Contacts of the helix formed by residues 362 - 378 (chain D) in PDB entry 4JGH
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 ASP 362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297D PHE* 3.7 25.4 - - + -
301D ASP* 5.4 0.3 - - - +
359D PHE 3.0 14.9 + - - +
360D GLN* 3.1 3.8 + - - +
361D ASP* 1.3 75.3 - - - +
363D PRO* 1.3 64.4 - - - +
364D ARG* 2.7 48.9 + - - +
365D PHE* 2.6 39.1 + - + +
366D LEU 3.1 8.3 + - - -
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Residues in contact with PRO 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ASP 3.1 8.7 - - - +
362D ASP* 1.3 92.3 - - - +
364D ARG* 1.3 60.1 + - + +
366D LEU* 3.8 12.9 - - + +
367D THR* 2.9 28.2 + - - -
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Residues in contact with ARG 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D PHE* 4.1 1.4 - - - -
301D ASP* 3.2 28.3 + - - -
307D ILE* 3.0 36.5 - - + +
311D LEU* 3.5 29.9 - - + +
362D ASP* 2.7 30.4 + - - +
363D PRO* 1.3 80.4 - - + +
365D PHE* 1.3 59.3 + - + +
367D THR* 3.7 6.8 + - - -
368D ALA* 3.2 17.5 + - - +
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Residues in contact with PHE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D PHE* 3.5 28.5 - + - -
307D ILE* 3.9 9.4 - - + -
310D MET* 3.8 30.7 - - + -
311D LEU* 3.4 24.9 - - + -
314D LEU* 3.7 24.6 - - + +
355D VAL* 4.3 11.6 - - + +
359D PHE* 3.6 56.5 - + + -
362D ASP* 2.6 30.3 + - + +
364D ARG* 1.3 73.1 - - - +
366D LEU* 1.3 60.9 + - - +
368D ALA* 3.1 16.1 - - - +
369D ARG* 3.1 10.6 + - - +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D VAL* 3.4 26.0 - - + -
361D ASP* 3.7 30.7 - - + +
362D ASP 3.1 12.7 + - - +
363D PRO* 3.8 14.8 - - + +
365D PHE* 1.3 72.7 - - - +
367D THR* 1.3 63.1 + - - +
368D ALA 3.0 1.3 - - - -
369D ARG* 3.0 33.3 + - - +
370D ASP* 2.8 37.3 + - - +
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Residues in contact with THR 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D PRO 2.9 16.1 + - - -
364D ARG* 3.7 9.0 - - - -
366D LEU* 1.3 78.5 - - - +
368D ALA* 1.3 62.7 + - - +
370D ASP* 4.0 7.4 - - - +
371D LYS* 3.2 34.9 + - + +
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 4.1 24.5 - - + +
314D LEU* 4.0 15.7 - - + -
315D GLU* 3.6 15.0 - - + +
364D ARG 3.2 9.5 + - - +
365D PHE* 3.1 19.3 - - - +
366D LEU 3.0 0.2 - - - -
367D THR* 1.3 80.7 - - - +
369D ARG* 1.3 61.8 + - - +
371D LYS* 3.8 4.4 - - - +
372D ALA* 3.0 24.1 + - - +
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Residues in contact with ARG 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D LEU* 4.8 0.8 - - + +
318D ILE* 3.8 25.8 - - + -
348D PHE* 4.0 23.0 - - + -
351D PHE* 4.6 7.4 - - + -
352D SER* 2.8 54.0 + - - +
355D VAL* 4.4 10.1 - - + -
361D ASP* 5.6 0.4 + - - -
365D PHE 3.1 7.7 + - - +
366D LEU* 3.0 36.7 + - - +
368D ALA* 1.3 75.8 - - - +
370D ASP* 1.3 83.6 + - - +
371D LYS 2.8 5.3 + - - -
372D ALA 2.7 6.6 + - - -
373D TYR* 2.6 43.4 + - + +
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Residues in contact with ASP 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D PHE* 4.9 4.4 - - - -
366D LEU* 2.8 17.8 + - - +
367D THR* 4.0 8.2 - - + +
369D ARG* 1.3 106.1 + - - +
371D LYS* 1.3 56.2 + - - +
373D TYR* 4.8 4.8 - - - -
374D LYS* 2.9 27.6 + - - +
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Residues in contact with LYS 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D GLU* 3.2 38.1 + - - +
319D ILE* 5.5 0.2 - - - +
367D THR* 3.2 26.7 + - + +
368D ALA* 3.8 3.1 - - - +
369D ARG 2.8 2.0 + - - -
370D ASP* 1.3 75.6 - - - +
372D ALA* 1.3 65.0 + - - +
374D LYS* 4.0 7.5 - - + +
375D ALA* 3.3 19.9 + - - +
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Residues in contact with ALA 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D GLU* 3.4 46.8 - - + +
318D ILE* 3.7 18.6 - - + -
319D ILE* 3.7 10.1 - - + +
368D ALA 3.0 8.3 + - - +
369D ARG 2.7 3.0 + - - +
371D LYS* 1.3 76.8 - - - +
373D TYR* 1.3 60.2 + - - +
375D ALA* 2.9 24.3 + - - +
376D VAL* 3.1 10.4 + - - +
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Residues in contact with TYR 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ILE* 3.9 11.5 - - + +
344D LEU* 3.6 36.4 + - + +
345D ASP* 4.7 3.1 + - - -
347D LEU* 5.2 3.1 - - + -
348D PHE* 3.3 54.0 - + + +
351D PHE* 5.1 9.2 - + + -
369D ARG* 2.6 31.5 + - + +
370D ASP* 4.8 3.8 - - - +
372D ALA* 1.3 67.8 - - - +
374D LYS* 1.3 58.4 + - + +
375D ALA 2.7 15.6 + - - -
376D VAL* 2.7 23.3 + - + +
377D VAL* 3.1 34.3 + - + +
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Residues in contact with LYS 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D ASP 2.9 23.5 + - - +
371D LYS* 4.0 7.6 - - + +
372D ALA 3.3 0.4 - - - -
373D TYR* 1.3 87.0 - - + +
375D ALA* 1.3 61.4 + - - +
377D VAL* 3.9 7.5 - - + +
378D ASN* 3.0 34.6 - - - +
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Residues in contact with ALA 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ILE* 4.0 22.7 - - + -
371D LYS 3.3 13.8 + - - +
372D ALA 2.9 14.8 + - - +
373D TYR 2.7 2.0 + - - -
374D LYS* 1.3 78.8 - - - +
376D VAL* 1.3 62.7 - - - +
377D VAL 3.2 1.3 - - - -
378D ASN* 3.1 14.2 + - - +
379D ASP* 3.3 20.0 + - - +
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Residues in contact with VAL 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ILE* 4.0 17.3 - - + +
319D ILE* 3.8 27.1 - - - +
322D GLY* 4.0 19.1 - - - +
323D LEU* 3.4 25.0 - - + +
326D MET* 4.9 2.7 - - + -
344D LEU* 4.7 16.6 - - + -
347D LEU* 5.1 3.4 - - + -
351D PHE* 5.7 0.9 - - + -
372D ALA 3.1 13.8 + - - +
373D TYR* 2.7 18.3 + - + +
375D ALA* 1.3 72.2 - - - +
377D VAL* 1.3 63.4 + - + +
379D ASP* 2.9 12.7 + - - -
380D ALA* 3.1 12.5 + - - +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D TYR* 4.2 7.5 + - - +
344D LEU* 4.3 22.2 - - + -
373D TYR* 3.1 44.7 + - + +
374D LYS* 3.9 11.7 - - + +
376D VAL* 1.3 78.4 - - + +
378D ASN* 1.3 69.0 + - - +
379D ASP 3.4 0.5 + - - -
380D ALA* 3.8 4.9 + - - +
381D THR* 3.8 12.1 + - - -
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Residues in contact with ASN 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LYS* 3.0 31.1 - - - +
375D ALA* 3.1 9.7 + - - +
377D VAL* 1.3 84.0 - - - +
379D ASP* 1.3 67.4 + - - +
380D ALA 3.7 0.4 - - - -
381D THR* 3.9 14.2 + - - -
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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