Contacts of the helix formed by residues 548 - 571 (chain B) in PDB entry 3RMD
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 548 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B TYR* 5.7 0.9 - - + +
489B MET* 4.6 3.5 + - - -
492B ALA* 4.6 2.2 - - + -
518B TYR* 3.1 39.2 - - + +
519B ARG* 3.2 37.7 - - + -
544B ARG* 3.4 16.0 + - - +
545B ALA 4.9 0.4 - - - -
546B GLN 3.0 0.2 - - - -
547B ARG* 1.3 76.7 - - - +
549B GLU* 1.3 64.8 + - - +
550B VAL 3.4 0.7 - - - -
551B ALA* 3.3 10.4 + - + +
552B GLY* 3.3 17.2 + - - -
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Residues in contact with GLU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET* 2.5 73.5 - - + +
492B ALA* 4.2 9.3 - - + +
493B GLN* 3.0 36.1 + - - +
546B GLN* 2.8 35.7 + - + +
548B THR* 1.3 80.0 - - - +
550B VAL* 1.3 69.0 + - + +
552B GLY 3.4 0.2 + - - -
553B MET* 3.3 8.1 + - - +
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 5.3 11.9 - - + +
546B GLN* 3.2 13.1 + - + +
547B ARG* 4.1 7.6 + - - +
549B GLU* 1.3 82.1 - - + +
551B ALA* 1.3 58.5 + - - +
552B GLY 3.2 1.1 - - - -
553B MET* 3.8 9.6 - - + -
554B THR* 3.2 33.4 + - - +
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Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 6.0 0.9 - - - -
485B HIS* 5.4 0.2 + - - -
544B ARG* 6.0 0.2 - - - +
547B ARG 3.9 13.0 + - - +
548B THR* 3.3 17.4 + - + +
549B GLU 3.2 0.6 - - - -
550B VAL* 1.3 80.0 - - - +
552B GLY* 1.3 57.9 + - - +
554B THR* 4.5 2.8 - - - -
555B ALA* 3.2 21.4 + - - +
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Residues in contact with GLY 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B HIS* 3.1 31.3 - - - +
488B TYR* 5.1 3.4 - - - -
489B MET* 3.7 12.3 - - - -
548B THR 3.3 8.7 + - - -
549B GLU 3.4 0.4 + - - -
550B VAL 3.2 0.4 - - - -
551B ALA* 1.3 79.4 - - - +
553B MET* 1.3 58.8 + - - +
555B ALA* 3.5 6.8 - - - +
556B GLN* 3.0 23.7 + - - +
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Residues in contact with MET 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET* 3.4 30.9 - - + +
549B GLU* 3.3 10.7 + - + +
550B VAL* 3.5 12.3 + - + +
551B ALA 3.4 0.2 - - - -
552B GLY* 1.3 74.4 - - - +
554B THR* 1.3 62.0 + - - +
555B ALA 3.0 1.3 - - - -
556B GLN* 2.9 26.1 - - - +
557B ILE* 2.8 48.5 + - + +
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Residues in contact with THR 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 5.4 5.9 + - - +
342B ASN* 3.7 28.2 + - - +
343B LEU* 4.0 19.7 + - + -
346B ASP* 3.5 27.8 - - + +
550B VAL* 3.2 23.8 + - - +
551B ALA* 4.7 3.6 - - - -
553B MET* 1.3 79.8 - - - +
555B ALA* 1.3 59.6 + - - +
557B ILE* 3.9 7.4 - - - +
558B ASN* 3.2 17.8 + - - +
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Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 3.9 11.6 + - - +
485B HIS* 3.4 35.2 - - + +
551B ALA 3.2 20.5 + - - +
552B GLY 3.5 4.9 - - - +
553B MET 3.0 0.2 - - - -
554B THR* 1.3 77.5 - - - +
556B GLN* 1.3 63.2 + - - +
558B ASN* 3.4 1.9 + - - +
559B ARG* 3.1 36.4 + - - +
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 3.9 31.2 + - + +
485B HIS* 4.1 4.9 - - + +
486B LYS* 3.0 42.9 - - + +
489B MET* 3.2 22.7 - - - +
552B GLY 3.0 10.4 + - - +
553B MET* 2.9 44.8 - - - +
555B ALA* 1.3 73.9 - - - +
557B ILE* 1.3 71.8 + - + +
559B ARG* 3.4 8.6 + - - +
560B LYS* 2.9 23.4 + - - +
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Residues in contact with ILE 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.8 23.8 - - + -
482B ARG* 6.3 0.2 - - - +
553B MET* 2.8 49.2 + - + +
554B THR* 3.9 6.7 - - - +
556B GLN* 1.3 81.7 - - + +
558B ASN* 1.3 57.5 + - - +
560B LYS* 3.3 20.7 - - + +
561B LEU* 2.9 39.3 + - + +
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Residues in contact with ASN 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.2 29.6 - - - +
346B ASP* 2.8 25.1 - - - +
347B MET* 3.1 50.0 + - + +
350B TYR* 5.9 1.6 - - + -
554B THR 3.2 10.0 + - - +
555B ALA 3.7 4.3 - - - +
556B GLN 3.2 0.4 - - - -
557B ILE* 1.3 77.7 - - - +
559B ARG* 1.3 71.8 + - - +
560B LYS 3.1 0.2 + - - -
561B LEU* 3.1 10.5 + - - +
562B LEU* 2.9 29.6 + - + +
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Residues in contact with ARG 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 4.5 8.1 + - - -
350B TYR* 3.2 40.1 - - - +
478B VAL* 2.7 46.7 - - + +
481B GLN* 2.5 38.6 + - - -
482B ARG* 3.5 23.6 - - + +
485B HIS* 3.4 28.6 + - - -
555B ALA* 3.1 27.5 + - - +
556B GLN 3.6 8.7 - - - +
558B ASN* 1.3 80.9 - - - +
560B LYS* 1.3 61.9 + - - +
562B LEU* 4.5 1.6 - - - -
563B ILE* 2.9 26.2 + - - +
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Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 4.4 20.9 - - - -
482B ARG* 3.0 37.4 - - - +
556B GLN 2.9 12.7 + - - +
557B ILE* 3.3 25.8 - - + +
559B ARG* 1.3 73.6 - - - +
561B LEU* 1.3 68.7 + - + +
562B LEU 2.7 13.5 + - - -
563B ILE* 2.7 19.7 + - - +
564B ASN* 3.0 27.4 + - - +
907B DTP 3.0 22.4 + - - +
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PHE* 4.0 21.8 - - + -
282B PHE* 3.9 31.4 - - + -
343B LEU* 3.7 38.6 - - + -
347B MET* 5.3 3.4 - - - -
557B ILE* 2.9 23.8 + - + +
558B ASN* 3.4 12.1 - - - +
560B LYS* 1.3 89.7 - - + +
562B LEU* 1.3 63.2 + - - +
564B ASN* 3.5 14.9 + - + +
565B SER* 3.5 14.4 + - - -
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B MET* 3.3 30.1 - - + -
350B TYR* 3.2 34.8 - - + -
364B THR* 3.6 10.5 - - + -
365B TRP* 3.4 22.9 + - + +
368B ILE* 3.6 17.9 - - + -
478B VAL* 3.9 21.1 - - + -
558B ASN 2.9 17.3 + - - +
559B ARG* 3.7 9.9 - - - +
560B LYS 2.7 3.8 + - - -
561B LEU* 1.3 65.9 - - - +
563B ILE* 1.3 57.8 + - - +
564B ASN 2.9 1.3 - - - -
565B SER* 2.7 35.2 + - - +
566B LEU 3.0 6.2 + - - -
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Residues in contact with ILE 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 4.6 1.8 - - - -
414B SER* 4.6 7.4 - - - -
417B PRO* 3.8 32.1 - - + +
475B ILE* 3.3 28.7 - - + -
478B VAL* 3.6 17.5 - - + +
479B PHE* 3.4 30.3 - - + -
482B ARG* 4.7 12.8 - - - +
559B ARG 2.9 24.0 - - - +
560B LYS* 2.7 13.5 + - - +
562B LEU* 1.3 76.4 - - - +
564B ASN* 1.3 67.3 + - - +
565B SER 3.3 4.2 + - - -
566B LEU* 3.7 9.6 + - - +
567B TYR* 4.7 2.8 + - - +
907B DTP 5.2 1.3 - - - +
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Residues in contact with ASN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B SER* 5.6 0.5 - - - -
417B PRO* 5.8 0.2 - - - +
482B ARG* 5.0 0.6 - - - +
560B LYS* 3.0 45.9 + - - +
561B LEU* 3.6 12.9 - - + +
562B LEU 2.8 2.0 + - - -
563B ILE* 1.3 89.0 - - - +
565B SER* 1.3 58.5 + - - +
567B TYR* 5.4 1.3 - - - -
907B DTP 3.7 46.9 + - + +
2G G 3.3 17.8 + - - -
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Residues in contact with SER 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PRO* 3.8 29.9 - - - +
365B TRP* 3.5 10.7 + - - -
561B LEU 3.5 10.2 + - - -
562B LEU* 2.7 19.4 + - - +
563B ILE 3.3 0.2 + - - -
564B ASN* 1.3 75.1 - - - +
566B LEU* 1.3 71.0 + - - +
567B TYR 3.2 2.2 - - - +
568B GLY* 3.1 4.0 + - - +
569B ALA* 3.1 21.1 + - - +
2G G 3.9 17.7 - - - +
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 3.4 55.9 - - + +
369B ILE* 5.4 1.1 - - + -
417B PRO* 5.8 3.4 - - + -
420B ILE* 4.5 8.5 - - + -
471B VAL* 4.3 20.4 - - + +
475B ILE* 3.8 33.7 - - + -
562B LEU 3.0 4.4 + - - -
563B ILE* 3.7 10.5 + - - +
565B SER* 1.3 79.9 - - - +
567B TYR* 1.3 58.7 + - - +
569B ALA* 3.0 3.9 + - + +
570B LEU* 2.7 46.0 + - + +
575B PHE* 4.8 7.9 - - + -
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Residues in contact with TYR 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B TYR* 2.4 46.8 + + - -
416B TYR* 4.2 35.7 - + + -
417B PRO* 6.0 3.5 - - + +
420B ILE* 5.7 2.2 - - + +
563B ILE 4.7 3.1 + - - +
564B ASN 6.2 0.7 - - - -
565B SER 3.2 1.4 - - - +
566B LEU* 1.3 80.1 - - - +
568B GLY* 1.3 54.3 + - - +
570B LEU* 2.8 15.8 + - + +
571B GLY* 2.7 36.3 + - - -
583B ALA* 4.7 6.1 - - - -
586B ILE* 4.5 30.7 - - + -
587B THR* 3.3 17.3 - - + +
907B DTP 4.9 8.3 - + + -
3G T 3.2 29.4 - - - -
4G CTG 5.3 3.4 + - - -
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Residues in contact with GLY 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B SER* 3.1 9.8 + - - +
567B TYR* 1.3 80.0 - - - +
569B ALA* 1.3 60.2 + - - +
572B ASN* 3.3 18.5 + - - +
2G G 3.6 24.4 - - - +
3G T 3.5 37.5 + - - +
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Residues in contact with ALA 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PRO* 4.2 4.9 - - + +
362B ILE* 3.5 41.3 - - + +
365B TRP* 4.9 2.5 - - + -
565B SER 3.1 9.1 + - - +
566B LEU* 3.0 10.8 + - - +
568B GLY* 1.3 72.8 - - - +
570B LEU* 1.3 58.4 + - - +
572B ASN* 2.7 27.7 + - - +
575B PHE* 3.3 27.2 - - + +
2G G 4.3 2.3 + - - -
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 3.5 32.1 - - + -
427B PRO* 6.0 0.9 - - + -
471B VAL* 4.0 21.1 - - + -
566B LEU* 2.7 32.3 + - + +
567B TYR* 2.8 19.7 + - + +
569B ALA* 1.3 73.7 - - - +
571B GLY* 1.3 54.0 - - - +
572B ASN 3.2 0.4 - - - -
575B PHE* 3.8 21.7 - - + -
577B TYR 4.3 14.8 - - - +
578B TYR* 3.4 21.5 - - - -
579B ASP 4.6 2.0 + - - +
582B ASN* 6.1 4.5 - - + -
583B ALA* 4.5 8.7 - - + +
586B ILE* 4.2 13.5 - - + -
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Residues in contact with GLY 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B TYR* 3.5 32.4 - - - -
567B TYR* 2.7 18.3 + - - -
568B GLY 3.8 4.5 - - - -
570B LEU* 1.3 72.5 - - - +
572B ASN* 1.3 58.7 + - - +
573B VAL 3.8 0.9 + - - -
578B TYR* 3.5 16.2 - - - -
583B ALA* 4.6 4.9 - - - -
3G T 3.6 16.1 - - - +
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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