Contacts of the helix formed by residues 540 - 559 (chain B) in PDB entry 6T2C
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 540 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A GLN* 5.1 2.6 - - - +
588A GLU* 3.3 23.8 + - - -
592A GLU* 4.9 8.1 - - - -
534B MET* 5.0 0.4 - - - -
538B ASP 3.2 6.7 + - - -
539B LEU* 1.3 79.7 - - - +
541B PRO* 1.3 70.6 - - - +
543B THR* 3.6 1.8 + - - -
544B ALA* 3.0 26.2 + - - +
238C THR* 5.6 2.0 - - - -
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Residues in contact with PRO 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 3.8 18.4 - - + -
433A ILE* 6.3 0.2 - - + -
434A ALA* 3.6 20.6 - - + -
437A ARG* 4.3 8.5 - - - +
588A GLU* 3.3 9.4 - - - +
592A GLU* 4.2 14.1 - - - +
534B MET* 4.6 3.8 - - + -
540B GLY* 1.3 84.4 - - - +
542B ALA* 1.3 56.2 + - - +
544B ALA* 3.2 5.0 + - + +
545B GLN* 2.9 32.2 + - - +
601B LEU* 3.7 19.7 - - + +
240C TRP* 3.6 29.8 - - + +
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Residues in contact with ALA 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA* 3.8 27.0 - - - +
437A ARG* 3.9 20.4 - - + +
438A ARG* 4.2 8.5 - - + +
584A LEU* 3.5 19.7 - - + +
588A GLU* 2.7 23.0 + - + +
541B PRO* 1.3 72.0 - - - +
543B THR* 1.3 59.8 + - - +
545B GLN* 3.3 5.9 + - - +
546B MET* 3.0 23.4 + - - +
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Residues in contact with THR 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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581A LEU* 3.6 29.4 - - + +
584A LEU* 4.0 9.0 - - - +
585A GLN* 3.6 37.5 + - + +
588A GLU* 2.3 30.5 + - - -
509B LEU* 5.2 0.4 - - + -
539B LEU* 3.8 19.3 - - + -
540B GLY 3.9 5.6 - - - -
541B PRO 3.3 0.2 - - - -
542B ALA* 1.3 77.0 - - - +
544B ALA* 1.3 57.3 + - - +
546B MET* 3.4 0.7 + - - -
547B ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ILE* 4.3 6.3 - - + +
534B MET* 3.7 34.3 - - + -
539B LEU* 4.3 7.6 - - + +
540B GLY 3.0 19.4 + - - +
541B PRO 3.2 6.5 + - - +
543B THR* 1.3 78.1 - - - +
545B GLN* 1.3 57.1 + - - +
547B ALA* 3.3 7.0 + - - +
548B ILE* 2.9 32.2 + - - +
601B LEU* 3.8 9.6 - - + -
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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
----------------------------------------------------------
423A LEU* 4.2 10.9 - - + +
426A ASP* 4.6 0.6 + - - -
431A GLU* 3.7 23.6 + - - +
434A ALA* 3.5 29.0 - - - +
435A SER* 3.5 7.6 + - - -
438A ARG* 3.0 32.6 + - - +
541B PRO 2.9 15.3 + - - +
542B ALA 3.3 4.7 + - - +
544B ALA* 1.3 76.6 - - - +
546B MET* 1.3 61.9 + - - +
548B ILE* 3.3 8.7 + - - +
549B GLN* 3.0 26.2 + - - +
600B ASN* 3.5 24.7 + - - +
601B LEU* 3.8 20.4 - - + +
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Residues in contact with MET 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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420A PHE* 3.7 33.4 - - + -
438A ARG* 4.0 16.5 - - + +
441A PHE* 4.4 10.1 - - + -
442A THR* 3.4 25.6 - - - +
580A LEU* 3.3 29.8 - - + +
581A LEU* 3.8 17.7 - - + -
584A LEU* 3.8 17.0 - - + -
542B ALA 3.0 16.6 + - - +
543B THR 3.9 0.2 - - - +
545B GLN* 1.3 76.1 - - - +
547B ALA* 1.3 57.6 + - - +
549B GLN* 3.3 10.6 + - - +
550B LEU* 2.9 33.2 + - + +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LEU* 3.6 8.7 - - + +
512B PHE* 3.8 38.0 - - + +
530B ILE* 3.9 12.3 - - + +
539B LEU* 5.0 1.3 - - + -
543B THR 2.9 18.1 + - - +
544B ALA* 3.6 8.5 - - - +
545B GLN 3.2 0.2 - - - -
546B MET* 1.3 74.8 - - - +
548B ILE* 1.3 59.9 + - - +
550B LEU* 3.4 4.6 + - - +
551B PHE* 2.9 31.0 + - - +
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Residues in contact with ILE 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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423A LEU* 3.7 20.2 - - + -
530B ILE* 3.9 21.3 - - + -
544B ALA 2.9 19.8 + - - +
545B GLN* 3.3 9.8 + - - +
547B ALA* 1.3 73.9 - - - +
549B GLN* 1.3 63.4 + - - +
551B PHE* 3.4 3.7 + - + +
552B ILE* 3.0 34.6 + - + +
597B ASN* 4.6 2.7 - - - +
599B TYR* 4.4 15.5 - - + -
600B ASN* 4.0 20.4 - - - +
601B LEU* 4.0 16.6 - - + -
604B LEU* 3.9 27.6 - - + -
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Residues in contact with GLN 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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420A PHE* 3.3 43.4 - - + +
421A ASP* 3.3 39.8 + - - +
422A GLU 4.8 3.1 - - - +
423A LEU* 3.8 20.7 - - + +
438A ARG* 3.3 35.3 + - - +
545B GLN 3.0 17.2 + - - +
546B MET* 3.6 11.5 - - - +
547B ALA 3.3 0.4 - - - -
548B ILE* 1.3 77.5 - - - +
550B LEU* 1.3 58.2 + - - +
552B ILE* 3.4 2.7 + - - -
553B LYS* 3.0 26.9 + - - +
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Residues in contact with LEU 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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420A PHE* 3.6 30.7 - - + -
577A ARG* 3.6 55.1 + - + +
578A ARG* 4.7 2.2 - - + +
580A LEU* 5.3 1.8 - - + -
581A LEU* 4.2 25.8 - - + +
512B PHE* 4.5 7.4 - - + +
546B MET* 2.9 22.7 + - + +
547B ALA* 3.4 5.1 + - - +
549B GLN* 1.3 75.7 - - - +
551B PHE* 1.3 57.7 + - - +
553B LYS* 3.4 6.0 + - + +
554B ASP* 3.0 30.5 + - - +
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Residues in contact with PHE 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B PHE* 3.3 26.2 + - + +
513B GLY 4.1 13.2 - - - -
514B VAL* 3.9 22.2 - - + -
522B ASP 3.4 24.2 - - - -
523B MET* 4.1 24.2 - - - -
526B GLY* 4.0 22.4 - - - -
527B THR* 4.7 5.4 - - + -
530B ILE* 4.5 11.9 - - + -
547B ALA 2.9 17.6 + - - +
548B ILE* 3.9 4.3 - - + +
550B LEU* 1.3 76.8 - - - +
552B ILE* 1.3 79.8 + - + +
554B ASP* 3.5 1.7 + - - +
555B TYR* 2.8 37.7 + + - +
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Residues in contact with ILE 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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421A ASP* 3.7 15.7 - - + +
523B MET* 4.3 21.5 - - + -
548B ILE* 3.0 25.0 + - + +
549B GLN* 4.0 1.3 - - - +
551B PHE* 1.3 97.2 - - + +
553B LYS* 1.3 57.9 + - - +
555B TYR* 3.6 5.7 - - + +
556B ARG* 2.9 55.7 + - + +
591B VAL* 4.9 6.3 - - + -
597B ASN* 3.7 36.1 - - + +
599B TYR* 5.3 2.9 - - + -
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Residues in contact with LYS 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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418A ILE* 5.5 4.5 - - - -
419A GLU* 3.3 30.8 + - - +
420A PHE* 5.4 5.2 - - + -
421A ASP* 3.1 24.2 + - - +
455A MET* 6.3 1.6 - - - -
577A ARG* 4.2 23.1 - - - +
549B GLN 3.0 18.5 + - - +
550B LEU* 3.7 10.5 - - + +
551B PHE 3.3 0.2 - - - -
552B ILE* 1.3 77.5 - - - +
554B ASP* 1.3 56.8 + - - +
556B ARG* 3.4 4.7 + - + +
557B TYR* 3.0 27.2 + - - +
562B HIS* 5.7 0.3 - - - -
33V C 3.6 24.5 + - - +
34V U 2.4 34.5 + - - -
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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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577A ARG* 5.4 4.6 - - - +
512B PHE 5.1 0.2 - - - +
513B GLY* 3.3 10.9 - - - -
514B VAL* 3.2 34.0 + - - +
550B LEU 3.0 17.2 + - - +
551B PHE 4.0 2.7 - - - +
553B LYS* 1.3 74.9 - - - +
555B TYR* 1.3 57.5 + - - +
557B TYR* 3.8 9.3 - - - -
558B THR* 2.4 45.8 + - - -
48C LYS* 3.6 17.6 + - - -
33V C 5.1 8.4 + - - +
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Residues in contact with TYR 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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514B VAL* 3.7 26.4 - - + +
519B GLU* 2.9 42.7 + - - +
522B ASP* 4.3 0.9 - - + -
523B MET* 3.6 29.2 - - + +
551B PHE* 2.8 31.6 + + + +
552B ILE* 3.6 8.7 - - + +
553B LYS 3.2 0.2 - - - -
554B ASP* 1.3 78.3 + - - +
556B ARG* 1.3 62.5 + - + +
558B THR* 3.1 1.3 + - - -
559B TYR* 3.1 48.0 + + - +
561B CYS* 4.0 14.1 - - - -
591B VAL* 3.6 33.0 - - + -
592B ALA* 4.1 6.7 + - - +
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Residues in contact with ARG 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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421A ASP* 3.7 24.2 + - - +
422A GLU* 3.0 37.6 + - - -
552B ILE* 2.9 31.8 + - - +
553B LYS* 4.0 4.9 - - + +
555B TYR* 1.3 74.3 - - - +
557B TYR* 1.3 61.6 + - - +
560B ARG 3.5 0.2 + - - -
561B CYS* 3.3 35.0 + - - +
562B HIS* 3.2 39.7 + - + +
563B ARG* 3.4 23.2 - - - +
591B VAL* 4.0 20.5 - - + +
594B GLY* 6.2 0.6 - - - -
595B GLY 3.3 21.8 + - - -
597B ASN* 3.7 7.7 - - - +
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Residues in contact with TYR 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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462A THR* 3.3 20.5 - - + +
466A ASN* 3.7 9.0 + - - -
574A MET* 5.4 0.8 - - + +
553B LYS 3.0 17.1 + - - +
554B ASP* 3.8 8.3 - - - +
555B TYR 3.2 0.2 - - - -
556B ARG* 1.3 79.0 - - - +
558B THR* 1.3 73.9 + - - +
560B ARG* 3.4 36.4 + - - +
562B HIS* 3.9 9.2 + + + -
48C LYS* 4.3 22.4 + - + +
32V G 3.4 23.2 + - - -
33V C 3.5 73.8 - + + +
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Residues in contact with THR 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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514B VAL* 3.8 19.7 - - + -
554B ASP* 2.4 41.4 + - - -
555B TYR* 3.1 3.7 + - - -
557B TYR* 1.3 81.8 - - - +
559B TYR* 1.3 72.1 + - + +
560B ARG* 3.1 20.1 + - - +
47C MET* 4.6 6.1 - - + +
48C LYS* 3.7 36.3 - - + -
51C MET* 3.6 12.5 - - - +
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Residues in contact with TYR 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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514B VAL* 4.3 6.9 - - + +
516B GLY* 3.9 9.2 - - - -
518B ASN 2.9 27.1 + - - -
519B GLU* 3.5 27.6 - - - +
522B ASP* 2.3 33.3 + - + -
555B TYR* 3.1 42.8 + + - -
558B THR* 1.3 86.9 - - + +
560B ARG* 1.3 69.7 + - - +
561B CYS* 3.2 13.1 + - - +
572B ARG* 3.3 19.8 + - - -
666B TRP* 4.6 3.8 - + - -
47C MET* 3.8 28.0 - - + +
51C MET* 4.0 20.0 - - + +
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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