Contacts of the strand formed by residues 354 - 360 (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 ALA 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ASN 3.7 5.2 - - - +
324B HIS* 3.9 25.6 - - + +
339B THR* 5.4 0.4 - - + -
342B GLY 3.0 13.7 + - - +
343B THR* 3.4 40.5 - - - +
352B SER 3.5 2.6 + - - -
353B ALA* 1.3 74.1 - - - +
355B SER* 1.3 60.4 + - - +
356B ARG 5.1 0.4 - - - +
464B LEU* 5.1 2.7 - - + -
521B CYS* 3.5 23.5 - - - -
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Residues in contact with SER 355 (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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320B GLY 4.7 1.4 + - - -
321B LYS* 3.1 46.7 + - - +
322B ASN 2.9 13.8 + - - -
353B ALA* 3.5 4.3 + - - -
354B ALA* 1.3 75.5 - - - +
356B ARG* 1.3 63.7 + - - +
458B GLU* 5.7 0.3 - - - -
459B PHE* 5.9 3.4 - - - -
460B PHE 6.4 0.2 - - - -
463B ILE 3.9 13.2 - - - +
464B LEU* 3.6 10.6 - - - -
465B THR* 3.1 20.6 + - - -
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Residues in contact with ARG 356 (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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321B LYS* 3.0 36.4 + - + +
322B ASN 3.2 3.8 + - - +
323B PHE* 3.3 34.4 - - + +
324B HIS* 2.9 25.6 + - - +
354B ALA* 5.2 0.7 - - - +
355B SER* 1.3 81.9 + - - +
357B LEU* 1.3 60.8 + - - +
358B TYR* 2.8 37.6 + - + -
455B MET* 3.3 38.2 + - + +
464B LEU* 3.8 3.0 - - - +
465B THR* 3.2 9.0 - - - +
481B ILE* 4.0 21.2 + - - +
484B THR* 4.9 8.9 - - - -
487B TYR 5.0 8.5 - - - +
488B ALA* 4.0 9.7 - - - +
511B SER* 5.3 0.8 + - - -
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Residues in contact with LEU 357 (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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324B HIS* 3.3 28.7 - - + +
326B VAL* 4.0 21.5 - - + -
339B THR* 4.2 5.4 - - + +
356B ARG* 1.3 76.3 - - - +
358B TYR* 1.3 66.2 + - - +
359B LEU* 3.8 22.7 - - + -
367B PHE* 3.5 32.8 - - + -
368B LEU* 4.9 3.4 - - + -
455B MET* 4.5 0.9 - - - +
464B LEU* 4.0 27.8 - - + -
465B THR 2.9 10.3 + - - +
466B VAL* 3.4 10.5 - - + +
467B TYR* 3.0 26.9 + - - +
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Residues in contact with TYR 358 (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* 4.0 10.8 - - + -
324B HIS 2.8 19.2 + - - +
325B LEU* 3.7 17.3 - - + -
326B VAL* 2.9 34.8 + - - +
356B ARG* 2.8 45.6 + - + -
357B LEU* 1.3 73.5 - - - +
359B LEU* 1.3 61.8 + - - +
450B PRO* 4.9 9.3 + - + -
455B MET* 3.4 26.6 - - + +
467B TYR* 3.4 19.3 - + + +
469B TYR* 3.8 7.9 - - + -
477B ILE* 3.9 21.3 - - + -
480B ILE* 5.6 3.6 - - + +
481B ILE* 3.5 35.9 - - + +
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Residues in contact with LEU 359 (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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326B VAL* 3.9 21.5 - - + -
357B LEU* 3.8 16.4 - - + -
358B TYR* 1.3 73.2 - - - +
360B PRO* 1.3 64.3 - - + +
363B LYS* 5.8 0.4 - - + -
364B SER* 3.8 21.1 - - - +
367B PHE* 3.7 48.5 - - + -
368B LEU* 3.8 18.8 - - + -
466B VAL* 3.8 19.5 - - + -
467B TYR 2.9 10.5 + - - +
468B GLU* 3.2 5.5 - - + +
469B TYR* 2.7 38.1 + - - -
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Residues in contact with PRO 360 (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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326B VAL* 3.1 33.2 - - + +
327B HIS 4.2 1.3 - - - -
328B PRO* 3.9 23.6 - - + -
359B LEU* 1.3 85.6 - - + +
361B GLU* 1.3 66.8 + - - +
362B SER 4.5 0.2 - - - +
363B LYS* 3.0 25.7 + - + -
364B SER* 2.9 12.2 + - - -
469B TYR* 3.2 22.4 - - + +
471B ASP* 3.5 22.0 - - - +
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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