Contacts of the helix formed by residues 567 - 579 (chain C) in PDB entry 3QHE
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 567 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530C VAL* 4.2 2.5 - - - +
564C ARG 3.0 13.8 + - - -
565C GLU 3.1 2.4 + - - -
566C VAL* 1.3 79.5 - - - +
568C SER* 1.3 65.6 + - - +
569C VAL 3.2 3.8 + - - -
570C LYS* 3.6 6.5 + - - +
571C ALA* 3.2 23.6 + - - +
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Residues in contact with SER 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C VAL* 3.9 14.7 - - - +
548C LEU* 4.4 7.7 - - - +
563C LEU* 2.8 37.5 + - - +
564C ARG 4.4 0.2 + - - -
566C VAL* 3.4 12.7 + - - +
567C GLY* 1.3 75.4 - - - +
569C VAL* 1.3 63.8 + - - +
571C ALA* 3.9 1.7 - - - +
572C LEU* 3.0 35.7 + - - +
595C LEU* 3.9 22.2 - - - -
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Residues in contact with VAL 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C ARG* 5.3 6.2 + - - -
567C GLY 3.2 1.2 - - - -
568C SER* 1.3 78.9 - - - +
570C LYS* 1.3 59.5 + - - +
572C LEU 3.4 0.2 + - - -
573C MET* 3.0 27.7 + - - +
592C LEU* 3.7 9.5 - - + +
595C LEU* 4.2 21.3 - - + -
602C ASN* 3.5 46.7 - - + +
605C ASP* 4.1 16.6 - - + +
606C ILE* 3.5 34.3 - - + +
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Residues in contact with LYS 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C GLY* 3.6 7.4 + - - +
568C SER 3.5 0.2 - - - -
569C VAL* 1.3 77.3 - - - +
571C ALA* 1.3 61.6 + - - +
573C MET* 3.3 4.9 + - - +
574C GLU* 2.8 62.8 + - - +
605C ASP* 5.0 11.1 - - + +
609C VAL* 3.9 20.0 - - + -
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Residues in contact with ALA 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C VAL* 3.8 18.8 - - + +
533C LEU* 3.7 24.3 - - + +
534C LYS* 6.0 7.4 - - + +
567C GLY 3.2 17.9 + - - +
568C SER 3.9 1.3 - - - +
570C LYS* 1.3 79.3 - - - +
572C LEU* 1.3 56.7 + - - +
574C GLU* 3.4 8.7 + - - +
575C CYS* 2.8 30.5 + - - +
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Residues in contact with LEU 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C LEU* 3.8 30.7 - - + -
545C ALA* 4.1 20.4 - - + -
548C LEU* 4.1 15.9 - - + -
568C SER* 3.0 17.8 + - - +
571C ALA* 1.3 75.3 - - - +
573C MET* 1.3 57.8 + - - +
575C CYS* 3.3 3.9 - - - +
576C ALA* 2.8 25.8 + - - +
588C VAL* 3.3 24.8 - - + +
591C ALA* 3.7 21.5 - - + -
592C LEU* 3.7 13.2 - - + +
595C LEU* 3.4 32.8 - - + -
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Residues in contact with MET 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C VAL 3.0 18.5 + - - +
570C LYS* 3.8 3.6 - - - +
572C LEU* 1.3 76.2 - - - +
574C GLU* 1.3 62.9 + - - +
576C ALA* 3.3 27.4 + - + +
577C LEU* 3.4 12.9 + - + +
592C LEU* 3.5 27.9 - - + +
606C ILE* 3.9 21.5 - - + +
609C VAL* 4.0 19.1 - - + -
612C ALA* 3.7 35.2 - - + -
615C PHE* 4.0 19.3 - - + -
616C LEU* 4.4 10.5 - - + -
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Residues in contact with GLU 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C LYS* 4.6 18.9 + - - -
570C LYS* 2.8 53.4 + - + +
571C ALA* 3.7 5.6 - - - +
573C MET* 1.3 68.5 - - - +
575C CYS* 1.3 66.7 + - - +
577C LEU* 3.3 24.7 + - + +
578C GLU* 3.7 12.3 + - - +
609C VAL* 4.0 19.5 - - + +
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Residues in contact with CYS 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C LEU* 4.0 29.2 - - + +
541C GLN* 3.6 26.2 - - - +
571C ALA 2.8 19.0 + - - +
572C LEU* 3.3 9.6 - - - +
574C GLU* 1.3 72.2 - - - +
576C ALA* 1.3 65.1 + - - +
578C GLU* 3.0 15.4 + - - +
579C VAL* 3.0 18.3 + - - +
588C VAL* 3.8 24.2 - - - -
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Residues in contact with ALA 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C LEU 2.8 16.1 + - - +
573C MET* 3.3 28.7 + - + +
575C CYS* 1.3 73.0 - - - +
577C LEU* 1.3 61.2 + - - +
578C GLU 3.3 0.9 + - - -
579C VAL* 3.4 19.7 + - - +
585C LEU* 3.9 4.0 - - + +
588C VAL* 3.7 18.2 - - + -
589C LEU* 4.2 9.0 - - + -
592C LEU* 5.2 0.7 - - + -
615C PHE* 3.5 26.4 - - + -
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Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C MET* 3.4 19.3 - - + +
574C GLU* 3.3 12.5 + - + +
575C CYS 3.1 1.0 + - - -
576C ALA* 1.3 76.8 - - - +
578C GLU* 1.3 68.8 + - + +
579C VAL 4.7 1.9 - - - +
609C VAL* 4.1 17.0 - - + -
610C ASP 3.6 22.4 - - - +
611C GLY* 4.0 9.9 - - - +
612C ALA* 4.2 1.6 - - - -
615C PHE* 3.6 46.4 - - + -
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Residues in contact with GLU 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C GLU* 4.2 2.3 - - - +
574C GLU 3.9 11.9 - - - +
575C CYS* 3.0 7.8 + - - +
577C LEU* 1.3 84.4 - - + +
579C VAL* 1.3 66.6 + - - +
580C LYS* 3.5 12.5 + - - +
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Residues in contact with VAL 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C GLU* 3.8 5.6 - - - +
541C GLN* 4.1 5.6 - - - +
575C CYS* 3.0 41.7 + - - +
576C ALA* 3.4 16.5 + - - +
577C LEU 4.7 1.9 - - - +
578C GLU* 1.3 78.1 - - - +
580C LYS* 1.3 62.9 + - - +
581C LYS 3.4 23.3 - - - +
584C THR* 3.6 20.4 - - + -
585C LEU* 3.5 25.9 - - + +
588C VAL* 4.6 4.7 - - + -
615C PHE* 6.0 1.4 - - - -
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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