Contacts of the helix formed by residues 317 - 332 (chain B) in PDB entry 4R1Z
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 THR 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA* 2.8 20.9 + - - +
316B GLU* 1.3 76.6 - - - +
318B THR* 1.3 75.5 + - - +
319B THR 3.2 1.1 - - - -
320B THR* 2.9 15.8 + - - -
321B VAL* 3.0 15.1 + - - +
377B VAL* 4.1 11.2 - - + +
494B VAL* 4.2 3.6 - - + -
600B HEM 3.0 38.9 - - + +
601B AER 3.4 46.9 - - + +
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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
----------------------------------------------------------
188B VAL* 3.6 19.7 - - + -
313B ALA 4.3 0.4 + - - -
314B GLY 3.7 3.8 + - - -
315B VAL 4.1 1.0 + - - -
317B THR* 1.3 81.4 + - - +
319B THR* 1.3 65.1 + - - +
321B VAL* 3.3 3.2 + - - +
322B LEU* 3.0 25.0 + - + +
459B ALA* 4.7 4.1 - - - +
462B GLU* 3.5 40.8 + - + +
463B LEU* 4.3 16.2 - - + -
600B HEM 3.2 35.3 - - + +
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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
----------------------------------------------------------
184B LEU* 3.9 12.1 - - + +
185B THR* 3.4 48.7 + - + +
188B VAL* 3.5 20.7 - - + +
315B VAL* 2.5 26.1 + - - +
316B GLU* 5.0 0.7 - - - -
317B THR 3.2 0.8 - - - -
318B THR* 1.3 80.7 - - - +
320B THR* 1.3 60.9 + - - +
322B LEU* 3.2 3.2 + - - +
323B LYS* 2.9 36.1 + - - +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU 2.5 24.9 + - - -
317B THR 2.9 7.7 + - - -
319B THR* 1.3 77.1 - - - +
321B VAL* 1.3 65.0 + - - +
323B LYS* 3.2 11.8 + - - +
324B TRP* 3.1 31.0 + - + +
377B VAL* 4.5 7.0 - - + -
494B VAL* 3.4 13.3 - - + +
495B LEU 3.1 28.9 - - - +
496B GLN* 3.4 25.1 + - + +
497B PRO* 4.2 1.1 - - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B THR 3.0 4.6 + - - +
318B THR 3.7 5.6 - - - +
320B THR* 1.3 76.2 - - - +
322B LEU* 1.3 57.6 + - - +
324B TRP* 3.2 10.9 + - - +
325B SER* 2.7 36.3 + - - +
368B ILE 5.7 0.4 - - - +
371B VAL* 4.1 11.2 - - + -
372B LEU* 3.7 17.9 - - + -
375B ARG 5.8 0.4 - - - +
377B VAL* 3.4 26.5 - - + -
463B LEU* 3.5 30.1 - - + -
600B HEM 3.6 28.3 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.0 28.5 - - + -
188B VAL* 3.7 30.3 - - + -
318B THR* 3.0 17.0 + - + +
319B THR* 3.4 7.9 - - - +
321B VAL* 1.3 76.7 - - - +
323B LYS* 1.3 58.5 + - - +
325B SER* 2.9 22.4 + - - -
326B ILE* 2.9 18.4 + - + +
463B LEU* 3.6 20.6 - - + -
466B PHE* 4.2 32.8 - - + -
467B LEU* 4.3 21.5 - - + -
470B ILE* 6.3 0.7 - - + -
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 5.9 0.2 - - - +
181B GLY* 4.2 18.4 - - - +
184B LEU* 4.2 13.9 - - + -
185B THR* 3.9 18.0 - - - +
319B THR* 2.9 40.6 + - - +
320B THR* 3.2 8.9 + - - +
322B LEU* 1.3 76.4 - - - +
324B TRP* 1.3 62.0 + - - +
326B ILE* 3.3 12.1 + - + +
327B ALA* 3.0 20.8 + - - +
496B GLN* 5.5 6.6 + - - +
497B PRO* 4.2 21.8 - - + +
499B LYS* 6.4 0.2 - - - +
500B PHE* 3.7 13.2 - - + -
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Residues in contact with TRP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B THR* 3.1 31.6 + - + -
321B VAL* 3.4 11.0 - - - +
323B LYS* 1.3 73.6 - - - +
325B SER* 1.3 61.1 + - - +
327B ALA* 3.1 7.8 + - + +
328B TYR* 2.8 49.2 + + + -
371B VAL* 3.8 14.6 - - + -
375B ARG* 3.5 50.2 + - + +
377B VAL* 5.3 1.3 - - + -
486B ASP 4.8 0.2 - - - -
487B LEU* 3.2 39.7 - - + -
489B GLY* 3.9 10.5 - - - -
495B LEU* 3.0 25.7 + - + +
496B GLN 3.7 4.5 - - - -
497B PRO* 3.5 44.6 - - + +
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 2.7 28.3 + - - +
322B LEU* 2.9 10.6 + - - +
324B TRP* 1.3 72.0 - - - +
326B ILE* 1.3 68.6 + - - +
328B TYR* 3.3 1.6 + - - +
329B LEU* 2.9 31.2 + - - +
368B ILE* 5.9 0.5 - - - +
371B VAL* 3.9 26.4 - - - +
463B LEU* 5.0 0.5 - - - +
467B LEU* 4.2 31.3 - - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 5.0 11.7 - - + -
184B LEU* 4.2 22.4 - - + -
322B LEU* 2.9 20.6 + - + +
323B LYS* 3.5 8.7 - - - +
325B SER* 1.3 74.6 - - - +
327B ALA* 1.3 64.2 + - - +
329B LEU* 2.9 19.6 + - + +
330B VAL* 3.0 15.5 + - + +
467B LEU* 4.8 14.4 - - + -
470B ILE* 5.6 10.1 - - + -
476B LEU* 3.9 32.1 - - + -
500B PHE* 3.6 24.7 - - + -
502B VAL* 4.3 13.5 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LYS 3.0 10.4 + - - +
324B TRP* 3.1 19.7 + - + +
326B ILE* 1.3 80.6 - - - +
328B TYR* 1.3 63.8 + - - +
330B VAL* 3.4 3.7 + - - +
331B HIS* 3.2 29.7 + - - -
485B PRO* 5.0 7.9 - - + -
486B ASP 6.0 0.7 - - - +
487B LEU* 4.3 17.3 - - + -
497B PRO* 5.5 2.9 - - + -
500B PHE* 3.6 22.6 - - + -
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Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TRP* 2.8 43.1 + + + +
325B SER 4.0 3.1 - - - +
327B ALA* 1.3 75.5 - - + +
329B LEU* 1.3 61.7 + - + +
331B HIS* 3.9 4.0 - - + -
332B ASN* 3.0 35.0 + - - +
371B VAL* 4.7 6.5 - - + -
374B ILE* 3.6 19.5 - - + +
375B ARG* 3.2 55.2 + - + -
421B GLU* 4.7 2.7 + - - -
423B PHE* 3.4 57.2 - + + -
487B LEU* 3.4 28.1 - - + +
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Residues in contact with LEU 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 SER* 2.9 27.4 + - - +
326B ILE* 3.2 15.7 - - + +
328B TYR* 1.3 76.2 - - + +
330B VAL* 1.3 62.3 + - + +
332B ASN* 2.8 20.4 - - - +
333B PRO 3.7 0.2 - - - -
335B VAL* 4.0 26.2 - - + -
336B GLN* 2.8 39.9 + - + +
339B ILE* 4.3 10.3 - - + -
367B THR* 4.8 7.9 - - + -
423B PHE* 6.1 2.2 - - + -
467B LEU* 4.3 18.2 - - + -
471B LEU* 4.1 26.9 - - + -
476B LEU* 5.2 4.7 - - + -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 3.0 23.1 + - + +
327B ALA* 3.7 8.7 - - - +
329B LEU* 1.3 77.5 - - - +
331B HIS* 1.3 62.5 + - - +
332B ASN 3.3 0.3 + - - -
333B PRO* 4.1 12.1 - - - +
336B GLN* 4.2 3.6 - - - +
476B LEU* 3.8 32.9 - - + +
477B GLU 4.8 1.3 - - - +
478B MET* 3.3 44.0 - - + +
484B LEU* 3.8 11.7 - - + +
485B PRO* 3.9 18.2 - - + -
500B PHE* 4.8 1.1 - - + -
502B VAL* 4.7 3.4 - - + -
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Residues in contact with HIS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA 3.2 22.2 + - - +
328B TYR* 3.8 4.9 - - + +
330B VAL* 1.3 78.6 - - - +
332B ASN* 1.3 74.5 + - - +
333B PRO* 3.4 8.4 - - - +
334B GLN* 4.7 0.3 - - - +
484B LEU* 3.7 31.0 - - + +
485B PRO* 3.1 41.3 + - + -
487B LEU* 3.5 31.9 - - + +
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Residues in contact with ASN 332 (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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328B TYR* 3.0 24.0 + - - +
329B LEU 2.8 14.5 + - - +
331B HIS* 1.3 94.0 + - - +
333B PRO* 1.3 66.4 - - - +
334B GLN* 2.9 29.3 + - - +
335B VAL* 3.4 19.5 + - + +
336B GLN 3.5 7.1 + - - -
423B PHE* 4.1 32.0 - - + +
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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) + - + + + + + -
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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