Contacts of the strand formed by residues 213 - 219 (chain B) 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 ARG 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ASP* 3.2 33.2 + - - -
107B TRP 4.1 3.7 + - - +
108B VAL* 3.7 26.7 - - - +
155B PHE* 3.2 9.6 - - - -
156B ASN* 2.8 42.1 + - + +
158B ASP 4.7 0.6 + - - +
159B ALA* 2.7 35.6 + - - +
161B ASP 2.8 20.8 + - - -
162B THR* 5.5 0.4 - - - +
163B PRO* 4.1 24.6 - - - +
212B GLY* 1.3 75.8 - - - +
214B ILE* 1.3 74.8 + - - +
215B VAL* 4.2 6.7 + - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.9 12.3 - - + -
106B ASP* 3.0 8.0 - - - +
107B TRP* 2.8 52.6 + - + -
108B VAL 3.9 4.4 - - - +
109B VAL* 3.9 23.8 - - + -
116B VAL* 5.7 2.2 - - + -
135B LEU* 5.7 0.9 - - + -
137B VAL* 3.9 30.5 - - + -
153B LEU* 5.3 7.6 - - + -
154B GLY 3.5 7.9 - - - +
155B PHE* 4.2 11.4 - - + -
187B LEU* 5.7 3.6 - - + -
189B ILE* 4.3 8.1 - - + -
213B ARG* 1.3 76.5 - - - +
215B VAL* 1.3 73.0 + - - +
231B LEU* 6.2 0.7 - - + -
233B ILE* 5.1 7.9 - - + -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 4.1 13.9 - - + -
105B GLU 3.3 8.1 - - - +
106B ASP* 4.2 11.0 - - + -
152B ALA 3.8 0.2 - - - +
153B LEU* 3.3 7.7 - - - +
154B GLY 2.8 42.3 + - - +
156B ASN* 6.1 2.2 - - + +
163B PRO* 5.7 0.2 - - + -
164B PRO* 3.9 26.9 - - + -
170B PHE* 3.9 24.7 - - + -
173B LEU* 4.6 7.9 - - + -
213B ARG* 4.6 11.4 - - + +
214B ILE* 1.3 85.2 - - - +
216B LEU* 1.3 70.3 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 5.0 2.5 - - - +
93B THR 5.3 0.4 - - - +
94B VAL* 4.5 21.8 - - + -
104B PHE* 3.4 5.5 - - - -
105B GLU* 2.7 47.9 + - + +
107B TRP* 3.9 29.2 - - + -
151B VAL* 3.8 20.6 - - + -
152B ALA 3.4 11.9 - - - +
153B LEU* 3.7 17.5 - - + -
215B VAL* 1.3 78.3 - - - +
217B SER* 1.3 75.9 + - - +
218B THR* 4.3 5.8 - - - +
231B LEU* 4.4 11.4 - - + -
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 5.6 0.2 - - - +
103B SER 3.0 19.1 + - - -
104B PHE* 3.3 24.5 - - - -
150B ARG 4.1 0.2 - - - +
151B VAL* 3.7 2.1 - - - -
152B ALA* 2.9 46.1 + - - +
167B LYS* 4.2 13.2 - - - +
170B PHE* 4.5 6.7 - - - -
216B LEU* 1.3 78.1 - - - +
218B THR* 1.3 67.1 + - - +
219B TYR* 4.3 7.8 - - - -
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 4.1 15.5 - - + +
95B LYS 3.4 16.7 + - - +
97B THR* 3.0 55.6 + - - +
102B PRO* 5.7 0.3 - - - +
103B SER* 3.7 14.0 + - - -
150B ARG 3.6 6.0 + - - -
151B VAL* 4.8 2.6 - - - +
216B LEU* 4.3 8.2 - - - +
217B SER* 1.3 79.0 + - - +
219B TYR* 1.3 70.3 + - - +
221B PHE* 3.2 16.2 - - + -
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Residues in contact with TYR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 3.9 9.9 - - + -
102B PRO* 6.4 1.8 - - + -
150B ARG* 2.8 75.3 + - + +
152B ALA* 4.5 16.8 - - + -
167B LYS* 4.0 37.2 - - + +
171B TYR* 3.5 17.5 + - - -
178B GLU* 4.2 7.4 - - - +
217B SER* 4.3 6.3 - - - -
218B THR* 1.3 87.0 - - - +
220B GLY* 1.3 64.4 + - - +
221B PHE* 3.3 5.0 - - - -
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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