Contacts of the helix formed by residues 531 - 557 (chain B) in PDB entry 1FU1
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 LEU 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 5.9 1.8 - - - +
5A ILE* 3.3 30.7 - - + +
6A SER* 4.1 3.8 - - - -
7A ARG* 4.0 26.0 - - + +
19A PHE* 3.4 37.5 - - + -
130A CAS 3.3 13.0 - - + +
527B ILE* 2.9 17.1 + - + +
528B CAS 3.2 7.4 + - - +
530B CAS 1.3 74.7 + - - +
532B ASP* 1.3 66.4 + - - +
534B THR* 3.0 11.1 - - + +
535B ALA* 2.9 26.5 + - - +
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Residues in contact with ASP 532 (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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7A ARG* 3.0 27.0 + - - -
528B CAS 3.1 9.4 + - - +
529B TYR* 3.7 13.7 - - + +
531B LEU* 1.3 74.7 - - - +
533B THR* 1.3 54.6 + - - +
535B ALA* 3.3 5.0 + - - +
536B GLU* 2.7 40.5 + - + +
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Residues in contact with THR 533 (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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134A THR* 4.4 9.4 - - - +
529B TYR* 2.9 38.6 + - + +
530B CAS 3.0 28.6 + - + -
532B ASP* 1.3 75.3 - - - +
534B THR* 1.3 66.3 - - - +
536B GLU* 4.3 10.6 + - - -
537B ASN* 2.9 43.4 + - - +
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Residues in contact with THR 534 (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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4A LYS* 5.8 1.4 + - - -
130A CAS 3.3 32.7 - - + +
133A THR* 4.9 9.1 - - - +
134A THR* 6.1 1.8 - - - +
137A ASN* 5.3 8.8 + - - +
530B CAS 2.7 28.2 + - - +
531B LEU* 3.0 22.2 - - + +
533B THR* 1.3 73.6 - - - +
535B ALA* 1.3 57.1 + - - +
537B ASN* 3.9 2.9 - - - +
538B GLN* 3.0 31.9 + - - +
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Residues in contact with ALA 535 (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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531B LEU 2.9 17.5 + - - +
532B ASP* 3.7 5.6 - - - +
534B THR* 1.3 77.0 + - - +
536B GLU* 1.3 65.3 + - - +
538B GLN* 3.5 8.1 + - - +
539B ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ASP* 2.7 23.6 + - + +
533B THR* 3.8 9.6 + - - +
535B ALA* 1.3 71.7 - - - +
537B ASN* 1.3 71.2 + - - +
539B ALA* 3.3 8.6 + - - +
540B LYS* 2.9 56.6 + - + +
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Residues in contact with ASN 537 (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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134A THR* 4.5 12.1 + - - +
137A ASN* 4.6 14.9 - - + +
138A GLN* 3.7 22.6 + - - +
141A ASN* 3.0 19.9 - - - +
533B THR* 2.9 34.6 + - - +
534B THR* 4.0 3.4 - - - +
536B GLU* 1.3 90.6 + - - +
538B GLN* 1.3 65.0 + - - +
540B LYS* 3.0 15.2 + - - +
541B ASN* 2.9 19.2 + - - +
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Residues in contact with GLN 538 (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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137A ASN* 5.4 7.5 - - - +
534B THR* 3.0 20.7 + - - +
535B ALA* 3.8 7.8 - - - +
537B ASN* 1.3 74.9 - - - +
539B ALA* 1.3 62.9 + - - +
541B ASN* 3.0 26.6 + - + +
542B GLU* 3.0 43.3 + - + +
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Residues in contact with ALA 539 (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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535B ALA 3.2 10.5 + - - +
536B GLU* 3.5 11.2 - - - +
538B GLN* 1.3 77.7 + - - +
540B LYS* 1.3 61.0 + - + +
541B ASN 3.2 0.2 + - - -
542B GLU* 3.2 16.3 + - - +
543B HIS* 2.8 29.7 + - - +
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Residues in contact with LYS 540 (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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141A ASN* 3.9 10.1 - - + +
536B GLU* 2.9 43.2 + - - +
537B ASN* 3.0 20.1 + - - +
539B ALA* 1.3 73.9 - - + +
541B ASN* 1.3 60.2 + - - +
543B HIS* 3.7 7.0 - - - +
544B LEU* 2.8 37.1 + - + +
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Residues in contact with ASN 541 (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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140A LYS* 5.6 9.0 - - - +
141A ASN* 3.0 28.0 + - - +
144A LEU* 3.5 21.6 - - - +
537B ASN 2.9 8.3 + - - +
538B GLN* 3.0 18.2 - - - +
540B LYS* 1.3 75.1 - - - +
542B GLU* 1.3 58.6 + - - +
544B LEU* 2.8 7.0 + - - +
545B GLN* 2.7 45.8 + - - +
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Residues in contact with GLU 542 (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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538B GLN* 3.0 44.2 + - + +
539B ALA* 3.4 14.5 - - - +
541B ASN* 1.3 86.3 - - + +
543B HIS* 1.3 60.3 + - - +
545B GLN* 3.4 9.2 - - - +
546B LYS* 3.1 43.3 + - - +
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Residues in contact with HIS 543 (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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539B ALA 2.8 17.6 + - - +
540B LYS* 3.7 8.1 - - - +
542B GLU* 1.3 73.4 - - - +
544B LEU* 1.3 68.4 + - - +
546B LYS* 3.4 11.3 + - + +
547B GLU* 3.0 32.9 + - + +
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Residues in contact with LEU 544 (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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141A ASN* 3.6 28.9 - - + +
144A LEU* 4.0 17.0 - - + +
145A GLN* 3.4 41.5 - - + +
148A ASN* 3.6 29.7 + - + +
540B LYS* 2.8 24.4 + - + +
541B ASN 3.4 2.9 - - - +
543B HIS* 1.3 73.5 - - - +
545B GLN* 1.3 53.5 + - - +
547B GLU* 3.2 8.3 + - + +
548B ASN* 2.8 34.7 + - - +
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Residues in contact with GLN 545 (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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144A LEU* 3.8 18.1 - - - +
541B ASN* 2.7 29.6 + - - +
542B GLU* 3.4 15.9 - - - +
544B LEU* 1.3 71.8 - - - +
546B LYS* 1.3 60.1 + - + +
548B ASN* 2.9 15.9 + - - +
549B GLU* 2.8 58.6 + - + +
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Residues in contact with LYS 546 (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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542B GLU* 3.1 30.6 + - - +
543B HIS* 3.8 9.7 - - + +
545B GLN* 1.3 77.3 - - + +
547B GLU* 1.3 57.5 + - - +
549B GLU* 3.0 13.8 + - + +
550B ARG* 2.7 37.2 + - - +
553B ARG* 4.9 3.3 + - - +
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Residues in contact with GLU 547 (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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148A ASN* 3.6 18.5 + - - +
152A LEU* 5.7 0.5 - - - +
543B HIS* 3.0 27.7 + - + +
544B LEU* 3.4 14.1 - - + +
546B LYS* 1.3 75.1 - - - +
548B ASN* 1.3 60.5 + - - +
550B ARG* 2.7 42.7 + - - +
551B LEU* 3.2 28.5 + - - +
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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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144A LEU* 3.4 17.1 - - + +
147A GLU* 3.0 36.1 + - - +
148A ASN* 2.6 28.2 + - - +
151A LEU* 4.2 6.3 - - - +
544B LEU 2.8 10.7 + - - +
545B GLN* 2.9 21.6 + - - +
547B GLU* 1.3 74.4 - - - +
549B GLU* 1.3 69.5 + - - +
550B ARG 3.0 1.2 + - - -
551B LEU* 3.1 7.0 + - - +
552B LEU* 3.0 35.3 + - - +
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Residues in contact with GLU 549 (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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545B GLN* 2.8 54.7 + - + +
546B LYS* 3.6 9.2 - - + +
548B ASN* 1.3 81.8 - - - +
550B ARG* 1.3 65.9 + - - +
552B LEU* 3.4 14.0 + - - +
553B ARG* 3.1 48.6 + - - +
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Residues in contact with ARG 550 (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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546B LYS 2.7 20.0 + - - +
547B GLU* 2.7 41.2 + - - +
549B GLU* 1.3 71.6 - - - +
551B LEU* 1.3 82.9 + - - +
553B ARG* 2.9 32.6 + - - +
554B ASP* 3.1 44.2 + - - +
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Residues in contact with LEU 551 (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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148A ASN* 4.2 16.6 - - + +
151A LEU* 3.8 28.9 - - + -
152A LEU* 3.7 35.0 - - + -
547B GLU* 3.2 30.3 + - - +
548B ASN 3.1 6.1 + - - +
550B ARG* 1.3 102.3 - - - +
552B LEU* 1.3 62.2 + - - +
554B ASP* 3.3 10.0 + - + +
555B TRP* 3.2 24.4 + - - +
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Residues in contact with LEU 552 (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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147A GLU* 5.0 5.8 - - - +
151A LEU* 4.8 20.4 - - + -
548B ASN* 3.0 30.2 + - - +
549B GLU* 3.6 18.2 - - - +
551B LEU* 1.3 76.0 - - - +
553B ARG* 1.3 58.7 + - + +
555B TRP* 3.6 8.9 + - + +
556B ASN* 3.2 39.5 + - - +
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Residues in contact with ARG 553 (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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546B LYS* 4.9 3.0 + - - +
549B GLU* 3.1 36.5 + - - +
550B ARG* 2.9 34.8 + - - +
552B LEU* 1.3 75.1 - - + +
554B ASP* 1.3 68.5 + - - +
555B TRP 2.9 2.7 + - - -
556B ASN* 3.0 7.6 + - - +
557B ASP* 3.0 32.9 + - - +
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Residues in contact with ASP 554 (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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155A TRP* 5.4 2.0 - - + -
550B ARG* 3.1 47.4 + - - +
551B LEU* 3.3 10.4 + - + +
553B ARG* 1.3 77.2 - - - +
555B TRP* 1.3 60.3 + - - +
557B ASP* 3.3 11.3 - - - +
558B VAL* 3.2 32.4 + - + +
561B ARG* 5.0 8.0 + - - +
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Residues in contact with TRP 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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151A LEU* 3.5 30.5 - - + -
154A ASP* 3.5 23.1 - - + -
155A TRP* 3.4 61.4 - + + -
158A VAL* 3.5 23.5 - - + +
551B LEU* 3.2 10.0 + - + +
552B LEU* 3.7 12.8 - - + +
553B ARG 2.9 0.6 - - - -
554B ASP* 1.3 76.4 - - - +
556B ASN* 1.3 58.2 - - - +
557B ASP 2.8 11.0 + - - -
558B VAL* 2.9 17.3 + - + +
559B GLN* 3.6 26.5 + - + +
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Residues in contact with ASN 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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552B LEU* 3.2 25.8 + - - +
553B ARG* 3.0 7.7 + - - +
555B TRP* 1.3 78.5 - - - +
557B ASP* 1.3 57.7 + - - +
559B GLN* 4.1 22.5 + - - +
560B GLY* 4.6 2.3 + - - -
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Residues in contact with ASP 557 (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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553B ARG* 3.0 26.0 + - - +
554B ASP* 3.3 12.4 - - - +
555B TRP 3.0 0.6 - - - -
556B ASN* 1.3 78.5 - - - +
558B VAL* 1.3 62.6 + - - +
559B GLN 3.4 1.3 - - - -
560B GLY* 3.2 6.3 + - - +
561B ARG* 3.0 57.1 + - + +
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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
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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