Contacts of the helix formed by residues 599 - 609 (chain A) 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 CYS 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A ARG* 4.3 10.3 - - - -
596A SER 4.0 0.5 - - - +
597A ALA 3.5 1.0 - - - -
598A HIS* 1.3 82.6 - - - +
600A THR* 1.3 64.1 + - - +
601A GLU* 3.4 23.3 - - - +
602A ASN* 3.3 41.5 + - - +
603A LYS* 3.6 22.4 + - - +
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Residues in contact with THR 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A CYS* 1.3 73.1 - - - +
601A GLU* 1.3 65.0 + - - +
603A LYS* 3.1 16.3 + - + +
604A ALA* 3.0 26.8 + - + +
645A LEU* 4.4 24.7 - - + -
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Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A ARG* 2.9 40.6 + - - +
599A CYS* 3.4 20.0 - - - +
600A THR* 1.3 79.5 + - - +
602A ASN* 1.3 63.6 + - - +
604A ALA* 3.2 7.9 + - - +
605A ASP* 2.9 27.7 + - - +
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Residues in contact with ASN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A LYS 5.5 1.0 + - - -
564A ARG* 3.6 26.0 + - - +
569A VAL* 3.4 40.2 - - + +
595A LEU* 2.9 34.9 + - - +
596A SER* 4.6 2.5 - - - -
598A HIS* 3.6 19.2 + - - +
599A CYS* 3.3 23.7 - - - +
600A THR 3.3 0.2 - - - -
601A GLU* 1.3 74.5 - - - +
603A LYS* 1.3 57.5 + - - +
605A ASP* 3.4 3.7 + - - +
606A ILE* 3.1 27.4 + - - +
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Residues in contact with LYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A SER 3.1 28.3 - - - +
597A ALA* 4.6 10.3 + - - +
599A CYS 3.6 14.6 - - - +
600A THR* 3.1 16.9 + - + +
602A ASN* 1.3 72.5 - - - +
604A ALA* 1.3 60.4 + - - +
606A ILE* 3.4 4.0 + - - +
607A CYS* 3.0 33.6 + - - -
641A ASN* 2.7 31.5 + - - +
642A VAL* 3.8 24.2 - - + -
644A SER* 3.2 17.7 + - - +
645A LEU* 3.8 15.0 - - + -
379B SER* 5.9 4.8 - - - -
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Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A THR* 3.0 13.1 + - + +
601A GLU* 3.2 11.4 + - - +
603A LYS* 1.3 77.7 - - - +
605A ASP* 1.3 52.8 + - - +
607A CYS* 3.2 3.9 + - - +
608A ALA* 2.8 36.5 + - - +
645A LEU* 3.4 20.8 - - + +
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Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A ARG* 3.1 29.3 + - - +
569A VAL* 4.2 16.1 - - + +
570A LYS* 4.9 16.5 + - + +
601A GLU 2.9 15.4 + - - +
602A ASN* 3.6 10.8 - - - +
603A LYS 3.3 0.2 - - - -
604A ALA* 1.3 76.2 - - - +
606A ILE* 1.3 64.6 + - - +
608A ALA* 3.3 15.2 + - - +
609A VAL* 3.3 19.0 + - - +
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A VAL* 3.4 23.1 - - + -
573A MET* 3.8 27.4 - - + -
592A LEU* 4.1 21.1 - - + -
596A SER* 3.5 33.9 - - - +
602A ASN 3.1 16.3 + - - +
603A LYS 3.6 5.8 - - - +
604A ALA 3.3 0.2 - - - -
605A ASP* 1.3 73.9 - - - +
607A CYS* 1.3 65.0 + - - +
608A ALA 3.2 0.5 + - - -
609A VAL* 3.3 6.6 + - - +
612A ALA* 3.2 25.9 - - + +
613A LEU* 5.3 0.4 - - + -
616A LEU* 4.1 20.4 - - + -
638A ILE* 4.3 2.9 - - + -
642A VAL* 3.9 14.8 - - + -
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Residues in contact with CYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A LYS 3.0 22.9 + - - +
604A ALA* 3.7 6.1 - - - +
606A ILE* 1.3 76.4 - - - +
608A ALA* 1.3 60.7 + - - +
609A VAL 3.6 5.9 + - - +
613A LEU* 4.0 27.8 - - + +
642A VAL* 3.9 25.4 - - - -
645A LEU* 4.5 10.1 - - + -
646A ILE* 4.1 13.0 - - - -
652A HIS* 3.8 34.1 + - + +
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Residues in contact with ALA 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A ALA 2.8 20.9 + - - +
605A ASP* 3.6 11.2 - - - +
606A ILE 3.2 0.4 - - - -
607A CYS* 1.3 72.7 - - - +
609A VAL* 1.3 65.0 + - + +
610A ASP* 3.2 4.2 + - - -
652A HIS* 6.0 0.2 - - - -
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A LYS* 4.3 27.1 - - + +
573A MET* 3.9 28.7 - - + -
574A GLU* 4.2 17.7 - - + +
577A LEU* 3.8 26.2 - - + -
605A ASP 3.4 16.4 - - - +
606A ILE 3.3 7.4 + - - +
607A CYS 4.0 4.7 - - - +
608A ALA* 1.3 75.7 - - - +
610A ASP* 1.3 69.6 + - - +
611A GLY 3.1 0.7 + - - -
612A ALA* 3.0 19.2 + - + +
613A LEU 4.8 0.3 + - - -
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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