Contacts of the strand formed by residues 397 - 404 (chain B) in PDB entry 5FQD
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 HIS 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B HIS* 4.5 6.1 - + - -
388B VAL* 3.7 14.6 - - + -
389B ALA 3.7 4.3 - - - -
390B GLN* 4.4 6.5 - - + +
395B ALA 3.7 2.2 + - - -
396B SER* 1.3 71.0 - - - +
398B ILE* 1.4 59.2 + - - +
399B GLY* 2.8 38.7 + - - -
400B TRP* 3.4 37.8 + + - -
418B THR* 4.0 12.7 - - + +
421B ALA* 3.4 18.0 - - - +
38C THR* 5.7 0.2 + - - -
39C ASN* 3.4 36.5 + - + +
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Residues in contact with ILE 398 (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 CYS* 3.7 36.3 - - + -
331B ILE* 3.9 22.2 - - + -
368B LEU* 3.6 26.2 - - + -
389B ALA 2.9 6.2 + - - +
391B CYS* 3.7 8.5 - - + +
396B SER* 3.4 21.5 - - - +
397B HIS* 1.4 77.9 - - - +
399B GLY* 1.3 57.8 + - - +
417B LEU* 3.5 8.8 - - + +
418B THR* 2.9 30.9 + - - +
421B ALA* 3.9 15.7 - - + +
422B LEU* 3.9 24.2 - - + -
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Residues in contact with GLY 399 (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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388B VAL 3.7 0.2 - - - -
389B ALA* 2.8 32.9 + - - +
397B HIS* 2.8 24.5 + - - -
398B ILE* 1.3 80.7 - - - +
400B TRP* 1.3 68.8 + - - -
416B GLY 3.2 12.8 - - - -
417B LEU* 4.2 2.9 - - - +
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Residues in contact with TRP 400 (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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351B ASN* 6.3 0.4 - - + -
357B HIS* 3.6 31.0 - + - -
359B THR* 4.0 10.1 - - + -
380B TRP* 3.6 30.3 - + - -
386B TRP* 3.8 34.7 - + + -
387B THR 3.2 8.7 - - - +
388B VAL* 3.8 10.3 - - - +
389B ALA* 4.0 1.9 - - - +
397B HIS* 3.4 23.7 + + - -
399B GLY* 1.3 83.1 - - - -
401B LYS* 1.3 60.0 + - - +
402B PHE* 3.9 19.0 - + + -
415B TRP* 3.5 10.0 - - - +
416B GLY 2.8 44.0 + - - +
417B LEU* 5.2 0.8 - - - +
418B THR* 4.4 7.6 - - - -
39C ASN* 2.7 36.7 + - + -
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Residues in contact with LYS 401 (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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370B LEU* 3.7 32.5 - - + +
385B ALA 3.5 1.0 - - - +
386B TRP* 3.3 4.9 - - - -
387B THR* 2.9 35.3 + - - +
389B ALA* 4.5 0.2 - - - +
400B TRP* 1.3 72.8 - - - +
402B PHE* 1.3 64.4 + - - +
403B THR* 3.8 22.7 + - + +
413B LYS* 3.7 40.6 - - - +
414B PHE 3.6 10.3 - - - +
415B TRP* 3.6 42.6 - - + -
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Residues in contact with PHE 402 (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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359B THR* 4.9 0.7 - - + -
379B SER* 4.0 13.2 - - - -
380B TRP* 4.6 16.4 - + - -
381B PHE* 3.6 32.1 - + - -
384B TYR* 4.0 16.8 - - + -
385B ALA 3.2 11.2 - - - -
386B TRP* 3.7 23.1 - + + -
400B TRP* 3.9 23.6 - + + -
401B LYS* 1.3 72.3 - - - +
403B THR* 1.3 60.5 + - - +
413B LYS* 3.2 7.1 - - - +
414B PHE* 2.7 73.7 + + + +
416B GLY* 3.9 24.2 - - - -
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Residues in contact with THR 403 (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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374B PRO* 4.1 23.2 - - + +
384B TYR* 3.7 3.6 - - - -
385B ALA* 2.8 36.7 + - - +
387B THR* 5.0 2.6 + - - +
401B LYS* 3.8 33.8 + - + +
402B PHE* 1.3 77.7 - - - +
404B ALA* 1.3 66.7 + - - +
412B GLN 3.6 4.3 - - - -
413B LYS* 4.1 8.3 - - + -
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Residues in contact with ALA 404 (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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383B GLY 3.8 2.2 - - - -
384B TYR* 3.5 16.1 - - + -
403B THR* 1.3 77.1 + - - +
405B THR* 1.3 61.3 + - - +
406B LYS 3.7 9.0 - - - +
409B MET* 3.8 16.4 - - + -
412B GLN* 2.8 51.6 + - - +
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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