Contacts of the helix formed by residues 599 - 610 (chain B) in PDB entry 2QY0
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 ASN 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570B LEU* 3.6 30.8 - - + +
598B ALA* 1.3 72.5 - - - +
600B PRO* 1.3 71.0 - - - +
601B GLN* 3.0 29.9 + - - +
602B ALA* 2.9 27.9 + - + +
603B CYS* 3.0 13.0 + - - -
622B CYS* 4.2 0.4 - - - -
667B TYR* 5.3 0.6 - - - -
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Residues in contact with PRO 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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570B LEU* 6.4 0.4 - - + -
598B ALA 3.2 10.5 - - - +
599B ASN* 1.3 90.2 - - - +
601B GLN* 1.3 56.3 + - - +
603B CYS 3.8 0.2 - - - -
604B GLU* 3.0 32.8 + - + +
616B PHE* 3.6 19.6 - - + -
621B PHE* 6.2 1.1 - - - -
622B CYS* 3.9 13.0 - - - +
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Residues in contact with GLN 601 (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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599B ASN* 3.0 18.7 + - - +
600B PRO* 1.3 78.9 - - - +
602B ALA* 1.3 59.7 + - - +
604B GLU* 3.5 8.1 + - - +
605B ASN* 3.0 25.0 + - + +
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Residues in contact with ALA 602 (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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599B ASN* 2.9 22.5 + - + +
601B GLN* 1.3 78.0 - - - +
603B CYS* 1.3 61.7 + - - +
605B ASN* 3.2 10.0 + - + +
606B TRP* 3.0 28.9 + - - +
667B TYR* 3.6 22.9 - - - +
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Residues in contact with CYS 603 (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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598B ALA* 4.0 0.4 - - - -
599B ASN 3.0 11.4 + - - -
600B PRO 3.7 5.4 - - - +
602B ALA* 1.3 74.0 - - - +
604B GLU* 1.3 66.1 + - - +
606B TRP* 3.3 4.7 + - - +
607B LEU* 3.2 28.8 + - - +
616B PHE* 3.9 9.4 - - + -
622B CYS* 2.1 52.5 - - + -
667B TYR* 3.5 32.8 - - - -
669B PHE* 4.3 8.7 - - + -
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Residues in contact with GLU 604 (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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600B PRO 3.0 18.3 + - - +
601B GLN* 3.5 11.9 - - - +
602B ALA 3.3 0.2 - - - -
603B CYS* 1.3 77.9 - - - +
605B ASN* 1.3 56.4 + - - +
607B LEU* 3.4 10.7 + - - +
608B ARG* 2.8 32.1 + - - +
616B PHE* 3.3 38.1 - - + +
804B GOL 5.7 3.5 + - - -
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Residues in contact with ASN 605 (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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601B GLN* 3.0 16.5 + - + +
602B ALA* 3.2 13.9 + - - +
604B GLU* 1.3 75.9 - - - +
606B TRP* 1.3 59.8 + - - +
608B ARG* 3.3 34.1 + - - +
609B GLY* 2.9 23.7 + - - -
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Residues in contact with TRP 606 (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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602B ALA 3.0 15.9 + - - +
603B CYS 3.5 6.7 - - - +
605B ASN* 1.3 79.3 - - - +
607B LEU* 1.3 75.7 + - + +
609B GLY* 3.2 9.9 + - - -
610B LYS* 3.3 45.2 + - + +
626B PRO* 4.1 21.9 - - + +
661B ILE* 4.1 37.2 - - + -
665B ARG 4.7 2.8 + - - -
666B GLY* 3.5 22.0 - - - -
667B TYR* 3.6 50.0 - + + -
669B PHE* 4.0 13.7 - + - -
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Residues in contact with LEU 607 (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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603B CYS 3.2 14.3 + - - +
604B GLU* 3.7 14.4 - - - +
606B TRP* 1.3 86.1 - - + +
608B ARG* 1.3 66.3 + - - +
609B GLY 3.0 2.0 - - - -
610B LYS* 2.9 14.0 + - - +
611B ASN 3.1 9.5 + - - -
612B ARG* 3.2 32.1 + - + +
614B ASP* 4.7 10.1 - - + +
616B PHE* 4.4 14.6 - - + -
659B TRP* 4.1 23.8 - - + -
661B ILE* 4.0 26.2 - - + -
669B PHE* 4.0 18.6 - - + -
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Residues in contact with ARG 608 (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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604B GLU* 2.8 23.3 + - - +
605B ASN* 3.3 30.0 + - - +
607B LEU* 1.3 72.8 - - - +
609B GLY* 1.3 61.3 + - - +
611B ASN* 3.3 17.9 + - - +
612B ARG 5.2 2.2 - - - +
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Residues in contact with GLY 609 (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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605B ASN 2.9 14.7 + - - -
606B TRP* 3.2 7.2 + - - -
607B LEU 3.0 0.8 - - - -
608B ARG* 1.3 78.6 - - - +
610B LYS* 1.3 57.3 + - - +
611B ASN* 3.8 7.1 + - - -
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Residues in contact with LYS 610 (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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606B TRP* 3.3 48.7 + - + +
607B LEU* 2.9 5.1 + - - +
609B GLY* 1.3 77.5 - - - +
611B ASN* 1.3 71.8 + - - +
612B ARG* 3.2 20.1 + - + +
661B ILE* 3.9 31.9 - - + +
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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