Contacts of the helix formed by residues 584 - 594 (chain B) in PDB entry 1QAS
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 PRO 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583B GLY* 1.3 82.6 - - - +
585B GLU* 1.3 71.5 + - - +
587B ASP* 3.5 13.4 - - + +
588B VAL* 2.9 36.0 + - + +
659B GLU* 5.0 2.2 - - - +
661B HIS* 5.6 3.4 - - + -
701B ARG* 3.9 26.7 - - - +
703B MET* 6.2 1.6 - - + -
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Residues in contact with GLU 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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561B ASN* 3.7 33.0 + - + +
562B TYR* 3.2 36.7 - - - +
563B SER* 3.9 7.6 + - - +
564B PRO* 4.1 9.0 - - - +
577B LEU* 4.0 5.7 - - + +
582B PRO 5.2 0.3 - - - +
583B GLY* 2.9 6.0 + - - -
584B PRO* 1.3 93.5 - - - +
586B MET* 1.3 62.1 + - - +
588B VAL* 3.5 1.9 + - - +
589B TYR* 2.9 28.2 + - - +
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Residues in contact with MET 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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335B LYS* 4.6 4.7 - - - +
561B ASN* 3.6 12.3 - - - +
577B LEU* 4.2 11.2 - - - -
578B ASN 4.0 3.1 - - - +
579B PHE* 3.8 52.9 - - + +
581B THR 3.2 28.2 + - - +
582B PRO* 4.9 1.8 - - + -
583B GLY 3.0 9.3 + - - +
585B GLU* 1.3 80.2 - - - +
587B ASP* 1.3 56.7 + - - +
589B TYR* 2.9 10.3 + - - +
590B LEU* 2.7 77.6 + - + +
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Residues in contact with ASP 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 GLY* 2.9 24.2 + - - +
584B PRO* 3.5 9.5 - - - +
586B MET* 1.3 77.4 - - - +
588B VAL* 1.3 63.3 + - - +
590B LEU* 4.2 2.9 - - - +
591B GLY* 3.0 19.4 + - - -
701B ARG* 2.6 28.4 + - - +
715B PHE* 4.2 6.6 - - - -
718B GLN* 3.3 39.3 + - - +
720B THR* 3.4 9.6 + - - -
737B SER 5.0 3.8 - - - +
738B LYS* 4.8 9.0 - - - +
740B GLY* 5.6 2.9 - - - -
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Residues in contact with VAL 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B PRO* 4.6 5.8 - - + -
565B VAL* 3.7 28.9 - - + -
568B TRP* 3.7 6.7 - - + -
584B PRO 2.9 21.4 + - - +
585B GLU* 4.1 2.9 - - - +
587B ASP* 1.3 75.3 - - - +
589B TYR* 1.3 62.9 + - - +
591B GLY* 3.8 0.5 - - - -
592B CYS* 3.1 22.2 + - - +
661B HIS* 3.7 39.0 - - + +
699B LEU* 3.9 18.5 - - + +
701B ARG* 4.1 10.8 - - - -
720B THR* 3.9 9.4 - - + -
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Residues in contact with TYR 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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307B VAL 3.4 8.8 + - - -
308B SER* 3.9 3.8 - - - -
309B SER 2.9 17.8 + - - -
564B PRO* 3.5 27.1 - - + -
568B TRP* 3.7 18.4 + + - -
575B VAL* 2.6 35.5 + - + +
577B LEU* 3.6 15.9 - - + -
579B PHE* 3.8 33.7 - + - -
585B GLU 2.9 18.3 + - - +
586B MET* 2.9 13.9 + - - +
588B VAL* 1.3 77.4 - - - +
590B LEU* 1.3 67.1 + - + +
592B CYS* 3.1 12.3 + - - +
593B PHE* 3.2 39.9 + + - -
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Residues in contact with LEU 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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308B SER* 4.9 3.6 - - - +
335B LYS* 3.8 49.4 - - + +
579B PHE* 4.2 14.4 - - + -
586B MET* 2.7 48.2 + - + +
587B ASP* 4.5 3.4 - - - +
589B TYR* 1.3 74.0 - - + +
591B GLY* 1.3 58.5 + - - +
593B PHE* 3.2 6.8 + - + +
594B GLN* 2.9 45.0 + - - +
736B LEU* 6.4 1.8 - - + -
740B GLY* 5.2 10.5 - - - -
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Residues in contact with GLY 591 (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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587B ASP 3.0 18.7 + - - -
588B VAL 3.8 1.8 - - - -
589B TYR 3.1 0.4 - - - -
590B LEU* 1.3 79.2 - - - +
592B CYS* 1.3 59.4 + - - +
594B GLN* 3.5 18.0 + - - +
699B LEU* 4.2 4.9 - - - -
720B THR* 3.7 23.5 - - - +
722B PRO* 3.5 20.3 - - - +
736B LEU* 6.6 0.4 - - - -
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Residues in contact with CYS 592 (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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306B LEU* 4.3 16.6 - - - -
568B TRP* 3.3 44.9 - - + -
588B VAL 3.1 7.7 + - - +
589B TYR 3.4 2.5 - - - +
591B GLY* 1.3 76.6 - - - +
593B PHE* 1.3 73.3 + - - +
594B GLN 3.3 0.2 - - - -
595B ASP* 3.2 24.9 - - - +
602B VAL* 3.6 13.5 - - - +
699B LEU* 3.8 12.2 - - + +
722B PRO* 4.2 5.3 - - - +
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Residues in contact with PHE 593 (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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306B LEU* 3.0 40.8 - - + -
307B VAL 3.6 4.9 - - - -
308B SER* 3.5 30.3 - - - +
335B LYS 5.8 2.0 - - - +
336B GLY 6.5 0.4 - - - -
568B TRP* 3.8 16.2 - + - -
589B TYR* 3.2 53.7 + + - +
590B LEU* 3.2 15.0 + - + +
592B CYS* 1.3 79.3 - - - +
594B GLN* 1.3 62.2 + - - +
595B ASP 3.1 2.9 - - - +
598B GLY* 3.2 24.6 - - - +
600B GLY* 3.6 19.9 + - - -
602B VAL* 3.8 20.6 - - + -
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Residues in contact with GLN 594 (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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287B PHE* 3.7 26.8 - - + -
291B HIS 4.0 3.6 - - - +
292B ARG* 4.9 6.1 - - - -
590B LEU* 2.9 34.5 + - - +
591B GLY* 3.6 17.3 - - - +
592B CYS 3.3 0.4 - - - -
593B PHE* 1.3 83.5 + - - +
595B ASP* 1.3 65.2 + - - +
596B ASN 3.9 0.3 + - - -
597B GLY 4.0 3.3 + - - -
598B GLY* 3.3 14.5 + - - -
720B THR 4.9 2.5 - - - +
736B LEU* 4.5 19.9 - - + +
740B GLY 5.6 1.0 - - - +
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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