Contacts of the strand formed by residues 391 - 398 (chain B) in PDB entry 5F6K
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 VAL 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A SER* 6.0 0.2 - - - -
330B GLU* 3.7 36.6 - - + +
331B ILE 3.4 5.4 - - - +
332B THR* 3.7 29.8 - - + +
389B GLY 4.2 6.1 - - - +
390B ASP* 1.3 73.6 - - - +
392B LEU* 1.3 62.7 + - - +
393B GLY 3.9 0.3 + - - -
452B ASN* 2.9 34.9 + - - +
453B GLY 4.6 0.7 + - - -
489B LYS* 3.9 31.2 - - + +
490B TYR* 4.0 17.4 - - + -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 3.2 8.8 - - - +
331B ILE 2.7 44.3 + - - +
333B VAL* 3.7 18.6 - - + -
344B LEU* 4.3 7.0 - - + -
366B TRP* 3.6 29.4 - - + -
386B TYR* 3.6 48.2 - - + -
390B ASP* 3.7 8.3 - - + +
391B VAL* 1.3 77.1 - - - +
393B GLY* 1.3 60.3 + - - +
394B PHE* 3.6 22.9 - - + -
450B TYR 3.3 4.7 - - - +
451B LYS* 4.0 10.3 - - + -
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Residues in contact with GLY 393 (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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328B TYR* 3.1 26.5 - - - -
329B PHE 3.6 4.0 - - - -
330B GLU* 4.4 1.3 - - - -
366B TRP* 4.6 0.3 - - - -
391B VAL 3.9 0.6 + - - -
392B LEU* 1.3 73.2 - - - +
394B PHE* 1.3 69.9 + - - -
395B TYR 4.2 0.2 - - - -
449B PHE* 3.4 5.9 - - - +
450B TYR* 2.7 40.9 + - - +
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Residues in contact with PHE 394 (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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328B TYR* 3.2 29.7 - - - -
329B PHE* 2.9 51.7 + + + +
331B ILE* 3.6 19.1 - - + -
344B LEU* 3.4 42.2 - - + -
345B GLY* 3.7 9.9 - - - -
346B TRP* 3.5 11.2 - - - +
366B TRP* 4.4 4.9 - + - -
392B LEU* 3.6 36.3 - - + -
393B GLY* 1.3 72.9 - - - -
395B TYR* 1.3 59.7 + - - +
448B ILE 3.9 2.5 - - - -
449B PHE* 3.4 33.0 - + - -
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA* 3.6 15.5 - - + +
327B TRP 3.4 10.3 - - - -
328B TYR* 3.9 13.4 - + + -
346B TRP* 4.0 6.0 + - - +
394B PHE* 1.3 72.9 - - - +
396B ILE* 1.3 59.9 + - - +
397B ASN* 3.4 43.0 + - + +
446B GLU* 3.9 17.5 + - + -
447B ILE* 3.5 2.9 - - - -
448B ILE* 2.8 69.2 + - + +
450B TYR* 4.3 8.7 - + + -
492B PRO* 6.1 1.1 - - + -
495B LEU* 4.0 26.1 - - + +
496B THR 3.7 22.6 + - - -
497B TYR* 4.4 9.4 - + + -
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Residues in contact with ILE 396 (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 VAL* 4.1 7.9 - - + -
325B GLY 4.9 1.1 - - - +
326B ALA* 3.1 4.5 - - - +
327B TRP* 2.9 48.9 + - + +
346B TRP* 3.5 43.0 - - + +
395B TYR* 1.3 77.6 - - - +
397B ASN* 1.3 65.1 + - - +
398B LEU* 4.2 17.0 - - + -
446B GLU 3.7 3.4 - - - +
447B ILE* 4.1 14.4 - - + -
463B ILE* 4.2 6.1 - - + -
468B TYR* 3.7 43.1 - - + -
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Residues in contact with ASN 397 (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 GLY* 3.7 4.3 - - - +
326B ALA* 3.6 13.1 + - - +
395B TYR* 3.4 30.3 + - + +
396B ILE* 1.3 76.1 - - - +
398B LEU* 1.3 66.6 + - - +
399B PRO* 3.4 21.8 - - - +
444B SER 4.3 5.3 + - - -
445B SER* 3.1 26.0 - - - -
446B GLU* 3.0 31.7 + - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.6 22.4 - - + +
323B ARG* 3.4 34.8 - - - +
324B LYS* 3.4 7.3 - - - +
325B GLY 2.8 33.5 + - - +
396B ILE* 4.2 14.4 - - + -
397B ASN* 1.3 81.5 + - - +
399B PRO* 1.3 65.6 - - - +
400B GLU* 3.9 0.9 + - - +
445B SER* 3.9 8.7 - - - -
463B ILE* 3.8 28.7 - - + -
464B PHE 5.4 0.9 - - - +
465B GLU* 6.3 1.3 - - - -
466B GLY 4.2 2.9 - - - +
468B TYR* 3.9 18.4 - - + -
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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