Contacts of the strand formed by residues 339 - 344 (chain B) in PDB entry 4OC6
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 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B TYR* 3.4 57.7 + - + +
198B LEU 3.2 15.3 - - - +
199B ASN* 4.1 11.4 - - - +
200B VAL* 4.2 1.6 - - - -
206B TRP* 3.7 6.1 - - - -
334B ASP* 2.8 56.9 + - + +
337B ASN* 3.8 28.0 - - + +
338B ASN* 1.3 74.7 - - - +
340B VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER 3.6 1.6 - - - +
197B TYR* 3.2 7.6 - - - -
198B LEU* 2.8 38.2 + - + +
200B VAL* 4.2 2.9 - - + -
206B TRP* 3.8 24.2 - - + -
208B VAL* 4.2 21.8 - - + -
230B VAL* 4.2 9.4 - - + -
331B THR* 3.8 13.0 - - + -
332B VAL 3.2 10.8 - - - +
333B PHE* 4.3 8.1 - - + -
339B ARG* 1.3 77.9 - - - +
341B GLY* 1.3 60.7 + - - +
342B PHE* 3.7 33.7 - - + -
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.4 4.7 - - - -
196B SER 3.3 6.7 - - - -
197B TYR* 3.5 21.7 - - - -
330B TYR 4.1 0.7 - - - -
331B THR* 3.1 9.5 - - - +
332B VAL* 2.8 41.7 + - - -
340B VAL* 1.3 73.9 - - - +
342B PHE* 1.3 65.3 + - - -
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Residues in contact with PHE 342 (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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194B SER 4.2 0.9 - - - +
195B LEU* 3.6 3.0 - - - +
196B SER* 2.9 34.7 + - - +
198B LEU* 3.6 31.4 - - + -
208B VAL* 5.5 2.0 - - + -
230B VAL* 3.9 19.1 - - + -
278B LEU* 4.5 7.9 - - + -
283B TYR* 3.5 35.4 + + + +
321B LEU* 4.3 3.6 - - + -
325B PHE* 3.3 34.1 - + - -
329B TYR* 3.9 11.0 - - + -
330B TYR 3.2 4.9 - - - -
331B THR* 3.4 33.4 - - + -
340B VAL* 3.7 18.8 - - + -
341B GLY* 1.3 74.6 - - - -
343B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 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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191B TYR* 3.6 27.1 - - + -
192B LYS 3.9 7.6 - - - +
194B SER 4.1 11.7 - - - +
195B LEU* 3.5 20.0 - - + -
283B TYR* 6.0 0.2 - - - -
329B TYR* 3.4 6.3 - - - -
330B TYR* 2.9 26.9 + - - +
342B PHE* 1.3 76.8 - - - +
344B GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 344 (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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191B TYR* 3.4 1.4 - - - -
192B LYS* 2.8 66.6 + - + +
328B ARG* 3.4 34.0 + - - +
329B TYR* 3.8 19.8 - - + -
343B ALA* 1.3 71.0 - - - +
345B ALA* 1.3 69.0 + - - +
347B ARG* 4.5 8.5 + - - +
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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
------------------------------------------------------------
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