Contacts of the strand formed by residues 384 - 391 (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 TYR 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.6 31.5 - + - +
340B LEU* 4.5 2.0 - - + +
376B THR* 4.3 3.9 - - - +
379B SER* 2.7 30.2 + - - -
381B PHE* 3.0 21.9 + - + +
383B GLY* 1.3 84.9 + - - +
385B ALA* 1.3 57.0 + - - +
402B PHE* 4.0 21.1 - - + -
403B THR 3.5 4.9 - - - +
404B ALA* 3.5 28.7 - - + -
405B THR* 4.4 3.4 - - - -
409B MET* 4.8 7.6 - - + +
410B SER 3.7 5.5 + - - -
411B PRO* 2.6 48.1 + - - +
412B GLN 4.2 3.1 - - - -
414B PHE* 3.6 32.1 - + - -
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Residues in contact with ALA 385 (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* 3.7 21.8 - - + -
375B SER 3.2 18.8 - - - +
376B THR* 3.8 12.1 - - + -
384B TYR* 1.3 73.7 - - - +
386B TRP* 1.3 59.0 + - - +
401B LYS 3.5 0.9 - - - +
402B PHE* 3.2 7.3 - - - -
403B THR* 2.8 42.0 + - - +
405B THR* 4.2 6.3 - - + +
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Residues in contact with TRP 386 (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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373B ARG 4.1 2.4 - - - +
374B PRO* 3.4 1.4 - - - +
375B SER* 2.7 72.2 + - - -
377B GLU* 2.7 33.6 + - + -
378B HIS 4.5 0.8 - - - -
379B SER* 4.1 23.1 - - - +
385B ALA* 1.3 72.4 - - - +
387B THR* 1.3 65.5 + - - +
388B VAL* 4.0 11.2 - - + -
400B TRP* 3.8 25.4 - + + -
401B LYS 3.3 4.7 - - - -
402B PHE* 3.7 25.1 - + + -
35C ILE* 5.2 5.2 - - + -
39C ASN 4.1 0.7 - - - -
40C GLY* 3.7 39.3 - - - -
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Residues in contact with THR 387 (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* 3.9 32.2 - - + +
371B ILE 3.4 20.2 - - - +
372B GLY 3.9 17.9 - - - +
373B ARG 4.3 6.3 - - - +
374B PRO* 3.3 25.1 - - + +
386B TRP* 1.3 75.7 - - - +
388B VAL* 1.3 64.7 + - - +
400B TRP* 3.2 3.6 - - - -
401B LYS* 2.9 37.6 + - - +
403B THR* 5.0 2.8 + - - +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.5 3.5 - - - -
371B ILE* 2.9 45.6 + - + +
386B TRP* 4.0 7.5 - - + -
387B THR* 1.3 74.3 - - - +
389B ALA* 1.3 63.3 + - - +
390B GLN* 4.6 5.4 - - + +
397B HIS* 3.7 21.8 - - + -
399B GLY 3.7 5.4 - - - -
400B TRP* 3.8 7.5 - - + -
39C ASN* 3.4 28.3 - - - +
40C GLY 3.9 2.7 - - - -
41C GLU* 3.5 39.7 - - + +
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Residues in contact with ALA 389 (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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368B LEU* 4.2 14.4 - - + -
369B ASN 3.4 6.3 - - - +
370B LEU* 4.1 5.4 - - + -
387B THR 3.4 0.6 + - - -
388B VAL* 1.3 73.5 - - - +
390B GLN* 1.3 61.0 + - - +
397B HIS* 3.7 2.9 - - - -
398B ILE* 2.9 23.0 + - - -
399B GLY 2.8 27.4 + - - +
400B TRP* 4.2 2.2 - - - +
415B TRP* 3.9 32.3 - - + -
417B LEU* 5.9 0.4 - - + -
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Residues in contact with GLN 390 (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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368B LEU* 3.2 10.1 - - - -
369B ASN* 2.8 39.6 + - + +
371B ILE* 3.6 29.1 - - + +
388B VAL* 4.6 6.3 - - + +
389B ALA* 1.3 76.6 - - - +
391B CYS* 1.3 63.4 + - - +
395B ALA* 3.2 39.7 + - - +
396B SER 3.3 8.1 - - - +
397B HIS* 4.5 5.1 - - + +
41C GLU* 3.3 26.9 + - - -
75C HIS* 6.0 1.7 + - - -
77C ARG* 4.4 9.9 - - - +
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Residues in contact with CYS 391 (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* 4.1 7.2 - - - -
326B CYS* 3.9 19.3 - - - -
329B THR* 3.8 27.8 - - - -
331B ILE* 4.6 1.6 - - + -
367B ASN 3.6 8.1 - - - -
368B LEU* 4.3 0.4 - - - -
369B ASN* 4.6 3.1 + - - -
390B GLN* 1.3 72.6 - - - +
392B LYS* 1.3 63.0 + - - +
393B ILE 3.2 11.4 - - - -
394B CYS* 3.9 15.9 - - - -
395B ALA* 2.9 26.9 + - - +
396B SER 2.9 16.4 + - - +
398B ILE* 3.7 17.5 - - + +
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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