Contacts of the helix formed by residues 584 - 594 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583A GLY* 1.3 81.1 - - - +
585A GLU* 1.3 71.8 + - - +
587A ASP* 3.5 13.9 - - + +
588A VAL* 2.9 35.6 + - + +
659A GLU* 5.1 2.2 - - - +
661A HIS* 5.7 3.6 - - + -
701A ARG* 3.9 26.7 - - - +
703A MET* 6.3 1.3 - - + -
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Residues in contact with GLU 585 (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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561A ASN* 3.6 33.7 + - + +
562A TYR* 3.2 36.5 - - - +
563A SER* 3.9 7.5 + - - +
564A PRO* 4.1 9.0 - - - +
577A LEU* 3.9 6.1 - - + +
582A PRO 5.2 0.3 - - - +
583A GLY* 3.0 5.4 + - - -
584A PRO* 1.3 97.1 - - - +
586A MET* 1.3 58.8 + - - +
588A VAL* 3.9 1.9 - - - +
589A TYR* 2.9 28.2 + - - +
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Residues in contact with MET 586 (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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335A LYS* 4.6 3.8 - - - +
561A ASN* 3.6 12.3 - - - +
577A LEU* 4.2 13.5 - - + -
578A ASN 3.9 2.5 - - - +
579A PHE* 3.7 54.1 - - + +
581A THR 3.3 27.1 - - - +
582A PRO* 4.9 1.6 - - + -
583A GLY* 2.9 9.0 + - - +
585A GLU* 1.3 80.2 - - - +
587A ASP* 1.3 55.8 + - - +
589A TYR* 3.3 7.3 - - - +
590A LEU* 2.8 78.2 + - + +
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Residues in contact with ASP 587 (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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583A GLY 2.8 23.5 + - - +
584A PRO* 3.5 10.1 - - - +
586A MET* 1.3 77.4 - - - +
588A VAL* 1.3 58.3 + - - +
590A LEU* 3.9 2.7 - - - +
591A GLY* 2.9 27.2 + - - -
701A ARG* 2.6 29.4 + - - +
715A PHE* 4.2 7.0 - - - -
718A GLN* 3.4 38.7 + - - +
720A THR* 3.7 7.4 + - - -
737A SER 5.0 3.6 - - - +
738A LYS* 4.7 10.9 - - - +
740A GLY* 5.6 2.9 - - - -
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Residues in contact with VAL 588 (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 PRO* 4.6 5.2 - - + -
565A VAL* 3.7 29.6 - - + -
568A TRP* 3.7 9.4 - - + -
584A PRO 2.9 23.1 + - - +
585A GLU* 4.1 3.1 - - - +
587A ASP* 1.3 72.8 - - - +
589A TYR* 1.3 62.5 + - - +
591A GLY* 3.4 0.7 + - - -
592A CYS* 3.0 22.7 + - - +
661A HIS* 3.8 38.8 - - + +
699A LEU* 3.9 16.3 - - + +
701A ARG* 4.1 10.8 - - - -
720A THR* 4.0 9.2 - - + -
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Residues in contact with TYR 589 (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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307A VAL 3.5 8.5 + - - -
308A SER* 3.9 4.3 - - - -
309A SER 2.9 19.8 + - - -
564A PRO* 3.5 26.9 - - + -
568A TRP* 3.8 18.5 + + - -
575A VAL* 2.6 34.7 + - + +
577A LEU* 3.7 16.2 - - + -
579A PHE* 3.8 33.4 - + - -
585A GLU 2.9 18.2 + - - +
586A MET* 3.3 11.9 - - - +
587A ASP 3.1 0.2 - - - -
588A VAL* 1.3 80.8 - - - +
590A LEU* 1.3 66.8 + - + +
592A CYS* 3.3 1.7 + - - +
593A PHE* 3.2 47.9 + + - -
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Residues in contact with LEU 590 (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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308A SER* 5.0 3.6 - - - +
335A LYS* 3.7 48.2 - - + +
579A PHE* 4.2 15.0 - - + -
586A MET* 2.8 48.8 + - + +
587A ASP* 4.4 2.0 - - - +
589A TYR* 1.3 74.4 - - + +
591A GLY* 1.3 60.2 + - - +
593A PHE* 3.3 6.6 - - + +
594A GLN* 2.8 46.9 + - - +
736A LEU* 6.5 0.2 - - + -
740A GLY* 5.3 10.1 - - - +
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Residues in contact with GLY 591 (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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587A ASP 2.9 19.3 + - - -
588A VAL 3.7 2.0 - - - -
589A TYR 3.2 0.2 - - - -
590A LEU* 1.3 77.8 - - - +
592A CYS* 1.3 60.4 + - - +
594A GLN* 3.5 18.1 + - - +
699A LEU* 4.2 5.6 - - - -
720A THR* 3.6 24.0 - - - +
722A PRO* 3.5 19.4 - - - +
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Residues in contact with CYS 592 (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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306A LEU* 4.4 13.7 - - - -
568A TRP* 3.3 47.6 - - + -
588A VAL 3.0 7.5 + - - +
589A TYR 3.6 1.8 - - - +
591A GLY* 1.3 74.8 - - - +
593A PHE* 1.3 75.7 + - - +
594A GLN 3.2 0.2 - - - -
595A ASP* 3.2 26.2 - - - +
602A VAL* 3.7 13.3 - - - +
699A LEU* 3.8 12.5 - - + +
722A PRO* 4.2 4.9 - - - +
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Residues in contact with PHE 593 (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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306A LEU* 3.0 41.3 - - + -
307A VAL 3.6 5.4 - - - -
308A SER* 3.5 24.2 - - - +
335A LYS 5.8 2.0 - - - +
336A GLY 6.5 0.4 - - - -
568A TRP* 3.7 21.3 - + - -
589A TYR* 3.2 50.7 + + - +
590A LEU* 3.1 14.4 + - + +
592A CYS* 1.3 79.3 - - - +
594A GLN* 1.3 62.0 + - - +
595A ASP 3.1 4.9 - - - +
598A GLY* 3.2 25.3 - - - +
600A GLY* 3.5 28.9 + - - -
602A VAL* 3.9 16.2 - - + -
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Residues in contact with GLN 594 (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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287A PHE* 3.8 26.7 - - + -
291A HIS 4.1 2.4 - - - +
292A ARG* 4.9 6.1 - - - -
590A LEU* 2.8 39.1 + - - +
591A GLY* 3.6 14.6 - - - +
592A CYS 3.2 0.4 - - - -
593A PHE* 1.3 82.2 + - - +
595A ASP* 1.3 63.7 - - - +
596A ASN 3.9 0.2 + - - -
597A GLY* 4.0 3.3 + - - -
598A GLY* 3.3 15.4 + - - -
720A THR 4.9 2.7 - - - +
736A LEU* 4.6 18.6 - - + +
740A 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