Contacts of the helix formed by residues 455 - 474 (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 GLY 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 6.3 0.7 - - - -
453B CYS* 3.3 8.2 - - - -
454B LEU* 1.3 77.2 - - - +
456B GLU* 1.3 55.8 + - - +
457B ALA* 3.2 2.7 - - - -
458B LEU* 2.6 33.3 + - - +
459B ALA* 2.8 15.8 + - - +
600B HEM 3.6 33.4 - - - -
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Residues in contact with GLU 456 (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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446B PHE* 3.7 50.9 - - + +
452B VAL* 3.9 15.2 - - - +
453B CYS* 3.6 13.9 - - - +
454B LEU 3.4 2.4 - - - -
455B GLY* 1.3 75.3 - - - +
457B ALA* 1.3 66.4 + - - +
459B ALA* 3.3 1.0 + - - +
460B LYS* 3.1 56.1 + - + +
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 5.9 5.2 - - + -
145B LEU* 4.2 18.8 - - + -
358B ARG* 5.5 0.5 + - - -
454B LEU 5.0 3.1 + - - +
455B GLY 4.8 1.1 - - - -
456B GLU* 1.3 83.5 - - - +
458B LEU* 1.3 60.4 + - - +
460B LYS* 3.5 6.3 + - - +
461B MET* 3.4 30.0 + - + +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.1 28.7 - - + -
155B ILE* 4.4 11.0 - - + -
159B ILE* 4.3 10.1 - - + -
191B VAL* 4.1 14.8 - - + -
192B VAL* 5.3 9.4 - - + -
195B LEU* 4.8 13.7 - - + -
310B ILE* 5.8 1.6 - - + -
455B GLY* 2.6 16.0 + - - +
457B ALA* 1.3 73.7 - - - +
459B ALA* 1.3 63.1 + - - +
461B MET* 3.3 11.1 + - + +
462B GLU* 3.0 47.7 + - + +
600B HEM 5.0 19.3 - - + -
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Residues in contact with ALA 459 (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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318B THR* 4.7 2.7 - - + +
446B PHE* 4.1 12.6 - - + -
455B GLY 2.8 13.0 + - - +
456B GLU 3.8 3.8 - - - +
458B LEU* 1.3 76.6 - - - +
460B LYS* 1.3 58.2 + - - +
462B GLU* 3.3 10.1 + - - +
463B LEU* 2.8 38.0 + - + +
600B HEM 3.7 42.3 - - + +
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Residues in contact with LYS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 3.9 25.6 + - - +
365B GLU* 4.8 15.0 + - - +
368B ILE* 5.5 5.1 - - + +
369B ARG* 4.5 17.4 - - - +
372B LEU* 5.9 2.2 - - + -
446B PHE* 3.7 25.1 - - + -
456B GLU* 3.1 43.4 + - + +
457B ALA* 3.8 5.4 - - - +
459B ALA* 1.3 75.2 - - - +
461B MET* 1.3 63.9 + - - +
463B LEU* 4.4 7.4 - - + +
464B PHE* 3.2 25.3 + - - +
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Residues in contact with MET 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 5.2 10.3 - - + -
155B ILE* 4.9 22.9 - - + -
156B GLU 5.5 0.2 - - - -
159B ILE* 3.8 19.3 - - + -
355B LEU* 3.7 38.4 - - + -
358B ARG* 4.7 8.7 - - - +
457B ALA* 3.4 26.4 + - + +
458B LEU* 3.3 15.0 + - - +
459B ALA 3.2 0.6 - - - -
460B LYS* 1.3 76.4 - - - +
462B GLU* 1.3 70.8 + - - +
464B PHE* 3.9 0.3 - - - +
465B LEU* 3.1 25.6 + - - +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.9 16.2 - - + -
188B VAL* 3.3 37.0 - - - +
191B VAL* 3.8 19.1 - - + +
192B VAL* 5.5 2.6 - - - +
314B GLY* 4.8 2.4 - - - +
318B THR* 3.5 28.6 + - + +
458B LEU* 3.0 43.1 + - + +
459B ALA 3.7 3.4 - - - +
461B MET* 1.3 82.5 - - - +
463B LEU* 1.3 65.0 + - - +
465B LEU* 3.8 0.7 - - - +
466B PHE* 3.0 38.2 + - + -
600B HEM 4.6 3.5 - - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR* 4.3 11.7 - - + +
321B VAL* 3.5 38.6 - - + -
322B LEU* 3.6 35.2 - - + +
325B SER* 5.0 2.0 - - - +
368B ILE* 3.9 29.6 - - + -
372B LEU* 4.5 10.8 - - + -
446B PHE* 5.7 2.0 - - + -
459B ALA* 2.8 27.7 + - + +
460B LYS* 4.4 5.8 - - + +
462B GLU* 1.3 74.9 - - - +
464B PHE* 1.3 65.0 + - - +
466B PHE* 4.2 0.3 - - - +
467B LEU* 3.3 28.5 + - + +
600B HEM 5.0 4.9 - - + -
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PRO* 5.2 2.7 - - + -
354B GLN 4.2 18.6 - - - -
355B LEU* 4.3 2.5 - - + -
357B ASP* 4.2 3.1 - - + -
358B ARG* 3.5 52.9 - - + +
361B LEU* 3.9 29.8 - - + -
364B LEU* 3.6 32.9 - - + +
365B GLU* 4.4 12.6 - - - +
368B ILE* 3.7 12.3 - - + +
460B LYS 3.2 20.4 + - - +
461B MET 3.9 1.3 - - - +
463B LEU* 1.3 80.9 - - - +
465B LEU* 1.3 71.2 + - + +
467B LEU* 3.8 1.6 - - - +
468B ALA* 2.8 38.1 + - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 4.4 11.7 - - + -
159B ILE* 3.3 42.2 - - + -
160B CYS* 4.1 13.0 - - - -
163B ALA* 5.1 0.9 - - + -
353B PRO* 3.9 24.2 - - + +
354B GLN* 4.1 2.2 - - - -
355B LEU* 3.4 44.9 - - + +
461B MET 3.1 10.3 + - - +
464B PHE* 1.3 83.9 - - + +
466B PHE* 1.3 55.6 + - - +
468B ALA* 3.1 2.5 + - - +
469B TRP* 2.7 47.2 + - + +
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Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.3 14.1 - - + -
162B GLU* 4.0 11.0 - - + -
163B ALA* 3.7 33.4 - - + -
166B MET* 5.2 4.7 - - + -
184B LEU* 5.3 5.2 - - + -
187B ALA* 3.8 34.3 - - + -
188B VAL* 4.6 8.7 - - + -
191B VAL* 4.5 3.4 - - + -
322B LEU* 4.2 28.5 - - + -
462B GLU* 3.0 49.7 + - + +
463B LEU 4.2 2.5 - - - +
465B LEU* 1.3 76.5 - - - +
467B LEU* 1.3 62.2 + - - +
469B TRP* 3.6 3.7 + - - +
470B ILE* 3.1 43.2 + - + +
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Residues in contact with LEU 467 (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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322B LEU* 4.3 15.7 - - + -
325B SER* 4.2 31.9 - - - +
326B ILE* 4.8 10.5 - - + -
329B LEU* 4.3 19.3 - - + -
343B LEU* 4.9 0.2 - - - +
364B LEU* 4.3 15.7 - - + -
367B THR* 6.0 3.8 - - + -
368B ILE* 3.9 24.2 - - + -
463B LEU* 3.3 20.6 + - + +
464B PHE 4.0 1.6 - - - +
465B LEU 3.3 0.2 - - - -
466B PHE* 1.3 74.5 - - - +
468B ALA* 1.3 65.5 + - - +
470B ILE* 4.5 8.1 - - + -
471B LEU* 3.0 37.0 + - + +
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Residues in contact with ALA 468 (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* 3.7 14.4 - - + +
353B PRO* 3.7 26.8 - - + +
364B LEU* 4.0 19.4 - - + +
464B PHE* 2.8 26.9 + - + +
465B LEU* 3.4 5.6 - - - +
467B LEU* 1.3 77.1 - - - +
469B TRP* 1.3 64.4 + - - +
472B GLN* 3.1 24.8 + - - +
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Residues in contact with TRP 469 (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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160B CYS* 3.6 37.3 - - + -
163B ALA* 3.5 19.3 - - + -
164B SER* 3.5 41.5 - - - -
167B CYS* 4.0 6.2 - - - -
352B HIS* 3.4 36.1 - + + -
353B PRO* 3.2 35.4 + - + +
465B LEU* 2.7 37.3 + - + +
466B PHE 3.9 2.2 - - - +
468B ALA* 1.3 73.9 - - - +
470B ILE* 1.3 63.3 + - + +
472B GLN* 3.5 8.0 - - - +
473B ARG* 3.2 53.3 + - - +
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Residues in contact with ILE 470 (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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163B ALA* 5.7 0.9 - - + +
166B MET* 5.0 9.9 - - + -
167B CYS* 4.6 12.3 - - - -
170B LEU* 4.7 19.3 - - + -
180B LEU* 6.2 2.2 - - + -
184B LEU* 4.9 14.8 - - + -
322B LEU* 6.3 0.7 - - + -
326B ILE* 5.6 9.0 - - + -
466B PHE* 3.1 35.2 + - + +
467B LEU* 4.0 10.3 - - + +
468B ALA 3.2 0.2 - - - -
469B TRP* 1.3 75.1 - - + +
471B LEU* 1.3 70.5 + - + +
472B GLN 2.9 6.4 + - - -
473B ARG 3.1 2.9 + - - -
474B PHE* 2.8 45.8 + - + +
476B LEU* 4.6 18.2 - - + -
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Residues in contact with LEU 471 (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 LEU* 4.1 27.1 - - + -
336B GLN* 3.7 31.9 - - + +
339B ILE* 3.5 51.4 - - + -
340B GLN* 3.1 30.1 - - + +
343B LEU* 4.1 3.3 - - + +
467B LEU* 3.0 26.6 + - + +
470B ILE* 1.3 84.2 - - + +
472B GLN* 1.3 60.5 + - - +
474B PHE 3.4 11.5 - - - +
476B LEU* 4.9 5.8 - - + -
507B ARG* 3.2 1.4 + - - -
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Residues in contact with GLN 472 (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* 3.9 17.0 - - + +
344B ASP* 5.0 4.4 - - - +
347B ILE* 4.1 7.1 - - - +
348B GLY 3.7 19.4 + - - +
349B LYS* 5.1 2.6 - - - +
351B ARG 2.9 25.6 + - - -
352B HIS* 3.4 20.9 + - - -
353B PRO* 3.5 21.4 - - + +
468B ALA 3.1 19.5 + - - +
469B TRP 3.5 3.5 - - - +
470B ILE 2.9 1.2 + - - -
471B LEU* 1.3 77.2 - - - +
473B ARG* 1.3 71.7 + - + +
507B ARG* 2.8 26.3 + - - +
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Residues in contact with ARG 473 (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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164B SER* 5.3 2.2 + - - +
167B CYS* 3.2 34.1 - - - +
171B THR* 5.4 2.7 - - - -
352B HIS* 2.9 39.6 + - + -
469B TRP* 3.2 34.6 + - - -
470B ILE 3.1 2.2 + - - +
472B GLN* 1.3 92.3 + - + +
474B PHE* 1.3 88.3 + - + +
506B VAL* 3.5 10.3 - - + +
507B ARG* 3.0 32.0 + - - +
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Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B CYS* 3.2 44.0 - - + -
170B LEU* 3.5 30.3 - - + -
171B THR* 3.6 9.6 - - - -
174B GLN* 3.9 9.2 - - - -
340B GLN* 2.7 25.3 - - - +
470B ILE* 2.8 26.7 + - + +
471B LEU* 3.4 12.0 - - - +
473B ARG* 1.3 96.7 - - + +
475B THR* 1.3 58.9 + - - +
476B LEU* 4.2 15.7 - - + -
504B ALA* 4.4 6.1 - - + -
505B LYS 4.1 4.9 - - - -
506B VAL* 3.4 37.7 - - + -
507B ARG* 3.7 0.8 - - - -
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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