Contacts of the helix formed by residues 577 - 598 (chain B) in PDB entry 6RKU
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 577 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B ALA 4.4 3.8 + - - -
576B ALA* 1.3 76.0 - - - +
578B GLU* 1.3 61.5 + - - -
579B ALA 3.2 3.1 - - - -
580B LEU* 3.2 7.1 + - - +
581B GLU* 2.9 37.8 + - - +
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Residues in contact with GLU 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ALA 4.2 0.2 + - - -
577B GLY* 1.3 69.1 - - - -
579B ALA* 1.3 60.7 + - - +
581B GLU* 3.6 20.4 - - - +
582B LYS* 2.9 31.4 + - - +
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Residues in contact with ALA 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 4.8 14.1 - - + -
576B ALA 4.6 8.5 + - - +
577B GLY 3.2 0.6 - - - -
578B GLU* 1.3 77.9 - - - +
580B LEU* 1.3 56.8 + - - +
582B LYS* 3.3 5.8 + - - +
583B LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 4.7 14.6 - - + -
564B ALA* 5.0 7.4 - - + +
566B LEU* 4.9 11.7 - - + -
575B LEU* 4.7 15.1 - - + +
576B ALA* 4.3 17.5 - - - +
577B GLY 3.2 16.7 + - - +
579B ALA* 1.3 78.0 - - - +
581B GLU* 1.3 63.9 + - + +
583B LEU* 3.3 12.6 + - + -
584B VAL* 2.9 45.5 + - + +
707B ILE* 4.0 26.7 - - + -
719B PHE* 4.4 19.7 - - + -
726B LEU* 6.2 0.4 - - + -
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Residues in contact with GLU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 5.8 1.2 - - - +
561B LEU* 3.9 42.3 - - + +
577B GLY* 2.9 22.9 + - - +
578B GLU* 3.6 24.3 - - - +
579B ALA 3.3 0.2 - - - -
580B LEU* 1.3 77.5 - - + +
582B LYS* 1.3 56.0 + - - +
584B VAL* 3.3 2.6 + - - +
585B SER* 2.9 28.6 + - - -
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Residues in contact with LYS 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B GLU 2.9 17.6 + - - +
579B ALA* 3.8 5.6 - - - +
581B GLU* 1.3 75.7 - - - +
583B LEU* 1.3 57.6 + - - +
585B SER* 2.5 24.9 + - - +
586B GLU* 2.9 25.6 + - + +
696B LYS* 5.7 4.9 - - - +
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 5.5 7.4 - - + -
579B ALA 2.9 18.0 + - - +
580B LEU* 3.6 16.2 - - + +
582B LYS* 1.3 76.8 - - - +
584B VAL* 1.3 57.1 + - - +
586B GLU* 3.3 5.3 + - - +
587B TYR* 2.9 30.1 + - + +
693B LEU* 5.1 5.2 - - + -
696B LYS* 3.6 38.8 - - + +
697B LEU* 4.4 17.5 - - + -
700B LEU* 4.3 26.5 - - + -
719B PHE* 4.3 22.7 - - + -
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 5.2 5.2 - - + -
561B LEU* 4.5 24.5 - - + -
580B LEU* 2.9 39.3 + - + +
581B GLU 3.8 3.6 - - - +
583B LEU* 1.3 75.1 - - - +
585B SER* 1.3 57.4 + - - +
587B TYR* 3.3 6.3 + - - +
588B ASN* 2.9 49.2 + - - +
719B PHE* 4.2 15.3 - - + -
723B LEU* 3.7 24.0 - - + -
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Residues in contact with SER 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 5.7 8.5 - - - +
581B GLU 2.9 12.6 + - - -
582B LYS* 2.5 32.4 + - - +
584B VAL* 1.3 77.4 - - - +
586B GLU* 1.3 57.4 + - - +
588B ASN* 3.3 10.3 + - - +
589B ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LYS* 2.9 18.9 + - + +
583B LEU* 3.8 4.4 - - + +
585B SER* 1.3 81.6 + - - +
587B TYR* 1.3 58.1 + - - +
589B ALA* 3.3 7.4 + - + +
590B THR* 2.9 39.1 + - - +
692B THR* 5.6 1.4 + - - -
693B LEU* 4.7 18.5 - - + +
696B LYS* 3.0 33.1 + - - +
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Residues in contact with TYR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B LEU* 2.9 19.5 + - + +
584B VAL* 3.6 6.5 - - - +
586B GLU* 1.3 76.2 - - - +
588B ASN* 1.3 67.5 + - - +
590B THR* 3.3 5.0 + - - +
591B GLN* 2.9 70.1 + - + +
610B ILE* 4.6 10.1 - - + +
693B LEU* 4.2 20.8 - - + +
697B LEU* 4.4 19.5 - - + -
719B PHE* 4.6 18.8 - + + -
720B GLU* 3.2 40.0 + - + +
723B LEU* 4.4 19.7 - - + -
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Residues in contact with ASN 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 4.2 24.7 - - + +
584B VAL* 2.9 42.2 + - - +
585B SER* 3.3 6.5 + - - +
587B TYR* 1.3 81.1 - - - +
589B ALA* 1.3 60.9 + - - +
591B GLN* 3.3 7.0 + - - +
592B LYS* 2.9 29.8 + - - +
723B LEU* 4.6 11.3 - - - +
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Residues in contact with ALA 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B SER 2.9 17.3 + - - +
586B GLU* 3.6 8.1 - - + +
588B ASN* 1.3 76.4 - - - +
590B THR* 1.3 57.2 + - - +
592B LYS* 3.3 8.7 + - - +
593B MET* 3.0 27.5 + - - +
596B ARG* 5.4 0.2 + - - -
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Residues in contact with THR 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B GLU* 2.9 24.0 + - - +
587B TYR 3.7 2.2 - - - -
589B ALA* 1.3 76.2 - - - +
591B GLN* 1.3 59.6 + - - +
593B MET* 3.2 21.1 + - + +
594B ILE* 2.9 50.5 + - + +
689B ARG* 5.4 3.5 + - + +
690B ILE* 5.1 8.3 - - + -
693B LEU* 3.6 36.5 - - + +
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Residues in contact with GLN 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B TYR* 2.9 68.9 + - + +
588B ASN* 3.7 8.3 - - - +
590B THR* 1.3 78.5 - - - +
592B LYS* 1.3 56.4 + - - +
594B ILE* 3.3 19.7 + - - +
595B ASN* 2.9 44.1 + - - +
607B LYS* 5.5 7.0 - - - +
610B ILE* 3.9 17.6 - - - +
693B LEU* 5.6 0.6 - - - +
720B GLU* 5.2 2.0 + - - +
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Residues in contact with LYS 592 (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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588B ASN 2.9 16.9 + - - +
589B ALA* 3.6 9.2 - - - +
591B GLN* 1.3 77.3 - - - +
593B MET* 1.3 56.9 + - - +
595B ASN* 3.3 10.1 + - + +
596B ARG* 2.9 53.2 + - + +
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Residues in contact with MET 593 (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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589B ALA 3.0 13.0 + - - +
590B THR* 3.2 26.0 + - + +
592B LYS* 1.3 78.2 - - - +
594B ILE* 1.3 57.1 + - + +
596B ARG* 3.2 32.2 + - - +
597B MET* 2.9 51.1 + - + +
686B GLU* 4.3 20.9 - - + +
689B ARG* 3.6 52.9 - - + -
690B ILE* 4.7 3.4 - - + -
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Residues in contact with ILE 594 (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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590B THR* 2.9 40.3 + - + +
591B GLN* 3.7 24.2 - - - +
593B MET* 1.3 74.6 - - + +
595B ASN* 1.3 63.5 + - - +
597B MET* 3.2 19.4 - - + +
598B GLU* 2.9 29.0 + - + +
603B LYS* 5.4 9.2 - - + -
606B LEU* 4.1 42.4 - - + +
607B LYS* 5.7 4.9 - - + +
610B ILE* 5.3 6.7 - - + -
690B ILE* 4.8 14.6 - - + -
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Residues in contact with ASN 595 (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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591B GLN* 2.9 35.8 + - - +
592B LYS* 3.3 9.4 + - + +
594B ILE* 1.3 78.4 - - - +
596B ARG* 1.3 61.9 + - + +
598B GLU* 3.3 20.4 + - - +
599B ARG 4.6 0.9 + - - -
603B LYS* 4.1 21.8 + - - +
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Residues in contact with ARG 596 (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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589B ALA 5.4 0.2 + - - -
592B LYS* 2.9 41.6 + - + +
593B MET* 3.4 39.8 - - - +
595B ASN* 1.3 78.7 - - + +
597B MET* 1.3 61.4 + - - +
598B GLU 3.3 0.9 + - - -
599B ARG* 3.8 13.7 + - - +
686B GLU* 6.0 0.2 + - - -
689B ARG* 5.7 1.0 - - - +
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Residues in contact with MET 597 (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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593B MET* 2.9 49.4 + - + +
594B ILE* 3.2 21.5 - - + +
596B ARG* 1.3 71.9 - - - +
598B GLU* 1.3 64.1 + - - +
599B ARG* 3.0 5.5 + - - -
600B ARG* 3.0 29.8 + - - +
601B TYR* 3.9 3.1 + - - +
606B LEU* 4.3 22.0 - - + +
686B GLU* 3.4 41.5 - - + +
690B ILE* 4.4 16.4 - - + -
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Residues in contact with GLU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ILE* 2.9 14.4 + - + +
595B ASN* 3.3 19.2 - - - +
596B ARG 3.1 1.2 - - - -
597B MET* 1.3 77.7 - - - +
599B ARG* 1.3 65.5 + - - +
600B ARG 3.9 0.2 - - - -
601B TYR 2.8 31.6 + - - +
602B PRO* 5.0 2.1 - - - +
603B LYS* 3.8 41.1 + - + +
606B LEU* 4.7 4.7 - - + -
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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
------------------------------------------------------------
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