Contacts of the strand formed by residues 355 - 366 (chain B) in PDB entry 4QDQ
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 GLY 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B ALA 3.7 5.8 - - - -
348B ILE* 4.4 4.5 - - - -
353B GLN 3.6 2.2 + - - -
354B ASN* 1.3 73.1 - - - +
356B TYR* 1.3 64.7 + - - -
357B TYR* 4.8 1.8 - - - -
390B ALA* 3.8 15.7 - - - -
415B HIS* 3.7 11.5 - - - -
416B SER* 3.8 1.7 - - - -
701B GOL 2.6 39.8 + - - -
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TRP* 4.1 17.3 - + - -
319B THR* 5.7 1.1 - - - -
346B GLY* 3.2 0.5 - - - -
347B ALA 2.9 36.8 + - - +
349B SER* 4.3 11.7 - - - -
352B THR* 4.5 2.6 + - - +
354B ASN* 3.5 47.0 + - + -
355B GLY* 1.3 73.1 - - - -
357B TYR* 1.3 65.6 + - - +
390B ALA* 3.9 2.3 - - - +
415B HIS 3.6 3.6 - - - -
416B SER* 3.2 26.6 + - - -
417B GLY* 3.5 28.7 - - - +
418B ILE 5.2 1.1 - - - -
419B ALA* 3.4 21.9 - - + +
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Residues in contact with TYR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLY* 3.7 9.9 - - - -
355B GLY 5.3 0.4 - - - -
356B TYR* 1.3 80.5 - - - +
358B VAL* 1.3 61.0 + - - +
359B LYS* 3.8 12.9 - - + +
387B ASN* 3.6 29.8 - - + -
388B ASN* 2.7 29.1 + - - -
389B ASP* 3.3 35.0 - - - +
390B ALA* 3.7 4.0 - - + -
414B TRP* 3.2 3.3 - - - +
415B HIS* 2.7 80.3 + + + +
417B GLY 3.6 6.5 + - - -
419B ALA 3.8 7.6 - - - -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B THR* 6.1 0.2 - - - +
357B TYR* 1.3 72.2 - - - +
359B LYS* 1.3 59.2 + - - +
360B SER* 3.2 31.9 - - - +
361B TYR* 4.2 13.9 - - + -
386B ALA* 3.4 3.9 - - + +
387B ASN* 3.1 32.3 + - - +
409B ILE* 5.9 0.4 - - + -
411B PRO* 3.8 33.4 - - + -
413B THR 3.6 6.7 - - - +
414B TRP* 4.1 1.1 - - - +
418B ILE* 3.9 16.4 - - + -
419B ALA 3.8 16.6 + - - +
420B LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B TYR* 3.8 26.2 - - + +
358B VAL* 1.3 73.0 - - - +
360B SER* 1.3 58.5 + - - +
385B GLN* 3.7 10.3 + - - +
386B ALA* 2.7 28.3 + - - +
387B ASN 3.9 8.5 - - - +
413B THR* 2.8 22.0 + - - +
414B TRP 3.7 24.9 + - - +
415B HIS* 3.9 16.9 + - + +
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 3.2 12.1 - - - +
359B LYS* 1.3 79.4 - - - +
361B TYR* 1.3 61.9 + - - +
383B VAL* 3.8 16.0 - - - +
384B PHE 3.1 13.9 - - - -
385B GLN* 4.0 12.1 - - - -
386B ALA* 4.2 1.8 - - - +
412B GLN* 2.8 30.9 + - - +
413B THR* 2.6 30.3 + - - +
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Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.4 34.1 + - + +
344B THR* 3.8 21.2 - - + +
358B VAL* 4.2 5.8 - - + -
360B SER* 1.3 76.2 - - - +
362B LYS* 1.3 74.5 + - - +
363B LEU* 5.0 0.4 - - + -
383B VAL* 3.7 2.8 - - - -
384B PHE* 2.8 64.2 + + + -
386B ALA* 3.8 25.6 - - + -
394B VAL 5.6 0.2 + - - -
396B ASN* 3.5 21.0 + - - +
409B ILE* 3.7 35.9 - - + -
410B ARG 3.4 12.6 - - - +
411B PRO* 3.9 5.6 - - + -
412B GLN* 4.0 4.3 - - - +
420B LEU* 5.9 0.2 - - + -
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B TYR* 1.3 80.3 - - - +
363B LEU* 1.3 60.1 + - - +
374B VAL* 4.4 12.3 - - + -
381B HIS* 3.0 42.6 + - + +
382B LYS 4.0 16.4 - - - +
383B VAL* 4.1 16.8 - - + -
384B PHE* 4.6 0.4 - - - -
409B ILE* 3.7 4.0 - - - -
410B ARG* 2.8 47.2 + - + +
412B GLN* 3.6 35.5 + - + +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.3 3.6 - - + -
342B ILE* 3.9 28.3 - - + -
361B TYR* 5.0 1.1 - - + -
362B LYS* 1.3 75.1 - - - +
364B GLU* 1.3 58.0 + - - +
365B VAL* 4.0 13.5 - - + -
374B VAL* 3.3 7.6 - - - +
375B TYR* 2.8 47.6 + - + +
382B LYS 4.7 1.6 + - - -
384B PHE* 3.7 19.6 - - + -
398B LEU* 4.1 13.0 - - + -
402B LEU* 3.9 25.4 - - + -
407B VAL* 3.7 24.5 - - + -
408B ARG 3.4 13.9 - - - +
409B ILE* 4.2 2.5 - - + +
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Residues in contact with GLU 364 (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 LYS 4.2 0.2 - - - -
363B LEU* 1.3 74.2 - - - +
365B VAL* 1.3 65.1 + - - +
372B TRP* 3.4 35.2 - - + +
373B MET 3.2 15.9 - - - +
374B VAL* 3.8 19.7 - - + +
408B ARG* 2.7 61.4 + - + +
410B ARG* 2.8 40.5 + - - -
702B SO4 5.5 0.5 + - - -
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.7 0.9 - - + -
363B LEU* 4.0 15.7 - - + -
364B GLU* 1.3 79.7 - - - +
366B SER* 1.3 61.7 + - - +
371B ASP 3.7 0.2 - - - +
372B TRP* 3.3 7.5 - - - -
373B MET* 2.8 60.3 + - + +
375B TYR 5.8 0.9 - - - +
402B LEU* 3.8 30.7 - - + -
404B THR* 3.3 24.5 - - + +
406B PHE 3.4 9.6 - - - +
407B VAL* 4.5 4.7 - - + -
556B ASP* 4.6 1.0 - - - +
557B THR* 3.7 21.0 + - + +
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Residues in contact with SER 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B VAL* 1.3 76.9 - - - +
367B THR* 1.3 60.6 + - - +
368B ASN* 3.2 6.4 + - - -
369B GLY* 2.8 29.7 + - - -
371B ASP 2.6 26.0 + - - -
372B TRP* 3.6 22.9 - - - -
404B THR* 3.0 7.9 + - - -
405B ARG 3.1 0.5 + - - -
406B PHE* 2.8 32.2 + - - -
556B ASP* 3.6 3.8 - - - -
557B THR* 5.7 0.4 - - - -
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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
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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