Contacts of the strand formed by residues 322 - 326 (chain B) in PDB entry 4OE4
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 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLY 3.6 9.6 + - - -
321B LYS* 1.3 74.7 - - - +
323B PHE* 1.3 59.3 + - - +
350B LYS 4.8 0.4 + - - -
351B CYS 2.8 25.8 + - - -
352B SER* 3.0 8.6 - - - +
353B ALA 2.8 26.6 + - - +
354B ALA* 4.3 1.1 - - - -
355B SER* 2.9 28.2 + - - -
356B ARG* 3.2 8.0 + - - +
458B GLU* 5.4 0.2 + - - -
488B ALA* 4.4 0.2 - - - -
489B LEU* 3.2 15.9 + - - +
490B THR* 2.9 49.2 + - - +
521B CYS* 4.0 2.7 - - - -
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Residues in contact with PHE 323 (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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322B ASN* 1.3 76.6 - - - +
324B HIS* 1.3 69.7 + - - +
325B LEU* 4.2 10.8 - - + -
354B ALA* 5.2 0.2 - - - -
356B ARG* 3.3 42.2 - - + +
358B TYR* 4.0 9.6 - - + -
481B ILE* 4.1 19.7 - - + -
488B ALA* 4.5 1.6 - - + -
490B THR 3.4 6.3 + - - -
491B GLY* 3.3 24.1 - - - -
492B ALA 3.0 39.4 + - - -
508B LEU* 3.8 31.4 - - + -
511B SER* 3.9 26.9 - - - -
512B ALA* 4.4 2.7 - - + -
515B PHE* 4.1 9.9 - + - -
521B CYS* 4.2 0.7 - - - +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 1.3 83.8 - - - +
325B LEU* 1.3 60.8 + - - +
326B VAL 4.0 0.2 - - - -
338B SER 3.6 23.8 - - - -
339B THR* 3.1 26.4 + - + +
342B GLY* 4.8 0.7 - - - -
354B ALA* 3.9 13.7 - - + +
356B ARG 2.9 9.5 + - - +
357B LEU* 3.3 21.4 - - + +
358B TYR* 2.8 27.4 + - - -
464B LEU* 6.4 0.2 - - + -
492B ALA* 3.7 13.2 - - + +
494B PHE* 3.4 18.9 - + + -
520B LYS* 3.6 11.8 - - + +
521B CYS* 3.0 39.3 + - - -
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Residues in contact with LEU 325 (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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323B PHE* 4.1 11.4 - - + -
324B HIS* 1.3 70.8 - - - +
326B VAL* 1.3 63.0 + - - +
358B TYR* 3.7 22.7 - - + -
469B TYR* 4.3 7.0 - - + +
474B PHE* 3.6 32.1 - - + -
477B ILE* 3.8 20.9 - - + -
478B CYS* 3.9 18.4 - - - -
481B ILE* 4.5 8.5 - - + -
492B ALA 2.7 15.8 + - - +
493B ILE* 3.2 13.8 - - + +
494B PHE* 2.8 26.9 + - - -
504B ALA* 4.4 0.2 - - + -
508B LEU* 4.2 17.3 - - + -
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Residues in contact with VAL 326 (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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325B LEU* 1.3 78.1 - - - +
327B HIS* 1.3 65.0 + - - +
330B ALA* 3.9 13.7 - - + -
332B ILE* 4.3 15.5 - - + -
335B ALA* 4.2 5.8 - - + -
339B THR* 5.3 0.4 - - - +
357B LEU* 4.0 15.3 - - + -
358B TYR 2.9 15.5 + - - +
359B LEU* 3.9 20.9 - - + -
360B PRO* 3.1 21.6 - - + +
363B LYS* 5.7 0.2 - - + -
367B PHE* 4.1 11.4 - - + -
469B TYR* 2.7 26.1 + - - -
494B PHE* 3.8 18.6 - - + -
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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