Contacts of the helix formed by residues 558 - 576 (chain B) in PDB entry 6TXA
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 ASP 558 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B VAL* 5.4 0.7 - - - +
556B LYS* 3.9 9.9 - - - +
557B VAL* 1.3 83.4 + - - +
559B ARG* 1.3 64.2 + - - +
560B LYS* 3.3 12.1 + - - +
561B SER* 2.9 42.7 + - - -
562B LEU* 3.1 20.8 + - - +
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Residues in contact with ARG 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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558B ASP* 1.3 73.3 - - - +
560B LYS* 1.3 60.4 + - - +
562B LEU* 3.7 7.0 + - - +
563B TYR* 3.3 22.2 + - - +
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Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 4.2 23.2 - - + +
491B VAL* 4.1 20.8 - - + +
558B ASP* 3.3 10.5 + - - +
559B ARG* 1.3 77.4 - - - +
561B SER* 1.3 62.4 + - - +
563B TYR* 3.5 7.2 + - - +
564B ALA* 3.3 20.4 + - - +
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Residues in contact with SER 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B VAL* 4.4 13.0 - - - +
493B LEU* 3.7 15.3 - - - +
554B CYS* 4.9 0.4 - - - -
556B LYS* 3.7 31.1 - - - +
558B ASP* 2.9 32.0 + - - -
560B LYS* 1.3 73.4 - - - +
562B LEU* 1.3 60.6 + - - +
564B ALA* 3.3 7.6 + - - +
565B ALA* 2.8 31.3 + - - +
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Residues in contact with LEU 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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455B LYS* 4.0 37.7 - - + -
456B TYR 4.5 9.6 - - - +
457B VAL* 4.5 14.6 - - + -
554B CYS* 5.1 2.7 - - + -
556B LYS 4.6 4.4 + - - +
557B VAL 4.5 7.2 - - - +
558B ASP 3.1 16.6 + - - +
559B ARG* 3.9 7.4 - - - +
561B SER* 1.3 74.9 - - - +
563B TYR* 1.3 64.2 + - - +
565B ALA* 3.4 4.0 + - + +
566B ARG* 3.1 64.4 + - - +
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Residues in contact with TYR 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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487B VAL* 3.8 17.9 - - + +
488B LEU 4.6 9.8 + - - -
489B LEU* 4.5 10.5 - - + -
490B ASP* 4.8 16.2 - - - +
559B ARG 3.3 12.0 + - - +
560B LYS* 3.7 10.1 - - - +
561B SER 3.3 0.2 - - - -
562B LEU* 1.3 78.7 - - - +
564B ALA* 1.3 66.8 + - - +
566B ARG* 3.3 11.5 + - - +
567B GLN* 3.2 62.5 + - + +
587B ILE 4.6 5.6 - - - -
589B PRO* 5.7 5.6 - - + +
590B LEU* 4.2 11.1 - - - +
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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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489B LEU* 4.0 18.1 - - + +
490B ASP 5.7 0.7 - - - +
491B VAL* 3.9 25.1 - - + +
493B LEU* 4.0 11.4 - - + -
560B LYS 3.3 10.9 + - - +
561B SER* 3.3 10.7 + - - +
562B LEU 3.3 0.6 - - - -
563B TYR* 1.3 79.0 - - + +
565B ALA* 1.3 65.0 + - - +
567B GLN* 3.0 13.9 + - - +
568B TYR* 3.0 23.8 + - + -
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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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457B VAL* 4.0 12.5 - - + +
493B LEU* 3.7 10.3 - - + +
498B PHE* 3.9 18.9 - - + -
554B CYS* 3.9 26.9 - - + -
561B SER 2.8 18.1 + - - +
562B LEU* 3.6 7.0 - - - +
564B ALA* 1.3 75.6 - - - +
566B ARG* 1.3 55.8 + - - +
568B TYR* 3.3 3.5 + - - +
569B PHE* 2.9 29.8 + - - +
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Residues in contact with ARG 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR 4.9 6.1 + - - -
457B VAL* 3.8 22.4 + - + +
562B LEU* 3.1 54.8 + - + +
563B TYR* 3.5 13.6 - - - +
564B ALA 3.2 0.2 - - - -
565B ALA* 1.3 77.2 - - - +
567B GLN* 1.3 64.0 + - - +
569B PHE* 3.8 0.5 - - - +
570B VAL* 3.0 35.6 + - - +
587B ILE* 3.8 48.5 - - + +
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Residues in contact with GLN 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B PRO* 4.3 8.5 - - + -
487B VAL* 4.6 9.0 - - + +
489B LEU* 3.9 24.2 - - + -
563B TYR* 3.2 52.7 + - + +
564B ALA 3.0 6.5 + - - +
566B ARG* 1.3 75.5 - - - +
568B TYR* 1.3 65.8 + - - +
571B GLN* 3.1 26.3 + - - +
587B ILE 3.0 25.3 + - - -
588B ALA* 3.3 14.5 - - - +
589B PRO* 5.0 1.1 - - - +
590B LEU* 5.3 1.9 + - - +
591B ILE* 3.3 33.1 + - + +
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Residues in contact with TYR 568 (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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480B VAL* 3.6 20.8 - - + +
481B ALA* 3.7 10.8 - - - -
483B ALA* 3.6 29.2 - - - +
485B PRO* 4.0 8.5 - - + -
489B LEU* 3.6 24.5 - - + +
491B VAL 4.5 0.2 - - - -
492B LYS* 3.4 14.2 - - - +
493B LEU* 3.3 44.8 + - + -
498B PHE* 3.8 22.9 - + + -
564B ALA* 3.0 30.2 + - + -
565B ALA 3.6 5.6 - - - +
567B GLN* 1.3 75.8 - - - +
569B PHE* 1.3 57.1 + - - +
571B GLN* 3.5 5.0 + - - +
572B TRP* 2.9 30.5 + - - +
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Residues in contact with PHE 569 (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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457B VAL* 3.6 25.8 - - + -
458B GLY* 3.6 34.1 - - - -
459B GLU 3.8 13.2 - - - -
460B THR* 4.0 8.3 - - + -
480B VAL* 4.3 4.9 - - + +
550B ILE 5.0 0.2 - - - -
552B VAL* 3.4 38.6 - - + -
565B ALA 2.9 17.0 + - - +
566B ARG 3.8 1.1 - - - +
568B TYR* 1.3 77.2 - - - +
570B VAL* 1.3 67.0 + - + +
572B TRP* 3.1 11.7 + + - +
573B CYS* 3.0 54.7 + - - -
581B PRO* 3.5 21.1 - - + -
587B ILE* 4.6 2.7 - - + -
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ARG 3.0 21.6 + - - +
567B GLN 4.4 1.1 - - - +
569B PHE* 1.3 81.6 - - + +
571B GLN* 1.3 60.3 + - - +
573B CYS* 3.6 8.7 - - - +
574B ALA* 3.3 16.3 + - - +
581B PRO* 4.3 12.3 - - + -
584B GLY* 4.7 2.2 - - - +
587B ILE* 3.6 27.4 - - + -
588B ALA* 3.7 20.4 - - + -
591B ILE* 3.9 18.1 - - + +
592B THR* 4.0 20.6 - - + -
598B TRP* 3.6 13.4 - - + -
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Residues in contact with GLN 571 (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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483B ALA* 4.1 6.1 - - + -
484B LYS 4.1 7.1 + - - +
485B PRO* 3.5 35.2 - - + +
486B LYS 4.1 4.2 + - - -
567B GLN 3.1 18.5 + - - +
568B TYR 3.6 3.4 - - - +
570B VAL* 1.3 74.2 - - - +
572B TRP* 1.3 53.2 + - - +
574B ALA* 2.7 26.2 + - - +
575B ASP* 2.8 47.6 + - - +
591B ILE* 3.4 15.3 - - + +
594B GLN* 2.9 43.8 + - - +
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Residues in contact with TRP 572 (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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460B THR* 4.3 0.9 - - + -
476B LEU* 4.0 24.2 - - + -
479B GLU* 3.3 43.9 + - + +
480B VAL* 3.6 26.5 - - + -
483B ALA* 4.1 5.1 - - + +
500B VAL* 4.5 8.3 - - + -
550B ILE* 3.9 23.1 - - + -
552B VAL* 4.0 17.9 - - + -
568B TYR 2.9 18.5 + - - +
569B PHE* 3.4 22.9 - + - +
571B GLN* 1.3 76.3 - - - +
573B CYS* 1.3 62.6 + - - +
575B ASP* 3.5 12.1 + - + +
576B ARG* 3.1 37.0 + - + +
578B PHE* 3.6 29.4 - + - -
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Residues in contact with CYS 573 (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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460B THR* 3.7 21.5 - - - -
569B PHE* 3.0 50.4 + - - -
570B VAL 3.6 8.7 - - - +
571B GLN 3.0 0.2 + - - -
572B TRP* 1.3 75.0 - - - +
574B ALA* 1.3 63.4 + - - +
576B ARG 3.5 0.7 + - - -
577B ASN* 3.3 3.1 + - - -
578B PHE* 2.9 38.3 + - + +
579B THR 4.2 6.5 - - - +
581B PRO* 4.0 9.9 - - + -
598B TRP* 4.0 15.0 - - + -
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Residues in contact with ALA 574 (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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570B VAL 3.3 5.6 + - - +
571B GLN* 2.7 14.9 + - - +
573B CYS* 1.3 74.6 - - - +
575B ASP* 1.3 62.7 + - - +
577B ASN* 3.3 4.9 + - - +
594B GLN* 3.9 24.0 - - - +
595B LYS* 3.3 44.3 - - + +
598B TRP* 3.7 17.9 - - + -
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Residues in contact with ASP 575 (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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483B ALA* 3.7 27.5 - - - +
484B LYS 4.6 1.6 + - - -
571B GLN* 2.8 42.1 + - - +
572B TRP* 3.7 12.5 - - + +
573B CYS 3.3 0.2 - - - -
574B ALA* 1.3 73.3 - - - +
576B ARG* 1.3 62.2 + - + +
577B ASN* 3.7 0.7 + - - +
594B GLN* 4.9 0.2 - - - +
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Residues in contact with ARG 576 (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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466B ILE* 4.7 19.7 - - - +
468B ILE* 5.0 11.4 - - - +
472B ASP* 5.7 4.9 + - - +
476B LEU* 4.4 10.1 - - - +
479B GLU* 2.6 37.1 + - - -
572B TRP* 3.1 34.1 + - + +
573B CYS 3.5 0.4 + - - -
574B ALA 3.2 0.2 - - - -
575B ASP* 1.3 78.2 - - + +
577B ASN* 1.3 69.4 + - - +
578B PHE* 3.2 52.0 + - + -
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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