Contacts of the strand formed by residues 392 - 398 (chain F) in PDB entry 3GUT
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 LYS 392 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391F ALA* 1.3 73.8 - - - +
393F VAL* 1.3 64.5 + - - +
394F ILE* 4.3 7.2 - - + -
422F THR* 4.1 24.9 - - + -
423F VAL 3.8 4.5 - - - +
424F THR* 4.5 5.6 - - + +
461F ARG* 5.2 2.4 - - - +
463F TYR* 3.1 35.5 + - - -
515F THR 3.8 0.5 - - - +
516F ALA* 3.2 3.6 - - - +
517F PHE* 2.7 55.2 + - + +
525F PHE* 3.8 35.6 + - + +
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Residues in contact with VAL 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F LEU* 5.3 3.6 - - + -
382F VAL* 4.6 9.4 - - + -
384F ILE* 4.1 22.9 - - + -
391F ALA 4.3 0.2 - - - -
392F LYS* 1.3 80.3 - - - +
394F ILE* 1.3 69.4 + - - +
395F VAL* 5.1 0.7 - - - +
421F CYS 3.8 0.9 - - - +
422F THR* 3.5 2.4 - - - -
423F VAL* 2.9 45.2 + - + +
425F ALA* 4.7 7.2 - - + +
432F VAL* 4.7 7.9 - - + -
434F PHE* 4.3 18.8 - - + -
514F PHE* 4.4 14.1 - - + -
515F THR 3.3 10.3 - - - +
516F ALA* 4.0 15.5 - - + -
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Residues in contact with ILE 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F LYS* 4.3 9.2 - - + -
393F VAL* 1.3 76.5 - - - +
395F VAL* 1.3 63.9 + - - +
396F GLN* 4.0 19.1 - - - +
420F VAL* 4.2 5.8 - - + -
421F CYS 3.1 4.9 - - - +
422F THR* 3.2 27.8 - - + +
463F TYR* 3.7 39.0 - - + +
464F ASN* 4.7 0.4 - - - +
513F MET 3.5 1.0 - - - +
514F PHE* 3.3 7.1 - - - +
515F THR* 2.9 44.3 + - + +
517F PHE* 3.6 23.8 - - + -
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Residues in contact with VAL 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F ILE* 1.3 79.3 - - - +
396F GLN* 1.3 63.9 + - - +
411F LEU* 3.4 22.5 - - + +
420F VAL* 3.6 7.8 - - - +
421F CYS* 2.6 44.4 + - + +
434F PHE* 3.5 35.2 - - + -
437F LEU* 5.1 4.3 - - + -
512F LEU* 4.1 20.6 - - + -
513F MET 3.6 4.3 - - - +
514F PHE* 3.8 26.5 - - + -
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Residues in contact with GLN 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F ILE* 4.0 22.1 - - + +
395F VAL* 1.3 79.2 - - - +
397F LEU* 1.3 70.5 + - - +
398F VAL* 4.5 4.9 - - + -
406F LEU* 4.6 13.4 - - + +
411F LEU* 4.6 2.9 - - - -
419F GLY 4.7 4.7 - - - -
420F VAL* 4.4 16.8 - - + +
458F ALA* 4.7 6.2 - - - +
463F TYR* 3.8 24.5 + - - +
464F ASN* 3.5 22.6 + - - -
468F LEU* 3.9 10.3 - - - +
512F LEU* 3.5 2.9 - - - -
513F MET* 2.9 50.0 + - + +
515F THR* 4.4 2.2 + - - -
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Residues in contact with LEU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F GLN* 1.3 74.1 - - - +
398F VAL* 1.3 65.9 + - - +
406F LEU* 3.7 10.1 - - - +
407F HIS* 3.4 20.8 + - + +
409F HIS* 3.2 46.9 - - + +
410F SER 3.7 4.9 - - - +
411F LEU* 3.9 27.4 - - + +
419F GLY 5.0 3.0 + - - +
439F ILE* 4.1 10.1 - - + -
510F VAL* 3.6 31.4 - - + -
511F ARG 3.3 2.0 - - - +
512F LEU* 3.5 28.5 - - + -
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Residues in contact with VAL 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F GLN* 4.2 2.5 - - + +
397F LEU* 1.3 81.5 - - - +
399F THR* 1.3 61.5 + - - +
404F ILE* 3.6 19.1 - - + -
405F HIS 3.1 10.3 - - - +
407F HIS* 3.8 7.2 - - - -
468F LEU* 3.8 31.9 - - + -
510F VAL* 3.5 8.1 - - - +
511F ARG* 2.8 56.2 + - + +
512F LEU 4.3 1.3 - - - +
513F MET* 3.9 26.5 - - + -
533F VAL* 4.6 3.8 - - + -
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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