Contacts of the helix formed by residues 583 - 600 (chain B) in PDB entry 2XWU
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 LYS 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544B SER* 4.4 5.5 + - - +
581B ILE 5.8 0.7 - - - +
582B HIS* 1.3 74.0 - - - +
584B THR* 1.3 68.3 + - - +
585B SER* 3.2 1.8 - - - +
586B GLN* 2.8 31.6 + - - +
587B CYS* 3.1 8.0 + - - -
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Residues in contact with THR 584 (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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582B HIS 3.8 1.4 + - - -
583B LYS* 1.3 71.9 - - - +
585B SER* 1.3 65.3 + - - +
587B CYS* 2.9 14.3 + - - +
588B MET* 3.1 23.7 + - + +
639B HIS* 2.8 41.3 + - + +
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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
----------------------------------------------------------
583B LYS* 2.9 4.1 + - - +
584B THR* 1.3 80.8 - - - +
586B GLN* 1.3 76.2 + - - +
588B MET* 3.4 12.2 + - - +
589B TRP* 3.1 31.7 + - - -
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Residues in contact with GLN 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B SER* 3.5 26.5 - - - +
545B VAL* 3.1 35.3 - - + +
548B VAL* 3.5 15.2 - - + +
582B HIS* 4.2 7.8 - - + +
583B LYS* 2.8 26.5 + - - +
585B SER* 1.3 80.0 - - - +
587B CYS* 1.3 64.2 + - - +
588B MET 3.2 2.0 - - - -
589B TRP* 3.8 32.1 - - + -
590B LEU* 3.1 20.4 + - - +
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Residues in contact with CYS 587 (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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577B LEU* 4.2 22.0 - - + +
582B HIS* 3.3 32.3 - - - -
583B LYS 3.1 7.1 + - - -
584B THR* 2.9 9.7 + - - +
586B GLN* 1.3 77.6 - - - +
588B MET* 1.3 59.8 + - + +
590B LEU* 3.4 7.2 + - - +
591B MET* 3.1 31.0 + - - +
639B HIS* 3.6 30.3 - - + -
643B LEU* 3.9 9.8 - - + +
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Residues in contact with MET 588 (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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584B THR* 3.3 30.1 - - + +
585B SER* 3.6 10.3 - - - +
586B GLN 3.2 0.2 - - - -
587B CYS* 1.3 77.0 - - - +
589B TRP* 1.3 66.0 + - + +
591B MET* 3.3 5.4 + - - +
592B GLN* 3.0 28.6 + - - +
639B HIS* 3.5 28.7 - - + +
642B GLY* 3.4 18.2 - - - -
643B LEU* 3.1 33.7 - - + -
646B ASN* 3.1 37.8 - - - +
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Residues in contact with TRP 589 (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 VAL* 3.7 31.6 - - + -
548B VAL* 3.5 27.1 - - + +
549B SER* 4.3 15.5 - - - -
552B LYS* 4.3 24.6 - - + +
585B SER* 3.1 28.3 + - - -
586B GLN* 3.7 31.0 - - + +
587B CYS 3.3 0.4 - - - -
588B MET* 1.3 76.9 - - + +
590B LEU* 1.3 62.0 + - - +
592B GLN* 3.1 14.9 + - - +
593B ALA* 2.8 28.6 + - - +
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Residues in contact with LEU 590 (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 LEU* 4.4 16.4 - - + -
548B VAL* 3.6 11.2 - - + +
551B LEU* 5.0 8.1 - - + -
573B SER* 3.6 29.2 - - - +
576B VAL* 4.4 4.0 - - + -
577B LEU* 4.2 25.8 - - + -
582B HIS* 4.1 28.5 - - + +
586B GLN 3.1 14.0 + - - +
587B CYS* 3.5 6.1 - - - +
589B TRP* 1.3 80.0 - - - +
591B MET* 1.3 59.3 + - - +
593B ALA* 3.2 7.4 + - - +
594B LEU* 2.9 36.9 + - + +
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Residues in contact with MET 591 (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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577B LEU* 4.5 16.4 - - - -
587B CYS 3.1 19.6 + - - +
588B MET* 3.6 7.6 - - - +
589B TRP 3.2 0.2 - - - -
590B LEU* 1.3 75.8 - - - +
592B GLN* 1.3 59.5 + - - +
594B LEU* 3.2 18.5 + - + +
595B GLY* 2.9 22.2 + - - -
613B LEU* 4.5 11.0 - - + -
614B ILE* 6.3 0.7 - - + -
617B TYR* 6.1 1.1 - - - -
643B LEU* 3.6 49.8 - - + +
644B LEU* 5.7 1.3 - - + -
646B ASN* 4.1 6.3 - - + -
647B LEU* 3.5 53.0 - - + +
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Residues in contact with GLN 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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552B LYS* 2.4 40.0 + - - +
588B MET* 3.0 15.4 + - - +
589B TRP* 3.1 13.3 + - - +
591B MET* 1.3 72.5 - - - +
593B ALA* 1.3 68.5 - - - +
595B GLY 3.0 2.8 + - - -
596B PHE* 3.3 9.5 + - - -
646B ASN* 2.7 38.9 + - - +
649B THR* 5.3 5.9 - - - +
650B THR* 2.8 41.3 + - + +
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Residues in contact with ALA 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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548B VAL* 5.3 0.7 - - + +
551B LEU* 4.4 10.8 - - + +
552B LYS* 3.8 28.0 - - + +
555B CYS* 3.5 22.4 - - + +
589B TRP 2.8 13.6 + - - +
590B LEU* 3.3 14.6 - - - +
592B GLN* 1.3 80.0 - - - +
594B LEU* 1.3 63.6 + - + +
596B PHE* 3.2 10.5 + - - +
597B LEU 3.2 16.1 + - - -
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Residues in contact with LEU 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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551B LEU* 6.0 1.1 - - + -
555B CYS* 6.0 0.7 - - - -
569B ILE* 4.5 4.9 - - + -
570B VAL* 4.3 14.6 - - + -
573B SER* 3.7 22.9 - - - +
590B LEU* 2.9 35.7 + - + +
591B MET* 3.6 14.6 - - - +
592B GLN 3.2 0.2 - - - -
593B ALA* 1.3 74.9 - - + +
595B GLY* 1.3 65.6 + - - +
597B LEU* 3.6 22.8 - - + +
598B LEU* 2.9 30.6 + - + +
613B LEU* 3.4 40.8 - - + -
647B LEU* 4.2 7.6 - - + -
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Residues in contact with GLY 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 MET 2.9 10.7 + - - -
592B GLN 3.0 1.0 + - - -
594B LEU* 1.3 77.7 - - - +
596B PHE* 1.3 60.7 + - - +
598B LEU* 5.0 0.4 - - - -
599B SER* 3.0 23.6 + - - -
647B LEU* 3.8 17.7 - - - +
650B THR* 3.0 23.6 - - - -
651B LEU* 3.6 13.2 - - - +
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Residues in contact with PHE 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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552B LYS* 4.3 22.7 - - + -
555B CYS 3.3 16.4 - - - +
556B ARG* 3.6 55.0 - - + -
559B LYS* 3.8 27.6 - - + +
592B GLN 3.3 14.8 + - - -
593B ALA* 3.2 8.7 + - - +
595B GLY* 1.3 74.0 - - - +
597B LEU* 1.3 65.9 + - - +
599B SER* 2.5 25.4 + - - -
600B ALA 3.7 1.6 + - - -
650B THR* 3.5 37.7 + - + -
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Residues in contact with LEU 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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555B CYS* 4.2 11.8 + - - -
559B LYS* 4.7 6.9 - - - +
562B LEU* 3.8 31.0 - - + +
566B ALA* 3.8 18.2 - - + +
569B ILE* 3.7 38.6 - - + -
570B VAL* 3.6 31.4 - - + -
593B ALA 3.2 9.5 + - - +
594B LEU* 3.4 13.7 + - + +
596B PHE* 1.3 81.5 - - - +
598B LEU* 1.3 62.6 + - + +
600B ALA* 3.4 6.9 + - - +
601B LEU* 3.0 23.7 - - - +
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Residues in contact with LEU 598 (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* 4.1 23.3 - - + -
594B LEU* 2.9 26.6 + - + +
597B LEU* 1.3 75.3 - - + +
599B SER* 1.3 62.8 + - - +
600B ALA 2.9 7.0 + - - -
601B LEU* 3.0 32.8 + - + +
606B ILE* 3.2 32.3 - - + +
609B ASN* 4.0 24.0 - - + +
610B LEU* 4.5 14.6 - - + -
613B LEU* 4.3 20.0 - - + -
647B LEU* 5.4 1.8 - - + -
651B LEU* 3.9 16.2 - - + -
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Residues in contact with SER 599 (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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559B LYS* 3.5 19.6 + - - +
560B TYR* 5.5 2.4 - - - -
595B GLY 3.0 12.6 + - - -
596B PHE* 2.5 23.6 + - - -
598B LEU* 1.3 77.4 - - - +
600B ALA* 1.3 57.2 + - - +
601B LEU 3.5 3.3 + - - +
606B ILE* 4.6 3.7 - - - +
650B THR 4.4 2.0 + - - -
651B LEU* 3.5 14.3 - - - +
652B ASP* 4.0 29.0 - - - +
653B ILE* 4.8 12.3 - - - +
655B HIS 5.8 0.7 - - - -
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Residues in contact with ALA 600 (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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559B LYS* 3.3 41.5 - - + +
560B TYR* 4.1 20.2 - - + -
563B PRO* 4.2 11.7 - - + +
597B LEU 3.4 9.3 + - - +
598B LEU 2.9 1.6 - - - -
599B SER* 1.3 80.0 + - - +
601B LEU* 1.3 64.5 + - + +
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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