1.3 72.1 + - - +
133C THR* 3.8 21.9 + - - +
192C ASP 5.0 0.7 - - - +
193C GLY* 3.2 32.2 + - - -
194C LYS 3.5 14.6 - - - +
195C THR* 3.6 21.8 + - + +
237C ILE* 3.5 1.3 - - - -
238C VAL* 2.8 58.2 + - + +
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Residues in contact with ILE 132 (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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109C VAL* 3.9 19.7 - - + -
111C PRO* 5.8 0.4 - - + -
117C PHE* 5.2 2.2 - - + -
130C TYR* 4.1 16.9 - - + -
131C ARG* 1.3 76.8 - - - +
133C THR* 1.3 63.9 + - - +
134C ALA 3.8 21.1 - - - +
135C LEU* 4.1 20.0 - - + -
191C VAL* 2.8 28.8 - - + +
192C ASP* 4.0 4.0 - - - +
194C LYS 4.9 1.2 + - - -
211C PHE* 3.8 40.3 - - + -
235C TYR* 5.9 0.4 - - + -
236C THR 3.7 5.4 - - - +
237C ILE* 3.9 26.9 - - + +
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Residues in contact with THR 133 (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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131C ARG* 4.0 30.1 - - - +
132C ILE* 1.3 78.2 - - - +
134C ALA* 1.3 64.1 + - - +
191C VAL* 3.8 17.5 - - - +
236C THR* 2.8 31.6 + - - +
238C VAL* 4.1 20.0 - - + -
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Residues in contact with ALA 134 (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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132C ILE* 3.7 3.9 - - - +
133C THR* 1.3 84.3 + - - +
135C LEU* 1.3 63.7 + - - +
191C VAL* 4.3 3.4 - - - -
234C GLN 4.4 0.7 - - - -
235C TYR* 3.3 7.5 - - - +
236C THR* 2.9 46.2 + - - +
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Residues in contact with LEU 135 (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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109C VAL* 4.3 24.9 - - + -
117C PHE* 5.6 5.4 - - + -
132C ILE* 4.1 16.2 - - + -
134C ALA* 1.3 75.1 - - - +
136C THR* 1.3 69.4 + - - +
137C VAL* 5.8 0.2 - - + -
188C VAL* 3.9 1.0 - - - +
189C ILE* 3.0 49.9 + - + +
191C VAL* 4.4 6.8 - - + +
211C PHE* 4.1 23.6 - - + -
214C ILE* 5.3 4.5 - - + -
233C ILE* 4.1 20.0 - - + -
234C GLN 3.5 14.4 - - - +
235C TYR* 3.7 18.4 - - + -
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Residues in contact with THR 136 (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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135C LEU* 1.3 79.6 + - - +
137C VAL* 1.3 76.8 + - - +
138C LYS* 4.3 14.3 + - + +
186C ASP* 4.3 13.0 - - + +
187C LEU 3.4 16.4 - - - +
188C VAL* 4.1 14.7 - - + +
189C ILE* 4.7 0.4 - - - +
232C PHE 3.7 0.5 - - - +
233C ILE* 3.4 5.0 - - - +
234C GLN* 2.8 52.4 + - - +
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Residues in contact with VAL 137 (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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91C LEU* 4.7 4.9 - - + -
135C LEU* 5.8 0.4 - - + -
136C THR* 1.3 80.7 - - - +
138C LYS* 1.3 63.8 - - - +
153C LEU* 4.0 24.7 - - + +
185C LYS 4.2 0.2 - - - +
186C ASP* 3.3 2.6 - - - -
187C LEU* 2.8 42.2 + - + +
189C ILE* 4.7 12.1 - - + -
214C ILE* 3.9 35.4 - - + -
231C LEU* 4.1 20.9 - - + -
232C PHE 3.3 7.9 - - - +
233C ILE* 4.4 9.9 - - + -
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Residues in contact with LYS 138 (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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88C THR* 5.3 2.2 - - + -
136C THR* 4.3 11.5 - - + +
137C VAL* 1.3 77.9 - - - +
139C TYR* 1.3 62.2 + - - +
140C SER* 4.0 1.5 + - - -
185C LYS 3.8 0.2 - - - -
186C ASP* 3.4 33.1 + - - +
230C GLU 3.6 0.9 - - - +
231C LEU* 3.3 9.6 - - - +
232C PHE* 2.9 53.0 + - + +
234C GLN* 3.2 40.6 + - + +
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Residues in contact with TYR 139 (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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94C VAL* 4.2 13.9 - - + -
138C LYS* 1.3 75.6 - - - +
140C SER* 1.3 61.7 + - - +
141C PRO* 3.6 18.3 - - + +
151C VAL* 4.1 27.9 - - + +
153C LEU* 4.6 9.8 - - + +
179C THR* 4.2 14.4 - - + -
181C ALA* 2.7 31.1 + - - -
183C THR 3.8 18.6 - - - -
184C ALA* 3.2 25.0 - - - +
185C LYS* 2.9 19.6 + - + +
186C ASP* 5.0 0.5 - - - +
228C VAL* 3.4 23.9 + - - +
229C GLY* 4.1 15.5 - - - -
230C GLU 3.4 8.1 - - - -
231C LEU* 3.7 15.5 - - + -
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Residues in contact with SER 140 (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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138C LYS* 4.0 2.2 + - - -
139C TYR* 1.3 77.5 - - - +
141C PRO* 1.3 71.8 + - - +
142C ALA* 5.1 0.2 - - - +
184C ALA* 4.4 2.5 - - - -
229C GLY* 3.2 1.7 - - - -
230C GLU* 2.9 40.0 + - - +
232C PHE* 4.0 22.6 - - - -
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Residues in contact with PRO 141 (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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139C TYR* 3.6 13.7 - - + +
140C SER* 1.3 91.6 + - - +
142C ALA* 1.3 59.2 + - - +
143C CYS 3.8 10.5 - - - +
181C ALA 3.5 13.2 - - - +
182C GLN 3.5 21.1 - - - +
184C ALA* 3.5 36.8 - - + +
228C VAL 3.7 5.8 - - - +
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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