Contacts of the helix formed by residues 572 - 588 (chain A) in PDB entry 5M7R
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ASP* 2.9 22.9 + - - -
566A TYR* 3.3 25.9 - - - +
571A HIS* 1.3 73.7 - - - +
573A PRO* 1.3 80.4 - - - +
574A LYS 3.0 3.7 + - - -
575A GLY 3.1 2.4 + - - -
576A ALA* 3.0 16.1 + - - +
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Residues in contact with PRO 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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380A LEU* 6.3 0.2 - - + -
563A ASP* 3.4 17.9 - - - +
566A TYR* 4.6 12.6 - - + +
570A GLU* 5.8 1.6 - - - +
571A HIS 4.0 0.2 - - - -
572A GLY* 1.3 83.1 - - - +
574A LYS* 1.3 58.8 + - + +
576A ALA* 3.3 5.8 + - + +
577A GLN* 3.0 29.0 + - - +
580A ARG* 5.3 0.7 + - - -
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Residues in contact with LYS 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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556A GLU* 4.9 9.9 + - - +
559A GLN* 4.6 23.2 + - - +
560A LEU* 4.2 31.6 - - + +
563A ASP* 3.0 25.7 + - + +
573A PRO* 1.3 76.9 - - + +
575A GLY* 1.3 58.5 + - - +
577A GLN* 3.5 16.1 - - - +
578A MET* 3.2 33.6 + - + +
617A MET* 5.2 2.3 - - - +
620A LEU* 6.5 1.1 - - - -
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Residues in contact with GLY 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ASP* 4.0 11.0 - - - +
564A LEU* 4.3 8.4 - - - +
571A HIS* 4.4 2.5 - - - -
572A GLY 3.1 6.1 + - - -
574A LYS* 1.3 73.9 - - - +
576A ALA* 1.3 66.1 + - - +
577A GLN 3.1 1.3 - - - -
578A MET* 3.3 4.4 + - - +
579A LEU* 3.0 24.9 + - - +
685B LEU* 3.8 29.6 - - - +
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Residues in contact with ALA 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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571A HIS* 4.0 23.2 - - + +
572A GLY 3.0 11.9 + - - +
573A PRO* 3.7 9.4 - - + +
575A GLY* 1.3 76.6 - - - +
577A GLN* 1.3 56.2 + - - +
579A LEU* 3.4 7.1 + - - +
580A ARG* 2.9 41.8 + - - +
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Residues in contact with GLN 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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573A PRO 3.0 17.4 + - - +
574A LYS* 3.5 16.7 - - - +
576A ALA* 1.3 74.1 - - - +
578A MET* 1.3 59.6 + - - +
580A ARG* 3.2 30.7 + - - +
581A GLU* 2.9 42.2 + - + +
617A MET* 3.1 41.0 - - - +
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Residues in contact with MET 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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560A LEU* 4.0 20.6 - - + -
564A LEU* 4.9 4.5 - - + -
574A LYS* 3.2 18.5 + - + +
575A GLY* 3.3 5.6 + - - +
577A GLN* 1.3 76.9 - - - +
579A LEU* 1.3 63.6 + - - +
581A GLU* 4.6 1.3 - - - -
582A PHE* 3.0 21.1 + - - +
614A PHE* 3.4 24.6 - - + -
617A MET* 3.5 57.2 - - + +
618A CYS* 4.7 2.0 - - - -
620A LEU* 5.6 1.6 - - + -
621A VAL* 3.8 17.5 - - + -
651A MET* 4.0 24.9 - - + +
689B PHE* 3.8 11.0 - - + -
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Residues in contact with LEU 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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571A HIS* 4.3 8.1 - - + -
575A GLY 3.0 17.2 + - - +
576A ALA* 3.6 6.1 - - - +
578A MET* 1.3 77.5 - - - +
580A ARG* 1.3 56.4 + - - +
582A PHE* 3.3 2.0 + - + +
583A GLN* 3.0 55.7 + - - +
685B LEU* 4.2 11.4 - - + -
688B GLU* 3.7 41.5 - - + +
689B PHE* 3.6 24.2 - - + -
692B LEU* 3.9 19.3 - - + -
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Residues in contact with ARG 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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573A PRO 5.3 0.6 + - - -
576A ALA* 2.9 40.0 + - - +
577A GLN* 3.2 29.4 + - - +
579A LEU* 1.3 73.8 - - - +
581A GLU* 1.3 69.3 + - + +
583A GLN* 3.4 16.8 + - - +
584A TRP* 3.0 23.4 + - + +
610A ARG* 5.4 0.4 + - - -
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Residues in contact with GLU 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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577A GLN* 2.9 39.0 + - + +
578A MET* 4.0 4.3 - - - +
580A ARG* 1.3 77.8 + - + +
582A PHE* 1.3 58.2 + - - +
584A TRP* 3.3 4.7 + - - +
585A LEU* 3.0 34.1 + - + +
610A ARG* 3.1 58.5 + - - +
613A LYS* 5.8 1.8 - - + +
614A PHE* 4.2 17.5 - - + -
617A MET* 4.4 5.6 - - + -
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Residues in contact with PHE 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 MET 3.0 19.1 + - - +
579A LEU 3.8 2.9 - - - +
581A GLU* 1.3 75.9 - - - +
583A GLN* 1.3 61.4 + - - +
585A LEU* 3.4 5.5 + - + +
586A ARG* 3.1 32.2 + - + +
614A PHE* 3.8 13.0 - + + -
654A VAL* 3.7 23.8 - - + -
657A PHE* 3.7 32.3 - + - -
658A VAL* 3.7 31.4 - - + -
661A LEU* 5.2 1.1 - - + -
689B PHE* 3.6 27.1 - + + -
692B LEU* 3.8 35.2 - - + -
693B LEU* 4.3 6.3 - - + -
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Residues in contact with GLN 583 (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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579A LEU* 3.0 46.4 + - - +
580A ARG* 3.7 17.1 - - - +
581A GLU 3.4 0.2 - - - -
582A PHE* 1.3 76.0 - - - +
584A TRP* 1.3 62.2 + - - +
586A ARG* 3.4 7.5 + - - +
587A ALA* 3.1 25.5 + - - +
688B GLU* 5.3 2.8 + - - -
692B LEU* 3.9 24.9 - - + +
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Residues in contact with TRP 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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580A ARG 3.0 17.4 + - - +
581A GLU* 3.6 4.5 - - - +
583A GLN* 1.3 77.2 - - - +
585A LEU* 1.3 76.1 + - + +
586A ARG 3.3 0.2 + - - -
587A ALA* 3.4 2.0 + - - -
588A ASN* 2.8 65.0 + - + +
603A LYS 5.1 1.6 - - - -
606A GLU* 3.5 29.1 + - - -
607A TRP* 3.8 36.3 - + + -
610A ARG* 3.1 55.8 - - - +
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Residues in contact with LEU 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 GLU* 3.0 23.7 + - + +
582A PHE* 3.7 6.3 - - + +
584A TRP* 1.3 90.9 - - + +
586A ARG* 1.3 60.4 + - - +
589A SER* 3.3 11.6 + - - -
607A TRP* 3.0 54.4 + - + +
610A ARG* 4.2 5.8 - - + +
611A ALA* 3.8 28.5 - - + +
614A PHE* 3.9 37.5 - - + -
658A VAL* 4.3 16.2 - - + -
661A LEU* 4.1 2.5 - - + +
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Residues in contact with ARG 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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582A PHE* 3.1 34.1 + - + +
583A GLN* 3.7 7.2 - - - +
584A TRP 3.2 0.2 - - - -
585A LEU* 1.3 76.9 - - - +
587A ALA* 1.3 61.5 + - - +
589A SER* 3.1 24.4 - - - -
657A PHE* 4.3 20.8 - - + -
661A LEU* 4.4 7.0 - - + -
692B LEU* 3.3 52.8 + - - +
693B LEU 5.6 0.6 - - - -
694B PRO* 6.1 0.6 - - - +
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Residues in contact with ALA 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 GLN 3.1 14.6 + - - +
584A TRP* 4.2 2.9 - - - +
586A ARG* 1.3 82.6 - - - +
588A ASN* 1.3 61.1 + - - +
589A SER 3.3 1.7 + - - -
590A SER* 4.8 5.7 + - - -
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Residues in contact with ASN 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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584A TRP* 2.8 71.4 + - + +
585A LEU 3.7 3.6 - - - -
587A ALA* 1.3 81.3 - - - +
589A SER* 1.3 63.1 + - - +
590A SER* 3.2 5.4 + - - -
591A VAL* 3.4 26.9 + - + +
607A TRP* 3.4 19.5 - - + -
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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