Contacts of the helix formed by residues 550 - 571 (chain D) in PDB entry 5MG3
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 PHE 550 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D ILE* 4.0 17.9 - - + -
545D GLY 3.4 23.3 - - - -
546D TYR* 3.8 26.4 + + - +
547D ARG 5.3 0.2 + - - -
548D GLY* 3.3 0.8 - - - -
549D ALA* 1.3 80.8 - - + +
551D SER* 1.3 63.8 + - - +
552D SER 3.5 2.9 - - - -
553D ILE* 3.3 15.0 + - + +
554D PHE* 3.0 43.4 + - + -
593D ALA 4.3 0.2 - - - -
594D ILE* 3.6 33.7 - - + -
597D THR* 3.6 23.8 - - - -
598D ARG* 3.8 26.2 - - + -
601D VAL* 4.1 9.4 - - + -
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Residues in contact with SER 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D ARG* 5.5 1.2 + - - -
547D ARG 5.6 2.8 + - - -
548D GLY* 3.6 19.2 + - - -
549D ALA 3.6 0.8 - - - -
550D PHE* 1.3 78.6 - - - +
552D SER* 1.4 57.3 + - - +
554D PHE* 3.6 9.7 - - - +
555D ASP* 3.1 31.6 + - - +
164F ARG* 4.1 11.8 + - - -
219F ASP* 2.6 28.1 + - - -
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Residues in contact with SER 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D LEU* 3.4 14.5 - - - +
549D ALA 5.2 1.2 + - - -
550D PHE 3.5 0.4 - - - -
551D SER* 1.4 73.2 + - - +
553D ILE* 1.4 61.4 + - - +
554D PHE 3.4 0.2 - - - -
555D ASP* 3.9 9.8 - - - +
556D ALA* 3.0 31.5 + - - +
212F ASN 5.4 0.2 - - - -
215F ILE* 4.3 10.1 - - - +
216F VAL* 3.5 35.8 - - - +
219F ASP* 3.7 13.3 + - - +
247F ARG* 4.4 7.8 + - - -
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Residues in contact with ILE 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520D ALA* 3.9 22.0 - - + +
523D LEU* 3.9 15.7 - - + -
524D ILE* 3.7 29.2 - - + +
549D ALA 3.2 27.1 - - - +
550D PHE* 3.3 17.4 + - + +
552D SER* 1.4 75.7 - - - +
554D PHE* 1.4 60.7 + - - +
556D ALA* 4.0 0.3 - - - +
557D ASN* 2.8 38.9 + - - +
590D MET* 5.2 1.8 - - + +
593D ALA* 4.3 21.5 - - + -
594D ILE* 3.9 23.8 - - + +
597D THR* 5.6 1.3 - - - +
247F ARG* 5.7 0.9 - - - +
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Residues in contact with PHE 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D PHE* 3.0 37.1 + - + -
551D SER* 3.6 10.5 - - - +
553D ILE* 1.4 71.6 - - - +
555D ASP* 1.3 60.9 + - - +
557D ASN* 3.3 6.1 + - - +
558D ILE* 2.9 45.1 + - + +
590D MET* 4.4 22.0 - - + -
591D PHE* 6.1 2.9 - + - -
594D ILE* 3.4 45.5 - - + -
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Residues in contact with ASP 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D SER 3.1 17.2 + - - +
552D SER* 3.9 1.5 - - - +
554D PHE* 1.3 76.5 - - - +
556D ALA* 1.3 57.3 + - - +
558D ILE* 4.0 3.4 - - - +
559D THR* 2.9 36.5 + - - -
160F TYR* 2.9 21.4 + - + +
164F ARG* 2.6 47.5 + - - -
165F PHE* 3.7 11.8 - - + -
215F ILE* 3.8 25.7 - - + +
219F ASP* 4.4 1.6 - - - +
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Residues in contact with ALA 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D VAL* 4.7 6.7 - - + -
520D ALA* 6.5 0.4 - - + -
523D LEU* 4.2 14.1 - - + -
552D SER 3.0 19.0 + - - +
553D ILE 4.0 3.6 - - - +
555D ASP* 1.3 76.5 - - - +
557D ASN* 1.3 55.1 + - - +
559D THR* 3.3 6.0 + - - -
560D THR* 2.8 43.2 + - - +
208F GLY 5.6 2.2 - - - +
209F TYR* 6.1 3.6 - - + -
212F ASN* 4.9 14.1 - - + +
215F ILE* 4.8 6.1 - - + +
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Residues in contact with ASN 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D VAL* 3.2 35.8 - - - +
520D ALA* 4.5 10.5 - - - +
553D ILE* 2.8 33.7 + - - +
554D PHE 3.3 3.6 + - - +
556D ALA* 1.3 78.3 - - - +
558D ILE* 1.4 58.6 + - - +
560D THR* 3.4 4.8 + - - -
561D LEU* 2.9 29.1 + - - +
586D VAL* 3.6 14.9 - - + +
589D SER* 4.0 3.5 + - - -
590D MET* 3.9 45.2 + - + +
593D ALA* 5.6 1.0 - - - +
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Residues in contact with ILE 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D PHE* 2.9 39.2 + - + +
555D ASP* 4.0 4.0 - - - +
557D ASN* 1.4 68.2 - - - +
559D THR* 1.4 56.9 + - - +
561D LEU* 3.2 12.4 + - + +
562D ILE* 2.9 41.3 + - + +
590D MET* 4.9 14.1 - - + -
160F TYR* 3.5 40.6 - - + +
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Residues in contact with THR 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555D ASP 2.9 26.6 + - - -
556D ALA* 3.5 7.0 - - - +
558D ILE* 1.4 71.1 - - - +
560D THR* 1.3 62.6 + - - +
562D ILE* 3.8 12.5 - - - +
563D LYS* 3.3 21.2 + - - +
157F ILE* 3.6 31.9 - - + +
160F TYR* 3.7 21.3 - - - -
161F VAL* 5.6 0.5 - - - +
207F ILE 4.9 2.5 - - - +
208F GLY* 4.8 11.0 - - - -
211F LEU* 4.0 15.7 - - + -
215F ILE* 4.1 10.9 - - + +
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Residues in contact with THR 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D LEU* 4.2 9.2 - - + +
516D VAL* 4.2 11.0 - - + +
556D ALA 2.8 25.2 + - - -
557D ASN* 3.7 6.7 - - - -
558D ILE 3.2 0.2 - - - -
559D THR* 1.3 78.8 - - - +
561D LEU* 1.4 58.0 + - - +
563D LYS* 3.1 33.5 - - - +
564D VAL* 3.4 14.3 + - + +
582D THR* 4.9 3.6 - - + -
586D VAL* 4.0 18.2 - - + -
208F GLY* 5.7 2.1 - - - -
209F TYR* 2.9 32.6 + - - +
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Residues in contact with LEU 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D ASN 2.9 20.3 + - - +
558D ILE* 3.5 13.2 - - + +
560D THR* 1.4 67.6 - - - +
562D ILE* 1.3 66.1 + - + +
564D VAL* 3.0 3.0 + - - -
565D ILE* 2.9 58.4 + - + +
583D GLY* 4.9 4.7 - - - +
586D VAL* 3.7 29.1 - - + +
587D ALA* 4.9 7.2 - - + +
590D MET* 4.9 18.4 - - + -
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Residues in contact with ILE 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D ILE* 2.9 32.1 + - + +
559D THR* 3.8 10.5 - - - +
561D LEU* 1.3 79.4 - - + +
563D LYS* 1.4 65.1 + - - +
565D ILE* 3.9 9.1 - - + +
566D ILE* 3.1 29.2 + - + +
156F SER* 3.8 39.7 - - - +
157F ILE* 4.4 6.3 - - + +
160F TYR* 3.8 28.3 - - + -
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Residues in contact with LYS 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D LEU* 4.1 8.9 - - - +
559D THR* 3.3 11.7 - - - +
560D THR* 3.1 38.6 - - - +
562D ILE* 1.4 81.2 - - - +
564D VAL* 1.4 59.3 + - + +
566D ILE* 3.8 0.7 - - - +
567D LEU* 2.9 42.6 + - + +
153F ALA* 3.8 24.9 - - + +
156F SER* 5.8 0.2 - - - -
157F ILE* 4.3 16.4 - - + -
204F MET* 2.7 19.7 + - - +
205F SER* 2.7 31.3 + - - +
207F ILE* 3.0 23.9 + - + +
208F GLY* 5.7 0.2 - - - -
209F TYR* 3.9 9.2 - - - -
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Residues in contact with VAL 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D LEU* 4.1 15.5 - - + -
560D THR* 3.4 15.6 + - + +
561D LEU* 3.0 9.9 + - - +
563D LYS* 1.4 81.9 - - + +
565D ILE* 1.3 63.5 - - + +
567D LEU* 3.7 9.1 - - + +
568D TYR* 3.0 28.2 + - + +
578D PHE* 5.6 0.9 - - + -
579D ALA* 3.4 37.4 - - + +
582D THR* 3.9 21.8 - - + -
583D GLY* 4.0 17.0 - - - +
586D VAL* 5.1 2.5 - - + -
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Residues in contact with ILE 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 2.9 48.6 + - + +
562D ILE* 3.9 11.2 - - + +
564D VAL* 1.3 82.6 - - + +
566D ILE* 1.3 67.3 + - + +
568D TYR* 3.4 16.1 + - - +
569D ALA* 3.4 13.5 + - - +
583D GLY* 5.8 3.1 - - - -
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Residues in contact with ILE 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D ILE* 3.1 21.5 + - + +
563D LYS 3.8 3.4 - - - +
565D ILE* 1.3 78.3 - - + +
567D LEU* 1.3 62.3 + - - +
569D ALA* 3.4 6.5 + - + +
570D VAL* 3.3 30.3 + - + +
149F ALA 4.6 2.5 - - - +
152F ALA* 3.5 33.2 - - + +
153F ALA* 3.6 13.7 - - + +
156F SER* 3.9 24.9 - - - +
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Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D LYS* 2.9 38.1 + - + +
564D VAL* 3.7 10.8 - - + +
566D ILE* 1.3 72.1 - - - +
568D TYR* 1.4 63.6 + - - +
571D GLY* 3.0 21.7 + - - +
575D ILE* 3.4 36.9 - - + +
576D LYS 5.4 0.2 + - - -
578D PHE* 4.0 20.0 - - + -
579D ALA* 4.7 3.6 - - + -
149F ALA* 3.5 31.9 - - + +
150F LEU* 4.6 0.4 - - - +
153F ALA* 4.0 6.7 - - + -
200F VAL* 5.2 2.2 - - + +
201F ALA* 6.3 0.2 - - - -
204F MET* 3.8 31.4 - - + +
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Residues in contact with TYR 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D VAL* 3.0 19.5 + - + +
565D ILE* 3.4 7.6 + - - +
567D LEU* 1.4 75.0 - - - +
569D ALA* 1.3 61.8 + - + +
570D VAL 3.6 0.2 + - - -
571D GLY 4.4 0.2 - - - +
575D ILE* 5.1 1.8 - - - -
576D LYS* 2.8 65.1 + - + +
579D ALA* 3.9 15.4 - - + +
580D ILE* 3.6 31.1 - - + +
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Residues in contact with ALA 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE 3.4 9.8 + - - +
566D ILE* 3.8 9.9 - - + +
567D LEU 3.3 0.8 - - - -
568D TYR* 1.3 86.9 - - + +
570D VAL* 1.3 64.8 + - + +
576D LYS* 4.2 6.2 + - - -
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Residues in contact with VAL 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D ILE* 3.3 24.8 + - + +
569D ALA* 1.3 82.0 - - + +
571D GLY* 1.4 67.9 + - - +
572D THR* 4.5 0.5 - - - +
145F THR* 3.6 19.7 - - + +
148F MET* 3.7 36.3 - - + -
149F ALA* 4.1 12.3 - - - +
152F ALA* 5.1 6.3 - - + -
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Residues in contact with GLY 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU 3.0 17.7 + - - -
569D ALA 4.7 0.2 - - - +
570D VAL* 1.4 81.2 - - - +
572D THR* 1.3 65.2 + - - +
575D ILE* 4.1 10.8 - - - -
576D LYS* 3.2 26.2 + - - -
145F THR* 4.5 4.0 - - - -
149F ALA* 3.9 18.6 - - - +
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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
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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