Contacts of the strand formed by residues 404 - 413 (chain B) in PDB entry 5DK3
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 PHE 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B ASP* 5.3 6.5 - - + -
317B LYS* 5.2 0.2 - - - -
371B GLY 3.1 22.3 + - - -
372B PHE* 2.9 46.2 + - + +
373B TYR* 4.0 24.7 - + - -
375B SER* 3.7 31.6 - - - -
396B PRO* 3.7 19.7 - - + -
397B VAL 3.2 20.2 - - - -
398B LEU* 3.6 32.5 - - + -
399B ASP* 4.9 0.9 - - - -
403B SER* 1.3 77.5 - - - +
405B PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 4.2 2.7 - - + -
369B VAL 3.2 12.8 - - - +
370B LYS* 3.6 16.6 - - + -
372B PHE* 3.7 4.7 - - - -
396B PRO* 3.4 0.9 - - - +
397B VAL* 2.8 61.4 + - + +
398B LEU 4.9 0.4 - - - -
399B ASP* 3.9 10.8 - - - +
404B PHE* 1.3 75.4 - - - +
406B LEU* 1.3 66.0 + - - +
407B TYR* 3.9 26.9 - + - -
392G LYS* 3.5 45.3 - - + -
394G THR* 4.2 11.2 - - + -
409G ARG* 3.4 37.0 - - + +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 3.6 8.5 - - - +
369B VAL* 2.8 53.7 + - + +
372B PHE* 3.9 13.0 - - + -
377B ILE* 3.6 30.3 - - + -
379B VAL* 4.0 8.1 - - + -
393B THR* 3.8 22.2 - - + -
394B THR* 3.5 29.8 - - - +
395B PRO 3.8 3.4 - - - +
396B PRO* 4.1 10.3 - - + -
405B PHE* 1.3 78.8 - - - +
407B TYR* 1.3 69.7 + - - +
408B SER 4.5 0.7 - - - +
394G THR* 5.3 0.7 - - - -
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Residues in contact with TYR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 4.6 1.1 - - + -
366B THR* 3.5 23.3 - - + -
367B CYS 3.3 9.6 - - - -
368B LEU* 3.7 27.8 - - + +
392B LYS 4.3 0.2 - - - +
393B THR* 3.5 2.3 - - - +
394B THR* 2.9 35.2 + - + +
405B PHE* 3.9 20.2 - + - -
406B LEU* 1.3 80.3 - - - +
408B SER* 1.3 59.4 + - - +
366G THR* 2.7 42.7 + - + +
394G THR* 4.1 9.0 - - + -
405G PHE* 5.4 0.2 - - - -
407G TYR* 3.3 46.2 - + + -
408G SER 4.9 0.2 - - - -
409G ARG* 3.4 28.9 - - + +
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B THR* 3.4 6.2 - - - +
367B CYS* 2.9 37.4 + - - -
379B VAL* 3.7 23.1 - - - +
381B TRP* 2.8 30.8 + - - -
391B TYR* 4.6 0.7 - - - -
392B LYS 3.4 6.3 + - - -
393B THR* 2.7 26.1 + - - -
406B LEU* 4.5 1.1 - - - +
407B TYR* 1.3 73.2 - - - +
409B ARG* 1.3 60.5 + - - +
407G TYR* 4.6 1.1 - - - -
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Residues in contact with ARG 409 (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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364B SER* 2.9 30.9 + - - -
365B LEU 3.4 6.7 - - - +
381B TRP* 4.1 3.4 - - - -
391B TYR* 3.3 3.1 - - - -
392B LYS* 2.8 36.1 + - - +
408B SER* 1.3 74.6 + - - +
410B LEU* 1.3 63.2 + - - +
411B THR* 3.3 21.1 + - - +
368G LEU* 3.7 17.2 - - - +
370G LYS* 3.4 30.7 - - - +
399G ASP* 2.7 30.7 + - - -
405G PHE* 3.6 28.7 - - + +
407G TYR* 3.2 27.6 - - + +
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Residues in contact with LEU 410 (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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363B VAL 3.7 0.9 - - - +
364B SER* 3.5 3.2 - - - -
365B LEU* 2.7 45.1 + - + +
381B TRP* 3.7 40.3 - - + +
388B GLU* 4.0 35.2 - - + +
390B ASN 3.7 18.4 - - - +
391B TYR* 3.9 12.6 - - + -
409B ARG* 1.3 71.9 - - - +
411B THR* 1.3 67.1 + - - +
412B VAL* 3.6 21.8 - - + -
423B PHE* 3.8 19.1 - - + -
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Residues in contact with THR 411 (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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362B GLN* 3.6 38.6 - - + +
363B VAL 3.4 7.7 + - - +
364B SER* 4.7 0.2 - - - +
388B GLU* 5.6 0.3 - - - +
390B ASN* 3.5 39.7 + - - +
409B ARG* 3.3 32.8 + - - +
410B LEU* 1.3 75.3 - - - +
412B VAL* 1.3 68.9 + - - +
370G LYS* 6.2 1.1 - - - +
399G ASP* 5.2 2.3 + - - -
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Residues in contact with VAL 412 (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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362B GLN* 3.4 5.5 - - - -
363B VAL* 3.0 48.1 + - + +
365B LEU* 4.2 15.7 - - + -
388B GLU* 4.3 5.2 - - - +
410B LEU* 3.6 29.4 - - + +
411B THR* 1.3 81.7 - - - +
413B ASP* 1.3 75.3 + - - +
416B ARG* 4.5 9.0 - - + +
417B TRP* 4.3 10.1 - - + -
423B PHE* 3.9 23.3 - - + -
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Residues in contact with ASP 413 (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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361B ASN* 3.7 15.0 + - - +
362B GLN* 4.0 16.4 - - - +
412B VAL* 1.3 76.4 - - - +
414B LYS* 1.3 64.9 + - - +
415B SER* 3.6 19.0 + - - +
416B ARG* 3.1 26.1 + - + +
417B TRP 3.4 8.1 + - - -
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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