Contacts of the helix formed by residues 563 - 583 (chain D) in PDB entry 5D4C
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 PRO 563 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561D GLY 4.3 0.4 - - - +
562D ALA* 1.3 93.2 - - + +
564D GLU* 1.3 66.4 + - - +
565D ILE* 3.4 2.9 - - + +
566D ILE* 3.7 12.2 + - + +
567D ILE* 3.2 17.2 + - - +
136F LEU* 5.5 1.1 - - + -
140F ARG* 4.1 2.5 - - - +
185F GLN* 3.5 29.4 - - - +
188F ILE* 3.6 47.8 - - + -
189F GLU* 3.6 24.5 - - + +
192F LEU* 5.9 0.4 - - + -
221F ILE* 4.5 0.4 - - + -
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Residues in contact with GLU 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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132D TYR* 4.6 18.7 + - - +
563D PRO* 1.3 73.8 - - - +
565D ILE* 1.3 61.4 + - + +
567D ILE* 3.4 6.0 + - - +
568D ARG* 2.9 43.6 + - - +
571D LYS* 5.2 7.3 + - - -
136F LEU* 6.1 0.6 - - - +
140F ARG* 3.6 17.7 + - - +
189F GLU* 3.9 8.8 + - - +
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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
----------------------------------------------------------
159D ARG* 6.1 3.8 - - - +
563D PRO* 3.4 0.8 - - + +
564D GLU* 1.3 76.2 - - + +
566D ILE* 1.3 58.9 + - - +
568D ARG* 3.6 11.3 - - - +
569D ASN* 2.9 29.7 + - - +
84F TYR* 4.3 4.9 - - + -
87F GLU* 3.7 39.8 - - + +
88F ILE* 3.9 20.9 - - + -
91F VAL* 4.0 25.6 - - + -
189F GLU* 3.9 21.8 - - + +
192F LEU* 3.9 22.7 - - + -
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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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557D LEU* 3.6 25.8 - - + -
562D ALA* 4.2 3.4 - - + -
563D PRO* 3.7 20.4 + - + +
564D GLU 3.3 0.4 - - - -
565D ILE* 1.3 76.9 - - - +
567D ILE* 1.3 57.1 + - - +
569D ASN* 3.4 2.2 + - - +
570D GLU* 2.9 24.4 + - - +
84F TYR* 5.3 1.8 - - + +
188F ILE* 3.9 20.6 - - + -
192F LEU* 3.8 35.0 - - + -
214F GLN* 3.3 29.1 + - - +
217F ASN* 3.8 21.8 - - + +
221F ILE* 4.2 10.1 - - + -
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Residues in contact with ILE 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D LEU* 4.0 6.1 - - + -
557D LEU* 3.5 34.5 - - + +
558D LEU* 3.6 27.6 - - + -
562D ALA* 3.8 19.3 - - + +
563D PRO 3.2 17.7 + - - +
564D GLU* 3.4 10.2 + - - +
565D ILE 3.3 0.6 - - - -
566D ILE* 1.3 73.4 - - - +
568D ARG* 1.3 61.6 + - - +
570D GLU* 3.2 3.8 + - - +
571D LYS* 2.9 56.7 + - - +
140F ARG* 3.9 11.9 - - - +
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Residues in contact with ARG 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D PHE* 3.6 34.7 + - + -
132D TYR* 2.6 30.5 + - - -
155D ASP* 3.3 30.9 + - - +
159D ARG* 5.5 1.2 - - - +
456D MET* 3.8 18.6 - - - +
564D GLU* 2.9 33.5 + - - +
565D ILE* 3.6 9.2 - - - +
567D ILE* 1.3 75.7 - - - +
569D ASN* 1.3 63.4 + - - +
571D LYS* 3.3 10.7 + - - +
572D ARG* 2.9 27.2 + - - +
87F GLU* 3.0 42.1 + - - +
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Residues in contact with ASN 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 2.9 17.4 + - - +
566D ILE 3.6 1.6 - - - +
568D ARG* 1.3 77.2 - - - +
570D GLU* 1.3 63.4 + - - +
572D ARG* 3.2 28.3 + - - +
573D MET* 2.9 36.0 + - - +
84F TYR* 3.5 36.0 - - + +
87F GLU* 5.2 1.1 - - - +
210F LEU* 4.6 11.9 + - - +
213F ILE* 4.8 2.0 - - - +
214F GLN* 2.5 33.0 + - - +
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Residues in contact with GLU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D ARG* 3.3 28.4 - - - +
553D ARG* 3.1 35.4 + - - -
554D LEU* 3.6 30.5 - - + -
557D LEU* 3.7 15.4 - - + +
566D ILE 2.9 17.5 + - - +
567D ILE 3.6 4.5 - - - +
569D ASN* 1.3 76.2 - - - +
571D LYS* 1.3 56.5 + - - +
573D MET* 3.3 7.9 + - - +
574D LEU* 2.9 27.7 + - - +
214F GLN* 2.9 27.6 + - - +
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Residues in contact with LYS 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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97D THR* 3.9 27.1 - - + +
129D PHE* 3.5 35.1 - - + -
456D MET 5.9 1.0 + - - -
459D GLU* 3.8 18.4 + - - +
554D LEU* 3.7 24.7 - - + -
558D LEU* 5.1 7.7 - - - +
564D GLU* 5.2 6.5 + - - -
567D ILE* 2.9 40.8 + - + +
568D ARG* 3.6 3.8 - - - +
570D GLU* 1.3 74.1 - - - +
572D ARG* 1.3 65.6 + - - +
574D LEU* 3.1 5.3 + - - +
575D GLN* 2.9 22.7 + - - +
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Residues in contact with ARG 572 (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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127D LEU 5.6 0.2 - - - -
128D TYR* 3.3 29.2 + - + +
129D PHE* 3.6 17.6 + - + +
568D ARG* 2.9 25.3 + - - +
569D ASN* 3.3 32.5 + - - +
571D LYS* 1.3 76.7 - - - +
573D MET* 1.3 63.9 + - - +
575D GLN* 3.1 6.8 + - - +
576D GLU* 3.0 40.9 + - - +
80F PRO* 3.7 28.5 + - - +
83F GLN* 3.7 25.0 + - - +
84F TYR* 4.0 10.7 - - - +
87F GLU* 2.8 35.6 + - - -
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Residues in contact with MET 573 (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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550D ARG* 2.9 44.4 + - - +
553D ARG* 3.7 13.5 - - - +
569D ASN* 2.9 25.8 + - - +
570D GLU* 3.6 9.2 - - - +
572D ARG* 1.3 78.2 - - + +
574D LEU* 1.3 57.4 + - - +
576D GLU* 3.3 8.8 + - - +
577D ALA* 2.9 17.2 + - - +
210F LEU* 3.6 34.5 - - + -
211F ASP* 3.1 38.6 - - - +
214F GLN* 3.8 20.9 - - - -
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Residues in contact with LEU 574 (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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95D LEU* 4.0 20.0 - - + -
97D THR* 3.7 33.9 - - + +
99D ALA* 5.4 3.1 - - + -
547D LEU* 3.7 23.8 - - + +
550D ARG* 4.0 6.9 - - + +
551D ASN* 3.6 40.6 - - + +
554D LEU* 3.8 12.8 - - + -
570D GLU 2.9 14.2 + - - +
571D LYS* 3.1 9.8 + - - +
573D MET* 1.3 75.4 - - - +
575D GLN* 1.3 64.0 + - - +
577D ALA* 3.1 6.2 + - - +
578D VAL* 2.9 30.7 + - + +
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Residues in contact with GLN 575 (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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98D PRO 5.0 0.2 - - - +
99D ALA* 3.5 12.4 - - + +
100D ALA* 2.9 46.2 + - - +
102D ILE* 5.3 1.0 - - - +
105D VAL* 5.9 0.6 - - - +
127D LEU* 4.4 14.6 - - - +
128D TYR* 3.5 32.3 + - + -
129D PHE* 5.1 2.7 - - + -
458D ALA* 4.4 4.3 + - - +
571D LYS 2.9 13.4 + - - +
572D ARG* 3.4 11.4 - - - +
574D LEU* 1.3 75.9 - - - +
576D GLU* 1.3 56.7 + - - +
578D VAL* 3.2 7.4 + - - +
579D ASP* 2.7 64.1 + - - +
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Residues in contact with GLU 576 (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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128D TYR* 4.0 7.0 - - + -
546D ARG* 4.2 4.0 + - - +
550D ARG* 4.6 6.4 + - - +
572D ARG* 3.0 28.9 + - - +
573D MET* 3.8 11.6 - - - +
574D LEU 3.3 0.2 - - - -
575D GLN* 1.3 75.3 - - - +
577D ALA* 1.3 57.4 + - - +
579D ASP* 3.6 8.8 - - - +
580D ALA* 2.9 29.3 + - - +
587D ARG* 2.9 34.2 + - - +
591D VAL* 5.5 0.2 - - - +
80F PRO* 3.2 34.4 - - - +
210F LEU* 5.2 3.6 - - - +
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Residues in contact with ALA 577 (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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543D LEU* 5.2 2.8 - - - +
546D ARG* 3.8 16.7 + - + +
547D LEU* 3.7 29.4 - - + +
550D ARG* 4.0 18.8 - - - +
573D MET 2.9 14.1 + - - +
574D LEU* 3.3 10.5 - - - +
576D GLU* 1.3 75.4 - - - +
578D VAL* 1.3 65.5 + - - +
580D ALA* 3.3 3.8 + - - +
581D LEU* 2.9 22.9 + - - +
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Residues in contact with VAL 578 (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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95D LEU* 4.1 10.8 - - + -
99D ALA* 3.9 24.2 - - + -
100D ALA 4.6 8.5 - - - +
514D LEU* 4.1 25.4 - - + -
517D VAL* 4.6 8.3 - - + -
547D LEU* 3.5 28.5 - - + -
574D LEU* 2.9 15.7 + - + +
575D GLN 3.6 5.4 - - - +
577D ALA* 1.3 75.4 - - - +
579D ASP* 1.3 60.1 + - - +
581D LEU* 3.2 5.2 + - + +
582D LEU* 2.9 37.9 + - + +
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Residues in contact with ASP 579 (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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100D ALA 3.7 5.4 - - - +
102D ILE* 3.5 39.1 + - + +
128D TYR* 2.3 34.7 + - - -
575D GLN* 2.7 38.3 + - - +
576D GLU* 3.6 8.7 - - - +
577D ALA 3.2 0.2 - - - -
578D VAL* 1.3 76.4 - - - +
580D ALA* 1.3 56.8 + - - +
582D LEU 3.2 0.2 + - - -
583D ASP 2.8 37.8 + - - +
587D ARG* 4.5 7.9 + - + +
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Residues in contact with ALA 580 (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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543D LEU* 3.3 23.6 - - + +
546D ARG* 4.0 5.6 - - - +
576D GLU 2.9 19.1 + - - +
577D ALA 3.7 4.3 - - - +
579D ASP* 1.3 76.4 - - - +
581D LEU* 1.3 62.0 + - - +
584D ASN* 3.4 29.8 - - - +
591D VAL* 3.6 31.0 - - + -
602D SER* 3.6 1.4 - - - -
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Residues in contact with LEU 581 (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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1094C ALA 5.7 0.4 - - - +
517D VAL* 3.9 14.8 - - + -
518D PRO 5.1 0.2 - - - +
540D LEU* 4.7 7.1 - - + +
543D LEU* 3.9 26.5 - - + +
544D TYR* 3.5 50.5 - - + +
547D LEU* 3.7 23.8 - - + -
577D ALA 2.9 13.8 + - - +
578D VAL* 3.3 9.6 - - + +
579D ASP 3.2 0.2 - - - -
580D ALA* 1.3 78.9 - - - +
582D LEU* 1.3 78.2 + - + +
602D SER* 3.4 11.1 - - - -
603D LEU* 3.7 13.6 + - + +
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Residues in contact with LEU 582 (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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1094C ALA 4.1 9.9 - - - +
1095C LEU* 4.0 14.3 - - + +
101D HIS* 3.5 46.0 - - + +
102D ILE* 3.9 12.6 - - + +
103D TRP* 5.3 0.2 - - - +
514D LEU* 3.9 17.3 - - + -
517D VAL* 5.5 2.5 - - + -
578D VAL* 2.9 24.6 + - + +
581D LEU* 1.3 93.6 - - + +
583D ASP* 1.3 54.7 + - - +
584D ASN 4.2 0.2 - - - -
602D SER* 3.7 0.3 - - - -
603D LEU* 3.6 25.1 + - + +
604D THR* 2.7 34.4 + - - -
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Residues in contact with ASP 583 (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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102D ILE* 3.8 13.9 - - + +
103D TRP* 3.8 14.6 + - - +
579D ASP* 2.8 25.3 + - - +
582D LEU* 1.3 73.9 - - - +
584D ASN* 1.3 69.3 + - - +
585D GLY 3.8 0.3 + - - -
586D ARG* 3.2 44.4 + - + +
587D ARG 4.9 0.9 + - - -
602D SER* 3.9 0.7 - - - -
604D THR* 3.3 34.9 - - - +
605D ASP* 4.1 4.9 - - - +
1444D THR* 4.8 3.3 + - - +
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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
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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