Contacts of the helix formed by residues 572 - 585 (chain A) in PDB entry 5VOT
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 GLY 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A PHE* 3.3 6.3 - - - -
569A ASN 4.4 2.6 + - - -
570A GLU 2.7 13.9 + - - +
571A PHE* 1.3 75.8 - - - +
573A ILE* 1.3 66.1 + - - -
574A PHE* 3.2 4.0 + - - -
575A ASN* 3.5 11.6 + - - +
576A SER* 3.3 15.1 + - - -
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Residues in contact with ILE 573 (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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537A SER* 4.6 6.5 - - - +
538A VAL* 4.5 15.7 - - + -
541A PHE* 3.1 49.8 - - + -
572A GLY* 1.3 72.0 - - - -
574A PHE* 1.3 70.9 + - + +
576A SER* 3.1 4.5 + - - -
577A LEU* 2.9 27.8 + - + +
195F VAL* 4.6 24.0 - - + -
199F HIS* 6.2 3.8 - - + -
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Residues in contact with PHE 574 (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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572A GLY* 3.2 1.4 - - - -
573A ILE* 1.3 87.2 - - + +
575A ASN* 1.3 77.1 + - - +
577A LEU* 3.3 14.3 + - + +
578A TRP* 2.9 32.7 + + + +
594D ARG* 5.2 6.7 - - - -
596D LEU* 3.4 47.1 - - + -
599D ARG* 4.0 22.2 - - + -
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Residues in contact with ASN 575 (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 ASN 4.4 13.3 - - - +
570A GLU* 5.0 3.6 - - + -
572A GLY* 3.5 13.9 + - - +
573A ILE 3.3 0.4 - - - -
574A PHE* 1.3 88.1 - - - +
576A SER* 1.3 57.8 + - - +
578A TRP* 3.3 14.7 + - - +
579A PHE* 2.9 26.9 + - - +
591A ILE* 4.3 27.4 - - + +
594D ARG* 5.2 14.6 - - - +
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Residues in contact with SER 576 (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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537A SER* 4.6 16.9 - - - -
540A LEU* 5.0 9.8 - - - +
541A PHE* 4.3 12.8 + - - -
570A GLU* 3.3 34.8 + - - +
572A GLY 3.3 9.5 + - - -
573A ILE* 3.1 11.3 + - - -
575A ASN* 1.3 75.5 - - - +
577A LEU* 1.3 66.6 + - - +
579A PHE* 3.0 12.4 + - - +
580A SER* 3.0 20.5 + - - -
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Residues in contact with LEU 577 (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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533A TYR* 3.4 36.2 + - + +
534A ILE* 5.3 5.8 - - + -
537A SER* 3.3 33.0 - - - +
573A ILE* 2.9 18.0 + - + +
574A PHE* 3.6 17.7 - - + +
576A SER* 1.3 74.9 - - - +
578A TRP* 1.3 65.4 + - - +
580A SER* 2.9 13.2 + - - -
581A LEU 3.0 10.9 + - - -
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Residues in contact with TRP 578 (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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574A PHE* 2.9 24.0 + + + +
575A ASN* 3.3 19.3 - - + +
577A LEU* 1.3 76.9 - - - +
579A PHE* 1.3 65.5 + - - +
581A LEU* 3.2 26.4 + - + +
582A GLY* 2.9 21.2 + - - -
590A ASP* 3.6 26.7 + - + -
591A ILE* 6.4 2.5 - - + -
592D SER* 4.7 1.8 + - - -
593D PRO* 4.5 29.1 + - + -
599D ARG* 3.1 54.1 - - + -
602D GLY* 4.7 3.6 - - - -
603D GLY 4.3 5.2 - - - -
606D TRP* 3.7 32.9 - + - -
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Residues in contact with PHE 579 (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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540A LEU* 4.6 20.2 - - + -
570A GLU* 5.6 6.1 - - + +
575A ASN 2.9 13.2 + - - +
576A SER* 3.0 13.7 + - - +
578A TRP* 1.3 77.8 - - - +
580A SER* 1.3 66.5 + - - +
582A GLY* 3.4 0.8 + - - -
583A ALA* 2.9 37.1 + - + +
589A CYS* 3.6 24.0 - - + -
590A ASP 5.2 1.8 - - - -
591A ILE* 3.5 33.7 - - + +
593A PRO* 3.9 26.9 - - + -
602A GLY* 5.0 11.2 - - - -
605A TRP* 5.4 4.3 - + - -
606A TRP* 4.2 23.3 - + - -
587B GLN* 5.8 0.9 - - - -
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Residues in contact with SER 580 (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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533A TYR* 3.1 25.5 + - - -
536A VAL* 5.1 3.0 - - - +
537A SER* 3.2 28.2 + - - -
540A LEU* 5.6 4.9 - - - -
576A SER 3.0 8.1 + - - -
577A LEU 2.9 7.6 + - - -
579A PHE* 1.3 83.0 - - - +
581A LEU* 1.3 63.0 + - - +
583A ALA 3.4 0.2 + - - -
584A PHE* 2.9 23.4 + - - +
605A TRP* 3.6 23.2 + - - +
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Residues in contact with LEU 581 (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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533A TYR* 3.2 27.7 + - + +
577A LEU 3.0 8.4 + - - +
578A TRP* 3.5 35.7 - - + +
580A SER* 1.3 75.2 - - - +
582A GLY* 1.3 61.1 + - - +
584A PHE* 2.8 26.1 + - + +
585A MET* 3.0 31.9 + - + +
603D GLY* 4.1 21.1 - - - -
606D TRP* 4.6 9.0 - - + -
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Residues in contact with GLY 582 (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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578A TRP* 2.9 18.5 + - - -
579A PHE* 3.9 2.0 - - - -
581A LEU* 1.3 73.7 - - - +
583A ALA* 1.3 56.4 + - - +
585A MET 2.8 19.0 - - - +
587A GLN* 2.9 19.8 - - - +
588A GLY 4.8 8.1 - - - -
589A CYS* 6.2 0.7 - - - -
587B GLN* 4.8 0.4 - - - -
606D TRP* 3.7 27.7 - - - -
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Residues in contact with ALA 583 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A PHE* 2.9 30.8 + - + +
580A SER 3.8 3.1 - - - +
582A GLY* 1.3 76.3 - - - +
584A PHE* 1.3 61.7 + - - +
585A MET 2.8 12.5 - - - +
605A TRP* 3.9 21.1 - - + -
606A TRP* 4.0 12.7 - - + +
609A THR* 3.8 14.2 + - - +
587B GLN* 3.6 21.9 - - - +
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Residues in contact with PHE 584 (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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526A TRP* 4.5 19.3 - + - -
529A ILE* 4.0 27.6 - - + -
533A TYR* 5.0 7.0 - + + -
580A SER 2.9 14.1 + - - +
581A LEU* 2.8 20.7 + - + +
583A ALA* 1.3 71.7 - - - +
585A MET* 1.3 88.0 + - + +
586A ARG* 5.7 1.4 - - - -
605A TRP* 4.1 25.5 - + + +
608A PHE* 4.6 3.1 - + - -
609A THR* 3.2 23.5 + - - -
612A ILE* 4.3 14.4 - - + -
613A ILE* 3.5 40.6 - - + +
607D PHE* 5.8 1.6 - + - -
610D LEU* 5.7 1.3 - - + -
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Residues in contact with MET 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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581A LEU* 3.0 25.6 + - + +
582A GLY 2.8 12.2 - - - +
583A ALA* 2.8 16.3 - - - +
584A PHE* 1.3 108.2 - - + +
586A ARG* 1.3 63.1 + - - +
587A GLN* 3.1 16.7 - - + +
613A ILE* 5.7 0.2 - - - -
587B GLN* 4.7 1.2 - - - +
606D TRP* 4.3 24.9 - - + -
607D PHE* 3.5 39.9 - - + +
610D LEU* 4.3 27.1 - - + -
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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