Contacts of the helix formed by residues 574 - 590 (chain B) in PDB entry 1QCO
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 574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571B MET 3.6 1.2 + - - -
572B GLY 3.3 4.2 - - - -
573B LEU* 1.3 79.5 - - - +
575B GLN* 1.3 66.2 + - - -
576B ALA 3.4 2.0 - - - -
577B ALA* 3.1 13.2 + - - +
578B TRP* 3.2 29.6 + - - +
708B PRO* 3.5 22.2 - - - -
723B GLU 5.3 0.2 - - - -
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Residues in contact with GLN 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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574B GLY* 1.3 69.6 - - - -
576B ALA* 1.3 64.0 + - - +
578B TRP* 3.1 29.2 + - + +
579B LYS* 2.8 56.6 + - - +
722B HIS* 3.9 19.8 + - - +
723B GLU* 3.4 43.4 + - - +
1005B NI 4.3 8.1 - - - +
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Residues in contact with ALA 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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554B ALA* 4.1 12.6 - - + +
573B LEU 5.8 1.3 - - - +
574B GLY 3.4 1.2 - - - -
575B GLN* 1.3 78.9 - - - +
577B ALA* 1.3 62.2 + - - +
579B LYS* 3.6 6.1 + - - +
580B GLU* 3.1 24.3 + - - +
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Residues in contact with ALA 577 (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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554B ALA* 3.9 17.8 - - + +
555B LEU* 3.8 22.0 - - + +
570B PHE* 4.5 2.7 - - + -
573B LEU* 3.6 30.2 + - + +
574B GLY 3.1 9.6 + - - +
576B ALA* 1.3 75.8 - - - +
578B TRP* 1.3 63.5 + - + +
580B GLU* 3.7 1.2 - - - +
581B ALA* 2.9 31.5 + - - +
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Residues in contact with TRP 578 (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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519B TYR* 4.4 3.7 + - + -
570B PHE* 3.1 41.1 + + + -
571B MET 3.0 22.0 + - - -
574B GLY* 3.3 16.4 + - - +
575B GLN* 3.1 27.3 + - + +
577B ALA* 1.3 77.3 - - + +
579B LYS* 1.3 63.6 + - + +
581B ALA* 3.3 3.5 + - - +
582B ARG* 3.0 24.3 + - - +
707B GLY* 3.7 10.3 - - - -
708B PRO* 3.7 19.3 - - + -
722B HIS 5.3 0.7 - - - -
723B GLU 3.8 15.9 - - - -
724B HIS 4.5 0.2 - - - -
725B ILE 3.5 20.4 - - - -
726B PHE* 3.4 46.2 - + + -
767B ASP* 5.1 5.6 - - - +
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Residues in contact with LYS 579 (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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575B GLN* 2.8 53.5 + - + +
576B ALA* 4.0 5.2 - - - +
578B TRP* 1.3 74.3 - - + +
580B GLU* 1.3 63.9 + - - +
582B ARG* 3.4 4.1 + - - +
583B ALA* 3.0 24.7 + - - +
767B ASP* 3.3 37.5 + - - +
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Residues in contact with GLU 580 (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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550B PHE 5.3 0.2 - - - -
552B GLY* 3.1 25.5 + - - +
553B PRO* 3.4 14.0 - - - +
554B ALA* 2.9 28.5 + - + +
555B LEU* 3.0 32.0 + - + +
576B ALA 3.1 17.9 + - - +
577B ALA 3.7 3.8 - - - +
578B TRP 3.2 0.2 - - - -
579B LYS* 1.3 74.3 - - - +
581B ALA* 1.3 66.4 + - - +
583B ALA* 3.3 6.7 + - + +
584B SER* 2.9 35.3 + - - +
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Residues in contact with ALA 581 (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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519B TYR* 3.9 7.4 - - + +
550B PHE* 4.0 8.9 - - + -
555B LEU* 3.7 19.0 - - + +
562B PHE* 4.5 6.3 - - + -
570B PHE* 3.7 22.9 - - + -
577B ALA 2.9 16.8 + - - +
578B TRP 3.3 4.0 + - - +
580B GLU* 1.3 76.6 - - - +
582B ARG* 1.3 57.9 + - - +
584B SER* 3.3 2.6 + - - -
585B LEU* 3.0 35.8 + - + +
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Residues in contact with ARG 582 (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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515B GLN* 2.8 30.5 + - - +
516B ASN 2.8 22.8 + - - -
517B LEU* 4.0 10.5 + - + +
519B TYR* 4.1 9.5 + - - +
578B TRP 3.0 16.8 + - - +
579B LYS* 3.7 6.1 - - - +
581B ALA* 1.3 77.0 - - - +
583B ALA* 1.3 56.7 + - - +
585B LEU* 3.3 6.3 + - - +
586B GLN* 2.9 62.0 + - + +
765B PRO* 3.8 17.7 - - - +
767B ASP* 3.7 31.3 + - - +
768B ALA* 3.7 17.6 - - - +
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Residues in contact with ALA 583 (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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579B LYS 3.0 17.3 + - - +
580B GLU* 3.7 7.0 - - + +
582B ARG* 1.3 76.7 - - - +
584B SER* 1.3 63.6 + - - +
586B GLN* 3.4 7.7 + - - +
587B ASN* 3.0 24.6 + - - +
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Residues in contact with SER 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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549B LEU 5.2 3.7 + - - -
550B PHE* 3.7 28.4 - - - -
551B THR 5.5 0.9 + - - -
552B GLY 5.6 1.9 + - - -
580B GLU* 2.9 26.9 + - - +
581B ALA 3.6 4.7 - - - -
583B ALA* 1.3 76.1 - - - +
585B LEU* 1.3 57.2 + - - +
587B ASN* 3.3 5.6 + - - +
588B LEU* 2.8 40.1 + - - +
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Residues in contact with LEU 585 (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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517B LEU* 4.1 16.8 - - + -
519B TYR* 4.1 18.6 - - + +
534B VAL* 3.9 29.4 - - + -
541B LEU* 3.7 29.8 - - + -
543B LEU* 3.9 18.2 - - + -
546B ILE* 4.3 4.9 - - + -
550B PHE* 4.2 15.3 - - + -
581B ALA* 3.0 21.9 + - + +
582B ARG* 3.3 5.8 + - - +
584B SER* 1.3 74.1 - - - +
586B GLN* 1.3 60.2 + - - +
588B LEU* 4.3 4.5 - - + -
589B LEU* 2.8 37.7 + - + +
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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
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514B ILE* 3.1 40.9 + - + +
515B GLN* 4.3 4.9 - - - +
517B LEU* 3.6 15.3 - - + -
582B ARG* 2.9 51.7 + - + +
583B ALA* 3.9 6.9 - - - +
585B LEU* 1.3 75.0 - - - +
587B ASN* 1.3 61.4 + - - +
590B SER* 3.1 22.9 + - - -
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Residues in contact with ASN 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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583B ALA 3.0 17.3 + - - +
584B SER* 3.6 5.4 - - - +
586B GLN* 1.3 77.4 - - - +
588B LEU* 1.3 67.3 + - - +
590B SER* 3.1 14.0 + - - -
593B GLN* 3.0 50.1 + - - +
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Residues in contact with LEU 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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503B PHE* 3.3 17.5 - - - -
541B LEU* 6.0 0.2 - - + -
546B ILE* 4.3 15.9 - - + -
549B LEU* 3.9 36.3 - - + +
550B PHE* 5.5 3.1 - - + -
584B SER* 2.8 27.1 + - - +
585B LEU* 3.7 8.1 - - + +
587B ASN* 1.3 82.0 - - - +
589B LEU* 1.3 60.9 + - + +
590B SER 3.6 1.7 + - - +
593B GLN* 4.3 11.5 - - + +
595B ARG* 4.1 31.2 - - + -
596B LEU* 3.8 24.6 - - + +
597B ARG 4.8 0.9 + - - -
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Residues in contact with LEU 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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502B SER* 2.7 37.1 + - - +
503B PHE* 3.2 15.4 + - + -
504B ILE* 4.8 0.9 - - + -
514B ILE* 4.0 11.4 - - + -
517B LEU* 3.6 31.9 - - + -
534B VAL* 5.2 1.6 - - + -
536B ILE* 4.3 17.3 - - + -
541B LEU* 4.1 23.1 - - + -
585B LEU* 2.8 26.1 + - + +
586B GLN 4.0 0.4 - - - -
588B LEU* 1.3 72.5 - - + +
590B SER* 1.3 63.7 + - - +
596B LEU* 4.4 3.6 - - + -
607B PHE* 3.7 34.3 - - + -
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Residues in contact with SER 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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501B MET 3.8 8.8 + - - -
503B PHE* 3.6 5.5 - - - -
514B ILE* 4.1 4.3 - - - -
586B GLN 3.1 15.0 + - - -
587B ASN* 3.1 21.3 + - - -
589B LEU* 1.3 80.5 - - - +
591B ALA* 1.3 63.1 + - - +
592B SER* 3.1 19.6 + - - -
593B GLN* 3.1 23.6 + - - +
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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