Contacts of the strand formed by residues 342 - 347 (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 GLN 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B SER* 3.4 10.5 - - - +
253B ASN* 5.6 7.7 - - - +
285B ILE 4.2 0.2 - - - -
286B VAL* 3.3 5.0 - - - +
287B ARG* 2.8 62.0 + - + +
288B GLY* 6.3 0.4 - - - -
289B THR* 5.8 0.3 + - - -
314B ARG* 6.1 0.4 - - - +
340B PRO 4.8 4.7 - - - +
341B LEU* 1.3 77.8 - - - +
343B TRP* 1.3 65.8 + - - +
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Residues in contact with TRP 343 (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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250B GLN* 3.5 39.9 - - + -
251B ALA* 3.4 17.9 - - - -
252B SER* 2.5 58.8 + - - -
253B ASN* 5.5 0.3 + - - -
263B VAL* 4.0 14.4 - - + -
265B PRO* 4.3 19.2 - - + +
272B LEU* 4.7 11.7 - - + +
274B LEU* 4.0 33.1 - - + +
284B ILE* 4.5 7.2 - - + -
285B ILE 2.9 15.5 - - - +
286B VAL* 4.4 10.8 - - + -
287B ARG* 5.5 2.2 - - - +
341B LEU* 4.1 11.7 + - + -
342B GLN* 1.3 80.3 - - - +
344B VAL* 1.3 71.6 + - - +
345B VAL* 4.1 10.5 - - + -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B SER* 5.4 2.9 - - - -
250B GLN 3.0 7.9 - - - +
251B ALA* 3.7 21.1 - - + -
283B CYS 3.8 0.3 - - - +
284B ILE* 3.2 6.2 - - - +
285B ILE* 3.0 47.4 + - + +
287B ARG* 4.9 9.6 - - - +
343B TRP* 1.3 80.5 - - - +
345B VAL* 1.3 65.4 + - - +
346B TYR* 3.7 35.4 - - + +
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Residues in contact with VAL 345 (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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249B SER* 3.3 9.0 - - - -
250B GLN* 2.8 32.7 + - + +
262B TYR* 3.8 31.6 - - + -
263B VAL* 4.4 18.2 - - + -
282B TRP* 4.2 11.7 - - + -
283B CYS 3.3 7.6 - - - +
284B ILE* 3.9 23.1 - - + -
343B TRP* 4.1 21.5 - - + -
344B VAL* 1.3 79.9 - - - +
346B TYR* 1.3 71.7 + - - +
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Residues in contact with TYR 346 (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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248B ILE* 5.2 4.3 - - + -
249B SER* 3.6 30.7 - - - +
262B TYR* 4.8 1.6 - - - -
282B TRP* 3.5 5.9 - - - +
283B CYS* 2.8 49.9 + - + +
285B ILE* 4.2 17.0 - - + -
344B VAL* 3.7 34.1 - - + +
345B VAL* 1.3 79.4 - - - +
347B ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 347 (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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114B VAL* 4.2 11.2 - - - +
118B PRO* 2.8 31.9 + - - +
119B GLN* 4.5 1.4 - - - +
121B SER* 3.7 14.6 + - - -
122B LEU* 4.0 41.9 - - - +
248B ILE* 4.6 14.0 - - + +
262B TYR* 3.5 35.3 + - - +
281B LYS 4.1 4.7 - - - +
282B TRP* 3.8 23.7 - - + -
346B TYR* 1.3 78.1 - - - +
348B MET* 1.3 66.8 + - - +
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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