Contacts of the helix formed by residues 316 - 333 (chain B) in PDB entry 4DVQ
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 VAL 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B PHE* 3.8 8.1 - - + -
196B THR* 3.4 20.9 + - - +
197B ILE* 3.9 18.6 - - + -
200B SER* 5.8 0.2 - - - -
223B PHE* 3.6 27.4 - - + -
224B LEU* 3.6 30.7 - - + -
227B LEU* 3.8 14.1 - - + -
312B THR 3.8 12.1 - - - +
313B ALA 4.0 1.0 + - - +
314B GLY 3.4 2.6 - - - -
315B SER* 1.3 85.3 - - - +
317B ASP* 1.3 63.3 + - - +
319B THR 3.4 3.1 + - - -
320B ALA* 2.9 24.5 + - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.4 28.6 - - - -
224B LEU* 5.3 1.7 - - - +
227B LEU* 3.0 33.4 - - - +
228B GLU* 5.1 3.8 + - - +
231B PHE* 3.8 24.7 - - + -
313B ALA 4.6 2.2 + - - +
316B VAL* 1.3 70.8 - - - +
318B THR* 1.3 68.0 + - + +
319B THR 3.1 0.5 + - - -
320B ALA 4.3 0.2 - - - +
321B PHE* 3.1 38.9 + - + +
378B VAL* 4.5 1.2 - - - +
488B ILE* 3.6 22.2 - - + +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 5.7 0.4 - - + -
314B GLY 2.8 29.5 + - - +
315B SER 4.3 0.7 - - - -
317B ASP* 1.3 77.8 - - + +
319B THR* 1.3 69.7 + - - +
322B PRO* 3.0 24.8 - - - +
378B VAL* 3.3 16.6 - - + +
488B ILE* 5.0 6.7 - - + -
601B HEM 3.2 36.9 - - + +
602B 1CA 3.9 40.4 - - + -
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR* 3.7 18.6 - - + -
315B SER 3.9 6.0 + - - -
316B VAL 3.4 6.4 + - - -
317B ASP 3.1 0.4 - - - -
318B THR* 1.3 87.5 + - - +
320B ALA* 1.3 68.0 + - - +
321B PHE 3.3 1.6 - - - -
322B PRO* 3.3 9.2 - - - +
323B LEU* 3.3 6.5 + - + +
456B ALA* 3.7 20.1 - - - +
459B GLU* 3.7 19.1 + - + +
460B MET* 3.3 35.3 - - + +
601B HEM 3.9 13.3 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 3.8 7.3 - - + +
193B PHE* 3.5 45.1 - - + -
196B THR* 3.7 17.0 - - + +
316B VAL 2.9 21.2 + - - +
317B ASP 3.2 0.6 + - - +
319B THR* 1.3 72.7 - - - +
321B PHE* 1.3 58.1 + - - +
323B LEU* 3.2 5.3 - - - +
324B LEU* 3.0 32.3 + - - +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLN* 4.0 18.2 - - - -
193B PHE* 3.4 31.9 - + - -
317B ASP* 3.1 26.9 + - + +
320B ALA* 1.3 75.3 - - - +
322B PRO* 1.3 73.1 - - + +
324B LEU* 3.1 13.1 + - + +
325B MET* 2.9 27.8 + - - +
378B VAL* 4.9 8.1 - - + -
483B MET* 6.2 0.2 - - + -
488B ILE* 3.8 17.0 - - + -
489B LEU 5.0 1.3 - - - +
490B ARG* 3.6 38.1 - - + -
491B PRO* 3.5 39.0 - - + -
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Residues in contact with PRO 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR 3.0 28.9 - - - +
319B THR 3.3 5.2 - - - +
321B PHE* 1.3 92.7 - - + +
323B LEU* 1.3 52.0 + - - +
325B MET* 3.2 3.4 + - + -
326B THR* 2.6 38.8 + - - +
372B THR* 3.4 12.1 - - + +
373B LEU* 3.6 22.7 - - + -
376B TYR 5.2 3.1 - - - +
378B VAL* 3.2 23.6 - - + -
460B MET* 3.2 17.9 - - + -
601B HEM 4.0 2.9 - - + -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 4.2 16.4 - - + -
195B TYR* 4.0 31.2 - - + -
196B THR* 4.4 1.6 - - + -
319B THR* 3.4 19.5 - - + +
320B ALA 3.2 10.7 + - - +
322B PRO* 1.3 78.8 - - - +
324B LEU* 1.3 61.8 + - - +
326B THR* 3.3 5.1 + - - -
327B LEU* 3.1 29.2 + - + +
459B GLU 4.4 0.2 - - - +
460B MET* 3.0 45.9 - - + +
463B LEU* 4.4 12.6 - - + -
464B LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 4.0 19.7 - - + +
189B GLN* 3.5 38.1 - - + +
192B ILE* 4.1 15.3 - - + -
193B PHE* 4.0 14.8 - - + -
320B ALA 3.0 29.9 + - - +
321B PHE* 3.1 22.6 + - + +
323B LEU* 1.3 75.0 - - - +
325B MET* 1.3 70.0 + - + +
327B LEU* 3.2 8.7 + - - +
328B PHE* 2.9 28.8 + - - +
491B PRO* 5.3 1.6 - - + -
494B SER* 4.9 4.9 - - - +
495B PRO* 6.5 0.4 - - + -
497B LEU* 5.2 2.4 - - + +
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Residues in contact with MET 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE 2.9 18.4 + - - +
322B PRO* 3.2 8.0 + - + +
324B LEU* 1.3 88.5 - - + +
326B THR* 1.3 58.0 + - - +
328B PHE* 3.2 9.6 + - + +
329B GLU* 2.8 31.8 + - - +
372B THR* 3.7 15.7 - - + -
376B TYR* 3.9 31.0 - - + -
481B ILE* 4.2 26.2 - - + -
483B MET* 4.4 12.8 - - + +
491B PRO* 3.6 40.6 - - + -
493B THR 5.2 1.1 - - - +
495B PRO* 5.4 3.6 - - + -
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 2.6 23.8 + - - +
323B LEU* 3.7 6.1 - - - -
325B MET* 1.3 74.7 - - - +
327B LEU* 1.3 60.4 + - - +
329B GLU* 3.1 1.6 + - - +
330B LEU* 2.8 46.9 + - + +
365B LEU* 5.7 0.2 - - + -
368B ALA* 4.7 5.6 - - + +
369B LEU* 4.2 13.2 - - + +
372B THR* 3.0 19.2 + - - +
423B TYR* 3.2 23.6 - - - +
464B LEU* 4.0 25.6 - - + -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 6.4 0.4 - - + -
188B VAL* 4.5 13.2 - - + -
192B ILE* 4.2 30.7 - - + -
323B LEU 3.1 18.3 + - - +
324B LEU* 3.6 10.1 - - - +
326B THR* 1.3 77.2 - - - +
328B PHE* 1.3 62.7 + - - +
330B LEU* 3.5 9.1 + - + +
331B ALA* 3.1 23.6 + - - +
463B LEU* 4.9 7.4 - - + -
464B LEU* 3.8 22.6 - - + +
467B VAL* 4.5 20.2 - - + -
473B VAL* 4.1 12.2 - - + +
497B LEU* 3.8 14.6 - - + -
499B PHE* 4.5 16.2 - - + -
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Residues in contact with PHE 328 (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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324B LEU 2.9 13.6 + - - +
325B MET* 3.4 17.3 - - + +
327B LEU* 1.3 77.2 - - - +
329B GLU* 1.3 70.4 + - + +
331B ALA* 3.0 6.6 + - - +
332B ARG* 3.0 67.0 + - + +
376B TYR* 4.9 4.0 - + - -
475B THR* 4.6 7.4 - - - -
477B THR* 3.2 23.6 - - + -
479B GLU 3.5 18.4 - - - -
481B ILE* 3.4 37.2 - - + -
495B PRO* 3.8 24.9 - - + -
497B LEU* 4.5 6.7 - - + +
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Residues in contact with GLU 329 (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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325B MET 2.8 21.9 + - - +
326B THR 3.8 1.3 - - - +
328B PHE* 1.3 75.2 - - + +
330B LEU* 1.3 63.0 + - - +
332B ARG* 2.8 28.4 + - - +
333B ASN* 3.0 47.5 + - - +
372B THR* 5.2 0.2 - - - +
375B LEU* 4.3 5.5 - - - +
376B TYR* 2.4 39.4 + - + -
423B TYR* 3.5 49.0 - - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR* 2.8 34.7 + - + +
327B LEU* 3.8 9.2 - - + +
329B GLU* 1.3 73.5 - - - +
331B ALA* 1.3 59.3 + - - +
333B ASN* 3.2 21.1 - - - +
334B PRO 3.7 0.3 - - - -
336B VAL* 4.3 5.4 - - + -
337B GLN* 2.9 36.3 - - + +
340B LEU* 3.5 33.9 - - + -
365B LEU* 5.3 1.8 - - + -
423B TYR* 4.1 19.5 - - + +
464B LEU* 4.8 12.1 - - + -
468B LEU* 4.3 25.8 - - + -
473B VAL* 5.5 4.7 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU 3.1 16.0 + - - +
328B PHE 3.0 6.0 + - - +
330B LEU* 1.3 75.2 - - - +
332B ARG* 1.3 60.3 + - - +
334B PRO* 4.1 9.2 - - - +
473B VAL* 3.7 34.3 - - + +
474B GLU* 3.9 7.1 - - - -
475B THR* 3.4 30.6 + - - +
478B GLN* 4.3 5.2 + - - +
497B LEU* 4.0 6.1 - - + -
280F PHE* 5.9 1.4 - - - -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.0 42.1 + - + +
329B GLU* 2.8 42.4 + - - +
331B ALA* 1.3 74.9 - - - +
333B ASN* 1.3 70.1 + - - +
334B PRO* 3.3 10.7 - - - +
376B TYR* 3.7 6.9 + - - -
475B THR* 4.3 0.4 + - - +
478B GLN* 2.9 48.4 + - + +
480B ASP* 2.3 52.7 + - - +
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Residues in contact with ASN 333 (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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329B GLU* 3.0 43.4 + - - +
330B LEU* 3.2 7.6 - - - +
331B ALA 3.3 0.2 - - - -
332B ARG* 1.3 88.0 - - - +
334B PRO* 1.3 60.4 - - - +
335B ASP* 3.2 14.2 - - - +
336B VAL* 3.0 20.3 + - + +
337B GLN 3.0 21.3 + - - -
422B ARG* 6.1 0.7 - - - +
423B TYR* 4.0 22.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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