Contacts of the helix formed by residues 587 - 596 (chain U) in PDB entry 6QX2
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 587 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64R TYR* 5.6 1.8 + - - -
106R GLY 4.4 8.7 + - - +
107R GLN* 3.1 21.5 + - - +
108R GLY* 2.7 40.4 + - - +
442U SER* 5.1 0.4 - - - -
586U MET* 1.3 76.2 - - - +
588U ALA* 1.3 58.2 + - - +
589U ASP* 3.1 19.6 + - - +
590U GLN* 2.8 39.1 + - - +
591U LEU* 3.1 12.4 + - - +
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Residues in contact with ALA 588 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298R LEU* 3.3 25.6 - - + -
442U SER* 3.2 32.9 - - - +
445U SER* 3.5 12.6 - - - -
446U GLY* 3.6 5.7 - - - +
586U MET 4.3 0.2 + - - -
587U ASN* 1.3 70.1 - - - +
589U ASP* 1.3 65.6 + - - +
591U LEU* 3.4 4.5 + - - +
592U TRP* 3.0 26.5 + - - +
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Residues in contact with ASP 589 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298R LEU* 3.9 13.4 - - + +
587U ASN* 3.1 25.9 + - - +
588U ALA* 1.3 74.1 - - - +
590U GLN* 1.3 78.2 + - - +
592U TRP* 3.7 7.2 + - - +
593U GLU* 3.4 28.1 + - - +
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Residues in contact with GLN 590 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R GLN* 3.1 16.1 + - - +
580U TYR* 3.7 17.6 + - - +
586U MET* 3.7 17.1 - - + -
587U ASN* 2.8 62.7 + - - +
589U ASP* 1.3 86.4 + - - +
591U LEU* 1.3 62.5 + - - +
592U TRP 3.3 0.4 - - - -
593U GLU* 3.4 4.5 + - - +
594U THR* 2.9 37.6 + - + +
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Residues in contact with LEU 591 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442U SER* 3.8 17.7 - - - +
443U THR* 3.6 40.8 - - - +
446U GLY* 5.8 0.2 - - - -
506U MET* 4.7 7.4 - - + -
583U LEU* 3.9 35.7 - - + +
586U MET* 4.0 20.6 - - + -
587U ASN 3.1 17.4 + - - +
588U ALA 3.6 4.7 - - - +
590U GLN* 1.3 74.2 - - - +
592U TRP* 1.3 63.3 + - - +
594U THR* 4.1 0.7 - - - -
595U THR* 3.3 36.8 + - - +
596U MET* 3.5 12.8 + - - +
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Residues in contact with TRP 592 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298R LEU* 6.1 0.4 - - + -
299R ARG* 6.1 3.5 - - + +
446U GLY* 3.2 29.1 - - - +
447U ARG 4.2 0.2 - - - -
448U ASP* 3.6 24.7 - - + -
452U GLN* 3.4 22.9 - - - -
588U ALA 3.0 17.5 + - - +
589U ASP* 3.7 6.3 - - - +
591U LEU* 1.3 75.4 - - - +
593U GLU* 1.3 93.2 + - + +
596U MET* 3.1 31.7 + - + -
597U ASN* 2.8 62.1 + - + +
598U PRO* 4.1 7.2 - - + -
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Residues in contact with GLU 593 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589U ASP 3.4 16.4 + - - +
590U GLN* 3.4 6.4 + - - +
592U TRP* 1.3 103.2 + - + +
594U THR* 1.3 62.8 + - + +
597U ASN* 3.1 23.9 + - - +
600U HIS* 3.2 42.6 + - - +
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Residues in contact with THR 594 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541U GLN 4.9 4.9 - - - +
543U PRO* 3.6 31.4 - - + +
586U MET* 4.0 3.6 - - + +
590U GLN* 2.9 23.3 + - + +
591U LEU 3.8 1.0 + - - -
592U TRP 4.3 0.2 - - - -
593U GLU* 1.3 81.7 - - + +
595U THR* 1.3 76.2 + - - +
600U HIS 4.2 3.4 - - - +
601U ARG* 3.6 17.4 - - - -
602U ALA* 4.5 2.9 + - - +
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Residues in contact with THR 595 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432U PHE* 4.6 4.5 - - - -
506U MET* 3.5 29.4 - - + -
540U ALA* 3.9 14.1 - - + +
541U GLN 4.4 3.6 - - - +
542U PRO* 3.8 31.4 - - + +
543U PRO* 3.8 1.0 - - - +
591U LEU* 3.3 21.6 + - + +
594U THR* 1.3 93.2 + - - +
596U MET* 1.3 58.9 + - - +
601U ARG* 3.4 19.1 - - - +
602U ALA 5.3 0.6 + - - +
603U LEU* 4.1 10.9 - - - +
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Residues in contact with MET 596 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432U PHE* 4.0 33.0 - - + -
443U THR* 3.6 43.1 - - + +
446U GLY* 4.6 3.4 - - - -
447U ARG* 3.6 29.4 - - + -
452U GLN* 2.8 34.8 + - - +
454U ILE* 4.7 0.4 - - + -
506U MET* 4.4 11.4 - - - -
591U LEU* 3.7 19.1 - - + +
592U TRP* 3.1 19.4 + - + +
595U THR* 1.3 78.8 - - - +
597U ASN* 1.3 62.2 + - - +
598U PRO* 3.4 1.9 - - - +
601U ARG* 3.1 13.5 + - - +
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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