Contacts of the helix formed by residues 563 - 583 (chain N) in PDB entry 5D4E
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561N GLY 4.2 0.2 - - - +
562N ALA* 1.3 94.4 - - + +
564N GLU* 1.3 65.3 + - - +
565N ILE* 3.4 3.4 - - + +
566N ILE* 3.7 12.9 + - + +
567N ILE* 3.2 17.8 + - - +
136P LEU* 5.5 1.1 - - + -
140P ARG* 4.1 2.0 - - - +
185P GLN* 3.4 25.5 - - - +
188P ILE* 3.6 46.9 - - + -
189P GLU* 3.6 28.5 - - + +
221P ILE* 4.6 0.4 - - + -
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Residues in contact with GLU 564 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132N TYR* 4.4 13.5 + - - +
158N TYR* 6.4 0.7 - - + -
456N MET* 6.1 0.5 - - - +
563N PRO* 1.3 74.6 - - - +
565N ILE* 1.3 61.1 + - + +
567N ILE* 3.4 6.6 + - - +
568N ARG* 2.9 53.5 + - - +
136P LEU* 6.1 0.2 - - - +
140P ARG* 3.8 16.8 + - - +
189P GLU* 4.1 7.9 + - - +
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Residues in contact with ILE 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159N ARG* 5.9 5.4 - - - +
563N PRO* 3.4 1.2 - - + +
564N GLU* 1.3 77.4 - - + +
566N ILE* 1.3 58.3 + - + +
568N ARG* 3.3 13.3 + - - +
569N ASN* 2.9 28.1 + - - +
84P TYR* 4.1 15.7 - - + -
87P GLU* 3.7 42.4 - - + +
88P ILE* 4.3 2.9 - - + -
91P VAL* 3.9 27.4 - - + -
189P GLU* 4.5 18.2 - - + +
192P LEU* 4.0 25.6 - - + -
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Residues in contact with ILE 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557N LEU* 3.8 24.0 - - + -
562N ALA* 4.3 3.4 - - + -
563N PRO* 3.7 20.3 + - + +
564N GLU 3.3 0.4 - - - -
565N ILE* 1.3 75.9 - - - +
567N ILE* 1.3 58.4 + - - +
569N ASN* 3.3 2.0 + - - +
570N GLU* 2.9 25.3 + - - +
84P TYR* 5.0 2.2 - - - +
188P ILE* 4.0 20.2 - - + -
192P LEU* 3.9 26.2 - - + -
214P GLN* 3.3 31.0 + - - +
217P ASN* 3.8 31.9 - - + +
221P ILE* 4.4 9.6 - - + -
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Residues in contact with ILE 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554N LEU* 4.2 4.5 - - + -
557N LEU* 3.6 33.4 - - + +
558N LEU* 3.7 26.7 - - + -
562N ALA* 3.8 13.9 - - + +
563N PRO 3.2 18.8 + - - +
564N GLU* 3.4 8.4 + - - +
565N ILE 3.4 0.2 - - - -
566N ILE* 1.3 74.7 - - - +
568N ARG* 1.3 58.0 + - - +
570N GLU* 3.3 4.9 + - - +
571N LYS* 2.9 57.1 + - + +
140P ARG* 3.7 20.6 - - - +
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Residues in contact with ARG 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N PHE* 3.6 37.4 + - + -
130N SER 5.3 1.0 + - - -
132N TYR* 2.4 30.8 + - - -
155N ASP* 3.4 30.7 + - - +
159N ARG* 5.4 1.4 - - - +
456N MET* 3.8 18.4 - - - +
564N GLU* 2.9 37.0 + - - +
565N ILE* 3.5 10.5 - - - +
567N ILE* 1.3 77.1 - - - +
569N ASN* 1.3 62.8 + - - +
571N LYS* 3.3 8.7 + - - +
572N ARG* 2.9 25.3 + - - +
87P GLU* 3.2 37.8 + - - +
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Residues in contact with ASN 569 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565N ILE 2.9 14.0 + - - +
566N ILE 3.5 4.5 - - - +
568N ARG* 1.3 76.5 - - - +
570N GLU* 1.3 62.2 + - - +
572N ARG* 3.0 27.8 + - - +
573N MET* 3.0 36.2 + - - +
84P TYR* 3.5 36.8 - - + +
87P GLU* 4.9 0.8 + - - +
210P LEU* 4.3 16.9 - - - +
213P ILE* 4.5 2.0 - - - +
214P GLN* 2.4 38.8 + - - +
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Residues in contact with GLU 570 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550N ARG* 3.2 22.3 - - - +
553N ARG* 3.1 38.1 + - - -
554N LEU* 3.6 34.8 - - + -
557N LEU* 3.5 7.6 - - + +
566N ILE 2.9 16.1 + - - +
567N ILE 3.6 4.7 - - - +
569N ASN* 1.3 75.9 - - - +
571N LYS* 1.3 57.6 + - - +
573N MET* 3.3 17.3 + - - +
574N LEU* 2.9 26.7 + - - +
214P GLN* 2.9 27.0 + - - +
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Residues in contact with LYS 571 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N THR* 3.7 34.8 + - + +
129N PHE* 3.5 32.3 - - + -
459N GLU* 4.0 17.6 + - - -
554N LEU* 3.7 14.8 - - + -
558N LEU* 4.9 9.3 - - - +
567N ILE* 2.9 42.4 + - + +
568N ARG* 3.7 3.4 - - - +
570N GLU* 1.3 72.1 - - - +
572N ARG* 1.3 61.8 + - - +
574N LEU* 3.1 9.3 + - - +
575N GLN* 2.9 28.8 + - - +
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Residues in contact with ARG 572 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N TYR* 3.3 30.6 + - + +
129N PHE* 3.7 21.9 + - + +
568N ARG* 2.9 19.8 + - - +
569N ASN* 3.0 43.3 + - - +
571N LYS* 1.3 75.9 - - - +
573N MET* 1.3 58.1 + - - +
575N GLN* 3.2 5.3 + - - +
576N GLU* 3.0 37.7 + - - +
587N ARG* 5.9 0.9 - - - +
80P PRO* 4.2 31.3 + - - +
83P GLN* 3.6 30.8 + - - +
84P TYR* 4.3 5.9 - - - +
87P GLU* 2.6 35.8 + - - -
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Residues in contact with MET 573 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550N ARG* 2.8 38.8 + - - +
553N ARG* 3.3 30.3 - - - +
569N ASN* 3.0 25.5 + - - +
570N GLU* 3.3 27.1 - - - +
572N ARG* 1.3 77.7 - - + +
574N LEU* 1.3 57.0 + - - +
576N GLU* 3.4 8.4 + - - +
577N ALA* 2.9 17.5 + - - +
210P LEU* 3.5 46.7 - - + +
211P ASP* 3.8 9.2 - - - +
214P GLN* 3.6 9.0 - - + -
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Residues in contact with LEU 574 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 3.9 19.1 - - + -
97N THR* 3.7 26.9 - - + +
99N ALA* 5.5 1.8 - - + -
547N LEU* 3.7 27.8 - - + +
550N ARG* 4.3 8.0 - - + +
551N ASN* 3.9 30.7 - - - +
554N LEU* 3.7 26.2 - - + -
570N GLU 2.9 13.6 + - - +
571N LYS* 3.1 9.2 + - - +
573N MET* 1.3 74.2 - - - +
575N GLN* 1.3 65.4 + - - +
577N ALA* 3.0 5.8 + - - +
578N VAL* 2.9 30.3 + - + +
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Residues in contact with GLN 575 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N PRO 4.8 0.2 - - - +
99N ALA* 3.5 13.0 - - + +
100N ALA* 3.0 43.6 + - - +
102N ILE* 5.7 0.2 - - - +
127N LEU* 4.4 15.6 - - - +
128N TYR* 3.5 29.8 + - + -
129N PHE* 4.9 2.7 - - + -
458N ALA* 4.1 6.1 + - - +
571N LYS 2.9 12.0 + - - +
572N ARG* 3.5 11.0 - - - +
574N LEU* 1.3 76.5 - - - +
576N GLU* 1.3 57.5 + - - +
577N ALA 3.2 0.2 + - - -
578N VAL* 3.2 5.9 + - - +
579N ASP* 2.4 67.9 + - - +
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Residues in contact with GLU 576 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N TYR* 3.9 10.8 - - + -
546N ARG* 4.4 4.0 + - - +
550N ARG* 4.7 5.0 + - - +
572N ARG* 3.0 28.2 + - - +
573N MET* 3.8 10.4 - - - +
575N GLN* 1.3 75.7 - - - +
577N ALA* 1.3 56.6 + - - +
579N ASP* 3.7 8.6 - - - +
580N ALA* 2.9 28.8 + - - +
587N ARG* 2.6 35.8 + - - +
78P SER 4.8 0.5 - - - +
80P PRO* 3.3 35.9 - - - +
210P LEU* 5.1 2.9 - - - +
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Residues in contact with ALA 577 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543N LEU* 5.2 2.4 - - - +
546N ARG* 4.0 16.5 + - + +
547N LEU* 4.0 28.5 - - + +
550N ARG* 4.0 17.5 - - - +
573N MET 2.9 15.5 + - - +
574N LEU* 3.0 10.1 + - + +
576N GLU* 1.3 75.8 - - - +
578N VAL* 1.3 60.2 + - - +
580N ALA* 3.3 2.6 + - - +
581N LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 578 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 4.2 11.0 - - + -
99N ALA* 3.7 27.1 - - + -
100N ALA 4.7 6.3 - - - +
514N LEU* 4.3 15.3 - - + -
517N VAL* 4.5 9.6 - - + -
547N LEU* 3.5 22.9 - - + +
574N LEU* 2.9 16.0 + - + +
575N GLN 3.2 4.9 + - - +
577N ALA* 1.3 73.9 - - - +
579N ASP* 1.3 58.3 + - - +
581N LEU* 3.1 9.4 + - + +
582N LEU* 2.9 47.6 + - + +
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Residues in contact with ASP 579 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100N ALA 3.5 8.8 - - - +
102N ILE* 3.5 34.3 + - + +
128N TYR* 2.2 33.4 + - - -
575N GLN* 2.4 37.0 + - - +
576N GLU* 3.7 7.8 - - - +
578N VAL* 1.3 75.7 - - - +
580N ALA* 1.3 54.5 + - - +
582N LEU* 3.3 0.8 + - - -
583N ASP* 2.8 40.3 + - - +
587N ARG* 4.8 4.5 + - + +
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Residues in contact with ALA 580 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543N LEU* 3.7 13.6 - - + +
546N ARG* 4.2 5.8 - - - +
576N GLU 2.9 19.8 + - - +
577N ALA 3.3 5.1 + - - +
579N ASP* 1.3 74.5 - - - +
581N LEU* 1.3 62.8 + - - +
583N ASP 4.2 2.7 - - - -
584N ASN* 3.4 31.7 - - - +
591N VAL* 3.6 30.7 - - + -
602N SER* 3.6 5.0 - - - -
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Residues in contact with LEU 581 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094M ALA 5.7 0.4 - - - +
517N VAL* 3.8 24.0 - - + -
518N PRO 5.1 0.4 - - - +
540N LEU* 4.5 12.3 - - + -
543N LEU* 4.0 26.6 - - + +
544N TYR* 3.5 46.4 - - + +
547N LEU* 3.9 14.6 - - + -
577N ALA 2.9 13.3 + - - +
578N VAL* 3.3 9.4 - - + +
580N ALA* 1.3 76.4 - - - +
582N LEU* 1.3 76.0 + - + +
602N SER* 3.2 17.0 - - - -
603N LEU* 3.7 11.2 + - + +
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Residues in contact with LEU 582 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094M ALA 3.9 16.8 - - - +
1095M LEU* 3.8 24.5 - - + +
101N HIS* 3.5 45.8 - - + +
102N ILE* 4.4 10.8 - - + +
103N TRP* 5.5 0.4 - - - +
514N LEU* 3.9 18.8 - - + -
517N VAL* 5.4 2.2 - - + -
518N PRO* 6.2 0.4 - - + -
578N VAL* 2.9 25.9 + - + +
579N ASP* 4.2 1.3 - - - +
581N LEU* 1.3 93.2 - - + +
583N ASP* 1.3 60.9 + - + +
602N SER* 4.2 0.2 - - - -
603N LEU* 3.7 11.2 + - + +
604N THR* 2.9 29.5 + - - -
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Residues in contact with ASP 583 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N ILE* 3.9 19.4 - - + +
103N TRP* 4.0 8.8 + - - +
579N ASP 2.8 24.8 + - - +
580N ALA* 4.0 0.6 - - - -
582N LEU* 1.3 75.9 - - - +
584N ASN* 1.3 70.5 + - - +
585N GLY 3.8 0.3 + - - -
586N ARG* 3.3 43.4 + - + +
587N ARG 5.1 0.2 + - - -
602N SER* 3.7 2.8 + - - -
604N THR* 3.4 34.1 - - - +
605N ASP* 4.4 5.0 - - - +
1444N THR* 4.9 2.6 + - - +
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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
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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