Contacts of the helix formed by residues 316 - 333 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H PHE* 3.9 7.6 - - + -
196H THR* 3.3 14.8 + - - +
197H ILE* 3.9 23.3 - - + -
200H SER* 5.8 0.7 - - - -
223H PHE* 3.6 29.4 - - + -
224H LEU* 3.6 31.6 - - + -
227H LEU* 4.2 3.8 - - + -
312H THR 3.9 10.5 - - - +
313H ALA 4.8 2.7 - - - +
314H GLY 3.3 3.0 + - - -
315H SER* 1.3 83.9 - - - +
317H ASP* 1.3 78.4 + - - +
318H THR 3.3 1.4 + - - -
319H THR 3.4 2.3 + - - -
320H ALA* 3.2 19.1 + - - +
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Residues in contact with ASP 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H PHE* 3.6 27.0 - - + -
224H LEU* 4.9 2.3 - - - +
227H LEU* 3.4 34.6 - - - +
228H GLU* 5.1 4.2 + - - +
231H PHE* 3.7 26.2 - - + -
313H ALA 5.1 1.7 + - - +
314H GLY 4.9 0.6 + - - -
316H VAL* 1.3 76.4 - - - +
318H THR* 1.3 63.1 + - + +
321H PHE* 3.2 40.6 + - + +
378H VAL* 5.0 0.9 - - - -
488H ILE* 3.9 19.4 - - + +
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Residues in contact with THR 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H PHE* 6.1 0.2 - - + -
314H GLY 2.3 34.8 + - - +
315H SER* 4.0 1.4 - - - -
317H ASP* 1.3 78.1 - - + +
319H THR* 1.3 61.4 + - - +
322H PRO* 3.0 23.2 - - - +
378H VAL* 3.4 19.2 - - + +
488H ILE* 4.9 5.2 - - + -
601H HEM 3.2 37.8 - - + +
602H 1CA 4.1 40.2 - - + -
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Residues in contact with THR 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H THR* 4.2 9.6 - - + -
315H SER 4.5 3.0 + - - -
316H VAL 3.4 5.5 + - - -
317H ASP 3.3 0.4 - - - -
318H THR* 1.3 79.5 + - - +
320H ALA* 1.3 65.3 + - - +
321H PHE 3.4 0.4 - - - -
322H PRO* 3.2 6.9 - - - +
323H LEU* 3.0 22.7 + - + +
456H ALA* 3.8 26.0 - - - +
459H GLU* 3.9 24.8 + - + +
460H MET* 3.3 28.6 - - + +
601H HEM 3.9 17.4 - - - +
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Residues in contact with ALA 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H ILE* 3.8 10.5 - - + +
193H PHE* 3.6 39.3 - - + -
196H THR* 3.8 19.7 - - + +
316H VAL 3.2 16.1 + - - +
317H ASP 3.5 0.6 + - - +
319H THR* 1.3 78.4 - - - +
321H PHE* 1.3 58.5 + - - +
323H LEU* 3.0 4.6 + - - +
324H LEU* 2.8 31.4 + - - +
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Residues in contact with PHE 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H GLN* 4.0 17.5 - - - -
193H PHE* 3.4 33.9 - + - -
317H ASP* 3.2 23.8 + - - +
320H ALA* 1.3 80.8 - - - +
322H PRO* 1.3 63.6 - - + +
324H LEU* 3.4 8.1 + - + +
325H MET* 3.0 33.7 + - - +
378H VAL* 4.7 6.7 - - + -
488H ILE* 3.4 28.7 - - + -
489H LEU 5.0 1.1 - - - +
490H ARG* 3.5 35.7 - - + -
491H PRO* 3.6 34.1 - - + -
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Residues in contact with PRO 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H THR 3.0 30.1 - - - +
319H THR 3.2 11.0 - - - +
321H PHE* 1.3 91.4 - - + +
323H LEU* 1.3 57.7 + - - -
325H MET* 4.2 2.0 - - + -
326H THR* 2.8 34.8 + - - -
372H THR* 3.3 14.5 - - + +
373H LEU* 4.0 20.0 - - + -
376H TYR 5.1 3.6 - - - +
378H VAL* 3.8 15.0 - - + -
460H MET* 3.5 16.8 - - + -
601H HEM 4.0 7.0 - - + -
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Residues in contact with LEU 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H ILE* 3.6 19.1 - - + -
195H TYR* 3.9 15.3 - - + -
196H THR* 4.3 6.5 - - + -
319H THR* 3.0 14.3 + - + +
320H ALA 3.0 10.8 - - - +
322H PRO* 1.3 76.5 - - - +
324H LEU* 1.3 61.8 + - - +
326H THR* 3.1 14.5 + - - -
327H LEU* 3.1 16.0 + - + +
460H MET* 3.4 27.0 - - + +
463H LEU* 3.3 38.1 - - + -
464H LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H VAL* 3.8 20.9 - - + -
189H GLN* 3.6 60.6 - - + +
192H ILE* 4.0 13.2 - - + -
193H PHE* 5.4 1.3 - - + -
320H ALA 2.8 18.9 + - - +
321H PHE* 3.8 8.5 - - + +
323H LEU* 1.3 73.7 - - - +
325H MET* 1.3 70.0 + - + +
327H LEU* 3.5 9.9 + - + +
328H PHE* 3.1 28.2 + - - +
491H PRO* 4.8 9.2 - - + -
494H SER* 3.9 11.4 - - - +
495H PRO* 5.2 4.9 - - + -
497H LEU* 5.1 3.3 - - + +
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Residues in contact with MET 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PHE 3.0 21.6 + - - +
322H PRO* 3.9 4.9 - - + +
323H LEU 3.3 0.2 - - - -
324H LEU* 1.3 89.2 - - + +
326H THR* 1.3 58.6 + - - +
328H PHE* 3.6 11.4 - - + +
329H GLU* 3.0 33.4 + - - +
372H THR* 4.0 15.7 - - + -
376H TYR* 4.2 26.7 - - + -
481H ILE* 3.6 32.5 - - + -
483H MET* 4.2 14.4 - - + +
491H PRO* 3.9 34.1 - - + -
495H PRO* 4.9 3.4 - - + -
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Residues in contact with THR 326 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H PRO 2.8 20.6 + - - -
323H LEU* 3.1 8.5 + - - -
325H MET* 1.3 74.2 - - - +
327H LEU* 1.3 60.7 + - - +
329H GLU* 3.0 2.7 + - - +
330H LEU* 2.8 45.3 + - + +
365H LEU* 5.5 0.2 - - + -
368H ALA* 4.8 5.4 - - + -
369H LEU* 3.6 15.2 - - + +
372H THR* 2.7 23.4 + - - +
423H TYR* 3.8 15.3 - - - +
464H LEU* 3.7 31.4 - - + -
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Residues in contact with LEU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H PHE* 6.2 0.9 - - + -
188H VAL* 4.9 2.9 - - + -
192H ILE* 4.1 30.5 - - + -
323H LEU* 3.1 16.0 + - + +
324H LEU* 3.7 14.4 - - + +
325H MET 3.5 0.2 - - - -
326H THR* 1.3 75.1 - - - +
328H PHE* 1.3 57.9 + - - +
330H LEU* 3.2 10.2 + - + +
331H ALA* 3.0 28.3 + - - +
463H LEU* 4.8 10.3 - - + -
464H LEU* 3.5 24.2 - - + -
467H VAL* 4.8 7.6 - - + -
468H LEU* 6.5 0.7 - - + -
473H VAL* 4.0 16.7 - - + +
497H LEU* 4.2 13.2 - - + -
499H PHE* 4.6 26.5 - - + -
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Residues in contact with PHE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H LEU 3.1 15.4 + - - +
325H MET* 3.6 19.7 - - + +
327H LEU* 1.3 79.8 - - - +
329H GLU* 1.3 69.3 + - + +
331H ALA* 3.3 3.3 + - - +
332H ARG* 3.1 58.4 + - + +
376H TYR* 4.6 5.2 - - - -
475H THR* 4.9 2.0 - - - -
477H THR* 3.6 21.1 - - + -
479H GLU 3.8 11.7 - - - -
481H ILE* 3.4 40.2 - - + -
495H PRO* 3.6 28.9 - - + -
497H LEU* 4.4 14.5 - - + +
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Residues in contact with GLU 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325H MET 3.0 22.7 + - - +
326H THR 3.0 4.0 + - - +
328H PHE* 1.3 77.3 - - + +
330H LEU* 1.3 61.9 + - - +
332H ARG* 2.9 39.1 + - - -
333H ASN* 2.6 46.3 + - - +
375H LEU* 4.4 5.4 - - - +
376H TYR* 2.5 37.6 + - + -
421H GLU 5.8 0.2 - - - +
423H TYR* 3.8 41.5 - - + +
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Residues in contact with LEU 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H THR* 2.8 29.5 + - + +
327H LEU* 3.7 8.3 - - + +
329H GLU* 1.3 77.2 - - - +
331H ALA* 1.3 59.7 + - - +
333H ASN 3.3 19.8 - - - +
334H PRO 3.6 0.7 - - - -
336H VAL* 4.3 7.6 - - + -
337H GLN* 2.7 34.8 - - + +
340H LEU* 3.5 33.2 - - + -
365H LEU* 5.3 2.5 - - + -
423H TYR* 3.6 31.4 - - + +
464H LEU* 5.3 5.6 - - + -
468H LEU* 3.9 26.0 - - + -
473H VAL* 5.5 3.6 - - + -
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Residues in contact with ALA 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU 3.0 12.7 + - - +
328H PHE 3.4 9.9 - - - +
330H LEU* 1.3 75.9 - - - +
332H ARG* 1.3 62.7 + - - +
333H ASN 3.5 0.2 + - - -
334H PRO* 3.7 10.6 - - - +
337H GLN* 3.9 0.2 + - - -
473H VAL* 3.8 26.0 - - + +
474H GLU* 4.1 2.3 - - - -
475H THR* 3.5 31.7 + - - +
478H GLN* 4.3 5.2 + - - +
497H LEU* 4.0 14.1 - - + -
280L PHE* 5.9 2.1 - - - -
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Residues in contact with ARG 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H PHE* 3.1 45.0 + - + +
329H GLU* 2.9 42.0 + - - +
331H ALA* 1.3 77.0 - - - +
333H ASN* 1.3 67.2 + - - +
334H PRO* 3.2 9.4 - - - +
376H TYR* 3.6 8.5 + - - -
475H THR* 5.2 0.7 - - - +
477H THR 4.7 0.4 - - - +
478H GLN* 3.3 51.5 + - + +
479H GLU* 4.1 0.2 - - - +
480H ASP* 2.4 49.5 + - - +
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Residues in contact with ASN 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H GLU* 2.6 45.1 + - - +
330H LEU* 3.3 6.6 - - - +
331H ALA 3.3 0.2 - - - -
332H ARG* 1.3 85.9 - - - +
334H PRO* 1.3 60.7 - - - +
335H ASP* 3.2 5.6 - - + -
336H VAL* 3.0 22.0 + - + +
337H GLN 2.8 22.5 + - - -
423H TYR* 3.5 30.8 + - + +
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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) + - + + + + + -
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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