Contacts of the strand formed by residues 319 - 323 (chain B) in PDB entry 4OE5
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 ASN 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLY 3.4 12.7 + - - +
318B LYS* 1.3 73.0 - - - +
320B PHE* 1.3 61.4 + - - +
347B LYS 4.8 0.6 + - - -
348B CYS 2.8 26.4 + - - -
349B SER 3.2 6.9 - - - +
350B ALA 2.9 26.4 + - - +
351B CYS* 3.6 2.6 - - - -
352B SER* 3.0 28.7 + - - -
353B ARG* 3.2 8.9 + - - +
477B GLY* 6.1 0.2 - - - -
478B LEU* 3.3 14.8 + - - +
479B THR* 2.8 47.1 + - - +
510B SER* 4.5 1.1 - - - +
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 1.3 76.2 - - - +
321B HIS* 1.3 70.0 + - - +
322B PHE* 4.0 8.5 - - + -
351B CYS* 4.2 0.2 - - - -
353B ARG* 3.3 37.5 - - + +
355B TYR* 4.2 8.5 - - + -
470B VAL* 3.7 21.1 - - + -
477B GLY* 6.5 0.2 - - - -
479B THR 3.7 5.5 + - - -
480B GLY* 3.2 19.1 - - - -
481B ALA 3.0 45.7 + - - -
497B LEU* 3.6 37.7 - - + -
500B ALA* 3.5 33.7 - - + -
501B ALA* 4.5 2.7 - - + -
504B PHE* 4.5 4.3 - + - -
510B SER* 4.4 0.3 - - - -
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Residues in contact with HIS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 1.3 87.4 - - - +
322B PHE* 1.3 60.7 + - - +
335B GLY 3.5 27.6 - - - -
336B THR* 2.9 25.0 + - - +
339B SER* 3.7 8.3 - - - -
351B CYS* 3.7 12.4 - - + +
353B ARG 2.9 7.5 + - - +
354B LEU* 3.5 18.8 - - + +
355B TYR* 3.0 26.2 + - - -
481B ALA* 3.4 17.0 - - + -
483B PHE* 3.8 18.5 - + + -
509B LYS* 3.9 5.3 - - - -
510B SER* 3.1 33.7 + - - -
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 4.0 12.3 - - + -
321B HIS* 1.3 73.4 - - - +
323B VAL* 1.3 66.3 + - - +
324B HIS* 4.4 8.5 - - + -
355B TYR* 3.8 16.2 - - + -
458B TYR* 3.6 23.3 - + - -
463B TYR* 3.9 15.9 - + + -
466B THR* 3.8 24.9 - - + -
467B LEU* 3.6 42.8 - - + -
470B VAL* 4.0 13.2 - - + -
481B ALA 2.8 12.7 + - - +
482B VAL* 3.3 21.9 - - + -
483B PHE* 2.8 32.9 + - - -
489B VAL* 5.2 3.1 - - + -
497B LEU* 4.9 0.4 - - + -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 1.3 82.3 - - - +
324B HIS* 1.3 68.5 + - - +
327B ALA* 3.6 15.7 - - + -
332B VAL* 3.8 26.0 - - + -
354B LEU* 3.7 28.0 - - + -
355B TYR 2.9 14.1 + - - +
356B VAL* 4.2 3.4 - - + -
357B PRO* 3.3 18.3 - - + +
360B LEU* 4.3 1.8 - - + -
364B ILE* 4.1 12.6 - - + -
458B TYR* 2.7 29.5 + - - -
483B PHE* 3.7 9.2 - - + -
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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