Contacts of the helix formed by residues 563 - 583 (chain J) in PDB entry 4XLN
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562J ALA* 1.3 87.2 - - + +
564J GLU* 1.3 65.1 + - - +
565J ILE* 3.1 4.0 + - + +
566J ILE* 3.4 18.7 + - + +
567J ILE* 3.1 19.8 + - - +
151L LEU* 6.3 1.1 - - + -
199L ARG* 6.2 0.2 - - - +
200L GLN* 3.2 22.4 - - + +
203L ILE* 3.9 40.6 - - + -
204L GLU* 3.6 31.9 - - + +
207L LEU* 6.3 0.2 - - + -
236L ILE* 4.8 0.7 - - + -
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Residues in contact with GLU 564 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J TYR* 4.9 4.2 + - - -
562J ALA 3.6 1.6 + - - -
563J PRO* 1.3 72.0 - - - +
565J ILE* 1.3 63.4 + - + +
567J ILE* 3.5 8.5 + - + +
568J ARG* 2.9 57.9 + - - +
571J LYS* 3.5 13.7 + - - -
151L LEU* 5.4 14.4 - - + +
155L ARG* 3.3 25.5 + - - +
204L GLU* 5.0 1.0 + - - -
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Residues in contact with ILE 565 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563J PRO* 3.1 1.3 + - + -
564J GLU* 1.3 84.4 - - + +
566J ILE* 1.3 61.1 + - + +
568J ARG* 3.3 6.5 + - - +
569J ASN* 2.9 27.7 + - - +
99L TYR* 4.0 16.6 - - + -
102L GLU* 3.9 31.6 - - + +
103L ILE* 5.0 4.3 - - + -
106L VAL* 5.8 5.2 - - + -
204L GLU* 3.6 41.1 - - + +
207L LEU* 4.3 14.1 - - + -
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Residues in contact with ILE 566 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557J LEU* 4.0 17.3 - - + -
562J ALA* 5.4 2.2 - - + -
563J PRO* 3.4 29.9 + - + +
565J ILE* 1.3 74.4 - - + +
567J ILE* 1.3 57.9 + - + +
569J ASN* 3.4 0.4 + - - -
570J GLU* 2.9 25.2 + - - +
99L TYR* 3.7 16.6 - - - +
203L ILE* 4.2 14.8 - - + -
207L LEU* 4.0 10.5 - - + -
229L GLN* 3.2 35.3 + - + +
232L ASN* 3.6 33.2 - - + +
233L GLN 6.0 0.4 - - - +
236L ILE* 5.2 7.0 - - + -
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Residues in contact with ILE 567 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554J LEU* 4.3 2.1 - - + +
557J LEU* 3.3 46.9 - - + +
558J LEU* 3.7 30.5 - - + +
562J ALA* 3.6 16.4 - - + +
563J PRO 3.1 18.2 - - - +
564J GLU* 3.6 11.0 - - - +
565J ILE 3.2 0.4 - - - -
566J ILE* 1.3 76.4 - - - +
568J ARG* 1.3 58.1 + - - +
570J GLU* 3.1 8.6 + - - +
571J LYS* 2.9 56.3 + - + +
151L LEU* 5.8 3.1 - - + -
155L ARG* 5.1 0.7 - - - +
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Residues in contact with ARG 568 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J PHE* 3.8 25.9 + - + +
130J ASN 4.6 4.2 + - - -
132J TYR* 2.9 33.7 + - - -
155J ASP* 6.0 3.0 - - - +
456J MET* 3.4 33.7 - - + +
564J GLU* 2.9 43.6 + - - +
565J ILE* 3.6 6.5 - - - +
567J ILE* 1.3 74.9 - - - +
569J ASN* 1.3 64.0 + - - +
571J LYS* 3.0 18.8 + - - +
572J ARG* 2.9 23.6 + - - +
98L GLN* 5.0 0.2 - - - +
102L GLU* 2.9 36.3 + - - +
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Residues in contact with ASN 569 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565J ILE 2.9 15.5 + - - +
568J ARG* 1.3 75.6 - - - +
570J GLU* 1.3 57.0 + - - +
572J ARG* 2.5 40.7 + - - +
573J MET* 2.9 58.1 + - - +
99L TYR* 3.1 27.4 - - + +
102L GLU* 5.0 0.2 - - - +
225L LEU* 3.3 19.5 - - - +
229L GLN* 3.0 30.2 - - - +
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Residues in contact with GLU 570 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550J ARG* 3.2 26.9 - - - +
553J ARG* 2.8 44.1 + - - -
554J LEU* 3.5 32.3 - - + -
557J LEU* 3.6 11.7 - - + +
566J ILE 2.9 8.6 + - - +
567J ILE* 3.3 11.0 - - - +
569J ASN* 1.3 76.6 - - - +
571J LYS* 1.3 57.1 + - - +
573J MET* 3.3 10.3 + - - +
574J LEU* 2.9 27.2 + - - +
229L GLN* 2.8 25.7 - - - +
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Residues in contact with LYS 571 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J THR* 3.6 35.7 - - + +
129J PHE* 3.4 35.3 - - + -
459J GLU* 5.7 0.8 + - - -
554J LEU* 4.3 5.6 - - + -
558J LEU* 5.1 4.0 - - - -
564J GLU* 3.5 13.1 + - - -
567J ILE* 2.9 36.2 + - - +
568J ARG* 3.0 16.9 + - - +
570J GLU* 1.3 75.7 - - - +
572J ARG* 1.3 57.5 + - - +
574J LEU* 3.1 6.4 + - - +
575J GLN* 2.9 26.9 + - - +
155L ARG* 2.9 42.1 - - - +
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Residues in contact with ARG 572 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J TYR* 3.5 26.2 - - + +
129J PHE* 3.1 44.8 + - + +
568J ARG* 2.9 8.9 + - - +
569J ASN* 2.5 50.1 + - - +
571J LYS* 1.3 76.5 - - - +
573J MET* 1.3 61.5 + - + +
575J GLN* 3.0 6.5 + - - +
576J GLU* 2.9 33.0 + - + +
587J ARG* 5.8 2.5 - - - +
95L PRO* 4.1 21.8 + - + -
98L GLN* 3.4 27.6 - - - +
99L TYR* 4.2 3.4 - - - +
102L GLU* 3.6 21.2 + - - -
225L LEU* 4.4 1.6 - - - +
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Residues in contact with MET 573 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550J ARG* 3.1 42.8 + - + +
553J ARG* 3.4 25.1 - - - +
569J ASN* 2.9 39.4 + - - +
570J GLU* 3.5 10.3 - - - +
571J LYS 3.3 0.2 - - - -
572J ARG* 1.3 76.0 - - + +
574J LEU* 1.3 58.8 + - - +
576J GLU* 3.1 14.0 - - - +
577J ALA* 2.9 24.8 + - - +
225L LEU* 3.6 23.6 - - + -
226L ASP* 3.6 22.9 - - - +
229L GLN* 3.5 13.5 - - - -
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Residues in contact with LEU 574 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J LEU* 3.7 24.0 - - + -
97J THR* 3.6 26.9 - - + +
99J ALA* 5.3 1.6 - - + -
547J LEU* 3.8 19.1 - - + +
550J ARG* 4.4 5.6 - - + +
551J ASN* 3.7 37.0 - - + +
554J LEU* 3.6 25.1 - - + -
570J GLU 2.9 13.8 + - - +
571J LYS* 3.1 10.3 + - - +
573J MET* 1.3 75.2 - - - +
575J GLN* 1.3 60.0 + - - +
577J ALA* 3.3 4.2 + - - +
578J VAL* 2.9 34.7 + - - +
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Residues in contact with GLN 575 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J ALA* 3.3 16.8 - - + +
100J ALA* 3.1 43.2 + - - +
102J ILE* 5.2 1.6 - - - +
105J VAL* 5.5 2.6 - - - +
127J LEU* 4.0 17.6 - - - +
128J TYR* 3.6 27.7 + - + -
129J PHE* 4.7 2.9 - - + -
458J ALA* 3.5 12.2 - - - +
571J LYS 2.9 11.7 + - - +
572J ARG* 3.0 12.3 + - - +
574J LEU* 1.3 76.6 - - - +
576J GLU* 1.3 56.3 - - - +
578J VAL* 3.2 4.0 + - - +
579J ASP* 2.9 58.8 + - - +
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Residues in contact with GLU 576 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J TYR* 4.4 11.8 - - + -
546J ARG* 5.5 2.4 + - - -
550J ARG* 3.6 22.1 + - - +
572J ARG* 2.9 13.0 + - + +
573J MET* 3.1 31.2 - - - +
575J GLN* 1.3 76.9 - - - +
577J ALA* 1.3 56.3 + - - +
579J ASP* 3.5 12.1 + - - +
580J ALA* 2.9 26.9 + - - +
587J ARG* 4.8 8.1 - - - +
95L PRO* 3.9 28.2 - - - +
225L LEU* 4.8 3.3 - - - +
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Residues in contact with ALA 577 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543J LEU 5.4 0.2 - - - +
546J ARG* 5.0 1.3 - - + -
547J LEU* 3.9 29.8 - - + +
550J ARG* 3.7 21.3 - - - +
573J MET 2.9 18.4 + - - +
574J LEU* 3.6 5.4 - - - +
575J GLN 3.2 0.2 - - - -
576J GLU* 1.3 74.9 - - - +
578J VAL* 1.3 65.9 + - - +
580J ALA* 2.9 10.9 + - - +
581J VAL* 2.9 24.8 + - - +
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Residues in contact with VAL 578 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J LEU* 3.6 29.4 - - + -
99J ALA* 3.9 11.2 - - + -
100J ALA 4.0 20.9 - - - +
101J HIS* 5.4 0.7 - - + -
514J LEU* 6.4 2.2 - - + -
517J VAL* 4.6 15.5 - - + -
547J LEU* 3.6 18.4 - - + +
574J LEU 2.9 18.1 + - - +
575J GLN 3.5 7.6 - - - +
577J ALA* 1.3 74.8 - - - +
579J ASP* 1.3 58.3 + - - +
581J VAL* 3.0 8.2 + - + +
582J ILE* 2.9 40.0 + - + +
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Residues in contact with ASP 579 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J ALA 3.5 6.1 - - - +
102J ILE* 3.2 39.0 + - + +
128J TYR* 2.2 38.8 + - - +
575J GLN* 2.9 39.9 + - - +
576J GLU* 3.6 7.3 - - - +
578J VAL* 1.3 76.5 - - - +
580J ALA* 1.3 54.6 + - - +
582J ILE* 4.3 1.1 - - - +
583J ASP 2.8 40.4 + - - +
587J ARG* 6.2 0.2 - - + -
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Residues in contact with ALA 580 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543J LEU* 3.4 27.0 - - + +
546J ARG* 6.1 1.8 - - - +
576J GLU 2.9 16.0 + - - +
577J ALA* 2.9 15.4 + - - +
579J ASP* 1.3 75.9 - - - +
581J VAL* 1.3 58.6 + - + +
584J ASN* 3.4 17.5 - - - +
591J VAL* 4.0 15.7 - - + -
602J SER* 3.4 17.0 - - - -
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Residues in contact with VAL 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517J VAL* 5.1 4.9 - - + -
540J LEU* 4.3 4.3 - - + +
543J LEU* 3.9 32.1 - - + +
544J TYR* 3.6 38.1 - - + +
547J LEU* 3.7 24.7 - - + -
577J ALA 2.9 17.9 + - - +
578J VAL 3.0 7.8 + - - +
580J ALA* 1.3 78.8 - - + +
582J ILE* 1.3 65.9 + - + +
602J SER* 3.2 14.1 - - - -
603J LEU* 3.5 18.5 + - + +
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Residues in contact with ILE 582 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094I ALA 4.5 7.9 - - - +
1095I LEU* 4.5 3.6 - - + -
101J HIS* 3.3 50.5 - - + +
102J ILE* 3.8 19.3 - - + +
103J TRP* 4.3 2.0 - - + -
514J LEU* 6.3 2.0 - - + -
517J VAL* 5.5 7.4 - - + -
518J PRO* 6.3 0.9 - - + -
578J VAL* 2.9 33.9 + - + +
579J ASP* 3.1 2.7 + - - +
581J VAL* 1.3 81.7 - - + +
583J ASP* 1.3 61.1 + - - +
602J SER* 3.2 4.9 + - - -
603J LEU* 3.8 19.2 + - + +
604J THR* 2.9 37.4 + - - +
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Residues in contact with ASP 583 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102J ILE* 3.7 21.6 - - + +
103J TRP* 3.6 11.8 + - + +
579J ASP* 2.8 22.6 + - - +
582J ILE* 1.3 75.6 - - - +
584J ASN* 1.3 68.5 + - - +
585J GLY 3.7 2.1 + - - -
586J ARG* 3.7 41.3 + - + +
602J SER* 3.6 1.3 - - - -
604J THR* 3.2 28.5 - - - +
605J ASP* 3.5 9.5 - - - +
1444J THR* 4.6 1.9 - - - +
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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