Contacts of the helix formed by residues 363 - 376 (chain B) in PDB entry 3A4R
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 PRO 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A GLU* 4.4 23.1 - - + +
358B LEU* 4.3 1.4 - - - +
361B ASP 3.9 5.8 - - - +
362B SER* 1.3 88.7 - - - +
364B LEU* 1.3 60.6 + - - +
365B LYS* 3.6 20.0 - - + -
366B VAL* 2.9 35.1 + - + +
367B LEU 4.1 0.3 + - - -
393B GLY 3.5 14.1 - - - +
394B LYS* 4.5 5.8 - - - +
395B GLU 3.3 10.1 - - - +
396B LEU* 3.7 11.9 - - + -
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Residues in contact with LEU 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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358B LEU* 4.2 5.8 - - + -
363B PRO* 1.3 72.2 - - - +
365B LYS* 1.3 63.2 + - - +
367B LEU* 3.0 45.0 + - + +
368B MET* 3.0 15.6 + - + +
391B LEU* 4.1 27.4 - - + -
393B GLY* 3.3 7.5 + - - -
395B GLU* 2.9 40.5 + - - +
397B PRO* 3.9 29.2 - - + -
400B LEU* 4.1 17.0 - - + -
402B LEU* 4.2 12.6 - - + -
408B ILE* 4.6 3.6 - - + -
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Residues in contact with LYS 365 (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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-1A GLY 4.8 2.0 + - - -
0A SER* 3.9 19.3 - - - +
340A GLU* 3.4 26.5 - - - +
359A SER* 3.6 12.3 - - - +
360A PRO* 3.9 15.8 - - - +
361A ASP* 3.1 37.1 + - - +
363B PRO* 3.6 20.9 - - + -
364B LEU* 1.3 77.6 - - - +
366B VAL* 1.3 60.6 + - + +
368B MET* 3.6 15.7 - - - +
369B SER* 2.9 30.8 + - - -
392B SER 5.6 0.2 - - - +
393B GLY* 2.9 20.4 + - - +
394B LYS* 5.5 4.5 - - + +
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Residues in contact with VAL 366 (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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0A SER* 3.5 33.8 + - - +
357B SER 5.5 0.2 - - - +
358B LEU* 3.8 16.8 - - + -
362B SER* 4.2 10.8 - - - +
363B PRO* 2.9 32.6 + - + +
365B LYS* 1.3 78.9 - - + +
367B LEU* 1.3 62.5 + - - +
369B SER* 3.3 2.9 + - - -
370B HIS* 3.0 49.2 + - + +
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Residues in contact with LEU 367 (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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343B LEU* 3.8 28.9 - - + -
345B VAL* 3.8 41.1 - - + -
354B LEU* 4.6 0.7 - - - +
356B ILE* 3.9 15.9 - - + -
358B LEU* 4.1 12.0 - - + +
363B PRO 4.1 0.8 + - - -
364B LEU* 3.0 24.9 + - + +
366B VAL* 1.3 80.3 - - - +
368B MET* 1.3 62.1 + - + +
370B HIS* 3.3 9.5 + - - +
371B TYR* 2.9 26.3 + - - +
384B PHE* 4.4 6.5 - - + -
391B LEU* 5.9 0.2 - - + -
408B ILE* 4.0 22.4 - - + -
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Residues in contact with MET 368 (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 LEU* 3.0 13.6 + - + +
365B LYS* 3.6 11.9 - - - +
367B LEU* 1.3 77.4 - - + +
369B SER* 1.3 58.5 + - - +
371B TYR* 3.2 2.9 + - - +
372B GLU* 3.0 38.4 + - - +
384B PHE* 3.7 50.9 - - + -
391B LEU* 3.6 32.1 - - + +
392B SER 3.9 4.7 - - - +
393B GLY* 3.5 38.6 - - - +
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Residues in contact with SER 369 (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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-4A GLY 3.7 23.8 + - - +
-1A GLY* 3.9 18.8 - - - -
0A SER* 3.9 16.7 + - - -
365B LYS 2.9 18.0 + - - -
366B VAL 3.6 5.2 - - - -
367B LEU 3.2 0.2 - - - -
368B MET* 1.3 78.3 - - - +
370B HIS* 1.3 59.4 + - - +
372B GLU* 3.6 3.8 + - - +
373B GLU* 3.3 21.8 + - - +
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Residues in contact with HIS 370 (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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0A SER* 5.5 1.9 + - - -
2B EDO 2.7 36.0 + - - +
354B LEU* 3.8 13.2 - - + -
356B ILE* 3.7 31.0 - - + +
357B SER 5.2 1.5 + - - -
366B VAL* 3.0 45.8 + - + +
367B LEU* 3.7 4.7 - - - +
369B SER* 1.3 75.1 - - - +
371B TYR* 1.3 61.4 + - - +
373B GLU* 3.3 1.0 + - - -
374B ALA* 2.9 26.9 + - - +
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Residues in contact with TYR 371 (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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345B VAL* 3.5 42.8 - - + -
347B GLY* 3.3 26.4 - - - -
352B GLN* 3.4 18.5 + - - +
354B LEU* 3.6 17.0 - - + +
367B LEU 2.9 17.1 + - - +
368B MET 3.2 4.7 + - - +
370B HIS* 1.3 75.7 - - - +
372B GLU* 1.3 64.9 + - - +
374B ALA* 3.3 0.7 + - - +
375B MET* 3.0 46.9 + - + +
377B LEU* 3.8 19.3 - - + +
382B LEU* 4.0 9.4 - - + -
384B PHE* 3.9 19.1 - + + -
410B VAL* 3.9 21.6 - - + +
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Residues in contact with GLU 372 (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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-4A GLY* 2.8 33.0 + - - +
368B MET* 3.0 25.6 + - - +
369B SER* 3.9 5.6 - - - +
370B HIS 3.3 0.2 - - - -
371B TYR* 1.3 75.1 - - - +
373B GLU* 1.3 63.4 + - - +
376B GLY* 3.0 5.5 + - - -
377B LEU* 2.9 45.8 + - - +
378B SER* 3.8 17.5 + - - +
379B GLY 4.2 4.8 + - - -
380B HIS 4.6 8.1 - - - +
382B LEU* 4.2 17.0 - - + +
384B PHE* 5.0 6.6 - - + -
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Residues in contact with GLU 373 (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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2B EDO 3.8 20.0 - - - +
369B SER 3.3 14.6 + - - +
370B HIS* 3.7 3.4 - - - +
371B TYR 3.3 0.2 - - - -
372B GLU* 1.3 80.2 - - - +
374B ALA* 1.3 65.5 + - - +
375B MET 3.2 0.3 + - - -
376B GLY* 3.4 7.8 + - - -
378B SER* 6.4 0.4 - - - -
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Residues in contact with ALA 374 (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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2B EDO 4.0 9.4 - - - -
354B LEU* 4.0 25.4 - - + -
370B HIS 2.9 18.6 + - - +
371B TYR 3.7 4.7 - - - +
373B GLU* 1.3 78.8 - - - +
375B MET* 1.3 75.9 + - + +
376B GLY 3.7 0.2 + - - -
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Residues in contact with MET 375 (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 HIS* 4.3 17.9 + - - +
352B GLN* 3.8 24.4 + - + +
353B MET 3.4 43.1 - - - +
354B LEU* 3.8 14.1 - - + +
371B TYR* 3.0 38.2 + - + +
374B ALA* 1.3 88.0 - - + +
376B GLY* 1.3 63.0 + - - +
377B LEU* 3.6 26.9 + - + +
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Residues in contact with GLY 376 (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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372B GLU 3.0 6.3 + - - -
373B GLU* 3.4 8.2 + - - -
374B ALA 3.4 0.6 + - - -
375B MET* 1.3 79.6 - - - +
377B LEU* 1.3 63.4 + - - +
378B SER 3.6 3.4 + - - +
380B HIS* 4.3 6.2 - - - -
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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