Contacts of the helix formed by residues 547 - 568 (chain B) in PDB entry 1LJ1
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 GLY 547 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B GLY* 3.4 18.5 - - - +
172B MET 3.7 0.5 - - - -
173B ASN* 2.9 35.7 + - - -
236B MET* 4.2 5.1 - - - +
546B GLY* 1.3 70.9 - - - -
548B ASN* 1.4 57.4 + - - +
551B SER 3.7 6.1 + - - -
1800B FAD 3.1 17.5 + - - +
1801B FUM 2.7 15.4 + - - +
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Residues in contact with ASN 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ASN* 2.8 33.2 + - - +
192B MET* 3.6 13.2 - - - +
196B THR* 3.0 38.2 + - - +
212B LEU* 3.9 11.9 - - + +
540B HIS* 3.6 18.5 + - + +
544B ARG* 4.3 1.1 - - + -
545B LEU* 3.0 32.6 + - - +
547B GLY* 1.4 75.4 - - - +
549B ALA* 1.3 61.0 + - - +
550B ILE 3.5 0.2 - - - -
551B SER* 3.6 4.9 + - - -
552B ASP* 3.0 26.9 + - - +
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Residues in contact with ALA 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B HIS* 3.7 5.8 - - + -
540B HIS* 4.6 1.1 - - - -
544B ARG* 3.4 30.2 - - - +
548B ASN* 1.3 76.4 - - - +
550B ILE* 1.3 66.8 + - - +
552B ASP* 3.3 7.5 + - - +
553B ILE* 3.1 29.7 + - + +
1800B FAD 2.9 41.7 + - - +
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Residues in contact with ILE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 4.5 9.6 - - + +
168B ALA* 3.7 24.5 - - + -
171B GLY 4.0 9.6 - - - +
172B MET* 3.7 28.0 - - + -
253B VAL* 4.4 13.2 - - + -
254B GLY* 5.3 2.0 - - - -
257B VAL* 5.2 10.8 - - + -
549B ALA* 1.3 74.9 - - - +
551B SER* 1.3 64.2 + - - +
553B ILE* 3.4 22.4 + - + +
554B ILE* 3.3 28.2 + - + +
1800B FAD 2.9 42.6 + - + +
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Residues in contact with SER 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B MET* 4.0 13.3 - - - +
173B ASN* 3.0 30.6 + - - -
192B MET* 4.0 7.4 - - - +
212B LEU* 3.9 14.7 + - - +
216B SER* 4.0 10.9 - - - -
219B SER* 5.8 0.2 - - - -
547B GLY 3.7 11.4 + - - -
548B ASN* 3.6 11.4 + - - -
549B ALA 3.2 0.6 - - - -
550B ILE* 1.3 78.5 - - - +
552B ASP* 1.3 60.6 + - - +
554B ILE* 3.6 1.2 + - - +
555B THR* 3.2 27.0 + - - -
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Residues in contact with ASP 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 3.6 15.4 - - + +
505B HIS* 5.6 1.0 + - - -
533B GLY* 3.9 30.0 + - - +
534B GLU* 4.7 2.1 + - - -
536B THR* 4.9 1.0 + - - -
539B VAL* 4.3 10.9 - - - +
540B HIS* 2.9 29.5 + - + +
548B ASN 3.0 18.7 + - - +
549B ALA* 3.3 6.3 + - - +
551B SER* 1.3 74.5 - - - +
553B ILE* 1.3 59.6 + - - +
556B PHE* 2.8 47.6 + - - +
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Residues in contact with ILE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.5 26.0 - - - +
137B ALA* 3.5 23.4 - - + +
140B SER* 4.1 0.7 + - - -
165B ALA* 4.0 4.5 - - + -
257B VAL* 6.2 1.3 - - + -
533B GLY* 3.7 13.0 - - - -
534B GLU 4.4 1.1 - - - +
549B ALA* 3.1 14.2 + - + +
550B ILE* 3.5 35.7 - - + +
552B ASP* 1.3 77.7 - - - +
554B ILE* 1.3 66.0 + - + +
557B GLY* 2.9 26.3 + - - +
1800B FAD 3.4 43.3 - - - +
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Residues in contact with ILE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 4.3 4.3 - - - +
140B SER* 3.3 19.0 + - - +
172B MET* 3.9 22.7 - - + -
219B SER* 4.0 13.9 - - - +
222B TRP* 3.9 26.2 - - + -
223B MET* 3.9 27.1 - - + -
257B VAL* 4.3 9.4 - - + -
261B LEU* 4.2 13.2 - - + -
550B ILE* 3.3 19.0 + - + +
551B SER 4.2 0.2 - - - +
553B ILE* 1.3 82.6 - - + +
555B THR* 1.3 67.2 + - - +
557B GLY* 4.1 0.2 - - - -
558B ARG* 3.0 28.1 + - - +
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Residues in contact with THR 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B VAL* 3.8 27.8 - - + +
212B LEU* 4.6 5.1 + - - -
215B HIS* 3.7 34.4 + - + +
216B SER* 4.4 3.5 + - - -
219B SER* 2.7 27.2 + - - -
551B SER* 3.2 19.2 + - - -
552B ASP* 3.9 1.6 - - - -
554B ILE* 1.3 78.4 - - - +
556B PHE* 1.4 72.1 + - + +
558B ARG* 3.9 3.3 - - - +
559B LEU* 3.1 24.4 + - - +
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Residues in contact with PHE 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.7 41.5 - - + -
211B VAL* 3.7 24.7 - - + -
212B LEU* 4.5 9.2 - - + -
512B ILE* 3.9 26.9 - - + -
513B ASP 4.9 2.5 - - - -
514B THR 5.0 0.2 - - - -
516B ALA* 4.6 4.4 - - + +
531B GLY 5.2 0.9 - - - +
532B ALA* 3.7 18.0 - - + +
533B GLY 4.5 0.9 - - - +
536B THR* 6.1 0.2 - - - -
539B VAL* 4.3 18.8 - - + -
552B ASP* 2.8 42.1 + - - +
555B THR* 1.4 78.1 - - + +
557B GLY* 1.3 64.8 + - - +
559B LEU* 3.7 18.8 - - + +
560B ALA* 3.0 25.6 + - - +
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Residues in contact with GLY 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA 3.6 17.9 - - - -
140B SER* 4.2 1.1 - - - -
141B ALA* 3.1 19.2 - - - +
532B ALA* 4.0 13.6 - - - +
553B ILE* 2.9 21.3 + - - +
556B PHE* 1.3 77.2 - - - +
558B ARG* 1.3 61.3 + - - +
560B ALA* 3.4 0.7 + - - -
561B GLY 3.1 17.8 + - - -
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Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER* 3.9 5.3 - - - -
144B SER* 2.8 37.0 + - - -
218B ASP* 3.7 40.0 + - - +
219B SER* 4.8 7.2 + - - +
222B TRP* 3.4 55.8 - - + +
554B ILE 3.0 18.7 + - - +
555B THR* 3.9 3.4 - - - +
557B GLY* 1.3 75.7 - - - +
559B LEU* 1.3 63.1 + - - +
562B GLU* 3.1 33.6 + - - +
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Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B VAL* 4.3 13.7 - - + -
215B HIS* 4.9 16.8 - - + +
514B THR 3.2 29.4 - - - +
515B LYS* 4.2 12.1 - - + -
516B ALA* 4.4 1.3 - - + +
555B THR 3.1 15.3 + - - +
556B PHE* 3.7 24.5 - - + +
558B ARG* 1.3 79.4 - - - +
560B ALA* 1.4 64.1 + - - +
562B GLU* 3.2 9.6 + - + +
563B GLU* 2.9 46.3 + - + +
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Residues in contact with ALA 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ILE* 3.6 16.9 - - + +
516B ALA* 3.8 23.1 - - + -
530B TYR* 4.1 19.3 - - + -
532B ALA* 4.3 6.7 - - + -
556B PHE 3.0 18.3 + - - +
557B GLY 3.9 2.7 - - - +
559B LEU* 1.4 78.4 - - - +
561B GLY* 1.3 62.0 + - - +
563B GLU* 3.8 4.5 - - - +
564B ALA* 2.9 26.9 + - - +
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Residues in contact with GLY 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 3.5 17.0 - - - -
144B SER* 3.4 15.3 - - - -
145B ALA* 3.4 17.2 - - - +
310B ILE* 3.8 11.8 - - - +
557B GLY 3.1 12.5 + - - -
558B ARG 3.3 0.2 + - - -
559B LEU 3.3 0.4 - - - -
560B ALA* 1.3 76.0 - - - +
562B GLU* 1.3 61.1 + - - +
564B ALA* 3.5 0.5 + - - +
565B ALA* 3.1 18.4 + - - +
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Residues in contact with GLU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B SER* 4.0 14.6 - - - +
148B SER* 3.7 24.0 + - - +
558B ARG* 3.1 41.3 + - - +
559B LEU* 3.8 8.4 - - + +
561B GLY* 1.3 73.0 - - - +
563B GLU* 1.3 64.9 + - + +
565B ALA* 3.4 3.5 + - - +
566B LYS* 3.1 34.5 + - + +
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Residues in contact with GLU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B LYS* 3.7 50.9 + - + +
517B GLU* 4.8 2.9 - - - +
530B TYR* 3.6 24.1 + - + +
559B LEU* 2.9 34.2 + - + +
560B ALA 3.9 0.9 - - - +
562B GLU* 1.3 75.2 - - + +
564B ALA* 1.3 58.2 + - - +
566B LYS* 3.4 27.1 + - - +
567B TYR* 3.0 30.0 + - - +
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B VAL* 4.0 15.9 - - + +
308B ALA* 4.0 9.3 - - + +
310B ILE* 3.7 20.9 - - + -
530B TYR* 3.9 23.7 - - + -
560B ALA 2.9 18.5 + - - +
561B GLY 3.8 2.9 - - - +
563B GLU* 1.3 74.5 - - - +
565B ALA* 1.3 60.9 + - - +
567B TYR* 3.5 1.6 + - - +
568B SER* 2.9 30.3 + - - -
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Residues in contact with ALA 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B VAL* 4.4 1.4 - - - +
145B ALA* 4.1 1.8 - - - +
148B SER* 3.6 36.1 - - - +
150B ALA* 3.8 28.8 - - + +
561B GLY 3.1 14.5 + - - +
562B GLU 3.8 1.6 - - - +
563B GLU 3.4 0.2 - - - -
564B ALA* 1.3 75.6 - - - +
566B LYS* 1.3 63.7 + - - +
568B SER* 3.1 21.2 + - - +
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Residues in contact with LYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B SER* 5.8 2.5 - - - +
515B LYS* 6.0 1.2 - - - +
562B GLU* 3.1 23.1 + - + +
563B GLU* 3.7 33.0 + - - +
565B ALA* 1.3 73.5 - - + +
567B TYR* 1.3 64.7 + - - +
568B SER* 3.4 7.4 + - - -
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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
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288B THR* 4.0 12.6 + - - +
289B VAL 5.1 0.7 + - - -
307B ASP* 3.6 29.6 + - + -
308B ALA* 4.4 5.8 - - + -
527B PRO* 3.6 21.6 + - + +
528B GLY* 3.5 29.4 + - - -
530B TYR* 3.4 16.8 - - - +
563B GLU 3.0 17.5 + - - +
564B ALA 3.7 5.6 - - - +
566B LYS* 1.3 75.3 - - - +
568B SER* 1.3 67.1 + - - +
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Residues in contact with SER 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 3.4 32.0 - - - +
129B VAL* 4.8 1.6 - - - -
150B ALA* 5.4 0.3 - - - +
307B ASP* 3.1 43.2 - - - +
308B ALA* 5.1 0.9 - - - -
564B ALA 2.9 16.8 + - - -
565B ALA* 3.1 20.0 + - - +
566B LYS 3.4 5.7 + - - -
567B TYR* 1.3 83.1 + - - +
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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
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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