Contacts of the helix formed by residues 572 - 588 (chain B) in PDB entry 5M7T
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ASP* 2.9 31.3 + - - -
566B TYR* 3.4 16.7 - - - +
571B HIS* 1.3 74.2 - - - +
573B PRO* 1.3 78.0 - - - +
574B LYS 3.4 2.2 - - - -
575B GLY 3.0 3.3 + - - -
576B ALA* 2.9 20.2 + - - +
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Residues in contact with PRO 573 (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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563B ASP* 3.4 16.4 - - - +
566B TYR* 4.8 10.1 - - + +
570B GLU* 6.2 0.2 - - - +
571B HIS 4.6 0.9 - - - +
572B GLY* 1.3 81.3 - - - +
574B LYS* 1.3 65.4 + - + +
576B ALA* 3.4 5.7 + - + +
577B GLN* 3.0 26.2 + - - +
580B ARG* 4.9 1.2 + - - -
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Residues in contact with LYS 574 (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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556B GLU* 4.3 13.5 + - - +
559B GLN* 4.1 27.8 + - - +
560B LEU* 3.9 34.5 - - + +
563B ASP* 3.0 18.7 + - + +
564B LEU* 5.3 0.2 - - - -
573B PRO* 1.3 77.0 - - + +
575B GLY* 1.3 57.3 + - - +
577B GLN* 3.4 13.2 + - - +
578B MET* 2.8 35.5 + - - +
617B MET* 4.6 10.9 - - + +
620B LEU* 6.5 1.3 - - + -
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Residues in contact with GLY 575 (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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685A LEU* 4.0 29.4 - - - +
689A PHE* 4.8 0.2 - - - -
563B ASP* 4.0 11.3 - - - +
564B LEU* 4.1 11.3 - - - +
571B HIS* 4.6 0.7 - - - -
572B GLY 3.0 6.8 + - - -
574B LYS* 1.3 79.4 - - - +
576B ALA* 1.3 61.6 + - - +
578B MET* 3.1 6.4 + - - +
579B LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 576 (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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571B HIS* 4.1 21.1 - - + +
572B GLY 2.9 16.6 + - - +
573B PRO* 3.7 6.5 - - + +
575B GLY* 1.3 74.4 - - - +
577B GLN* 1.3 56.3 + - - +
579B LEU* 3.3 8.6 + - - +
580B ARG* 2.9 37.9 + - - +
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Residues in contact with GLN 577 (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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573B PRO 3.0 18.6 + - - +
574B LYS* 3.6 8.6 - - - +
576B ALA* 1.3 75.7 - - - +
578B MET* 1.3 64.1 + - - +
580B ARG* 3.4 30.9 + - - +
581B GLU* 3.0 34.6 + - + +
617B MET* 3.0 46.3 - - - +
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Residues in contact with MET 578 (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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685A LEU* 5.8 0.7 - - + -
689A PHE* 3.7 11.8 - - + -
560B LEU* 4.1 20.9 - - + -
564B LEU* 4.9 7.6 - - + -
574B LYS 2.8 22.4 + - - +
575B GLY* 3.6 5.8 - - - +
577B GLN* 1.3 75.2 - - - +
579B LEU* 1.3 58.8 + - - +
581B GLU* 3.6 1.1 + - - -
582B PHE* 3.0 24.6 + - - +
614B PHE* 3.3 19.3 - - + -
617B MET* 3.6 59.2 - - + +
618B CYS* 4.8 4.9 - - - -
620B LEU* 5.5 1.6 - - + -
621B VAL* 3.9 18.6 - - + -
651B MET* 4.2 21.8 - - - +
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Residues in contact with LEU 579 (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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685A LEU* 4.3 9.4 - - + -
688A GLU* 2.9 39.0 - - + +
689A PHE* 3.6 32.7 - - + -
692A LEU* 4.0 25.6 - - + -
571B HIS* 4.6 7.2 - - + -
575B GLY 3.1 11.8 + - - +
576B ALA* 3.5 9.4 - - - +
577B GLN 3.2 0.2 - - - -
578B MET* 1.3 77.1 - - - +
580B ARG* 1.3 58.6 + - - +
582B PHE* 3.2 2.6 + - + +
583B GLN* 2.9 49.2 + - - +
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Residues in contact with ARG 580 (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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573B PRO 4.9 1.0 + - - -
576B ALA* 2.9 18.5 + - - +
577B GLN* 3.5 43.0 + - - +
578B MET 3.4 0.2 - - - -
579B LEU* 1.3 76.1 - - - +
581B GLU* 1.3 61.2 + - + +
583B GLN* 3.4 13.7 + - + +
584B TRP* 3.0 28.7 + - + +
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Residues in contact with GLU 581 (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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577B GLN* 3.0 34.6 + - + +
578B MET* 4.0 4.0 - - - +
580B ARG* 1.3 76.9 + - + +
582B PHE* 1.3 61.0 + - - +
584B TRP* 3.5 2.7 + - - +
585B LEU* 2.9 37.2 + - + +
610B ARG* 2.5 68.3 + - - +
613B LYS* 5.2 6.6 + - - +
614B PHE* 4.1 16.6 + - + +
617B MET* 5.8 0.9 - - - -
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Residues in contact with PHE 582 (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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689A PHE* 3.9 26.9 - + + -
692A LEU* 3.7 45.3 - - + -
693A LEU* 4.2 5.4 - - + -
578B MET 3.0 18.7 + - - +
579B LEU 3.7 3.6 - - - +
581B GLU* 1.3 73.8 - - - +
583B GLN* 1.3 63.5 - - - +
585B LEU* 3.4 3.3 + - + -
586B ARG* 3.0 33.9 + - + +
614B PHE* 3.9 12.1 - + + -
654B VAL* 3.6 28.5 - - + -
657B PHE* 3.8 27.4 - + - -
658B VAL* 3.7 26.0 - - + -
661B LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 583 (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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692A LEU* 4.0 26.7 - - + -
579B LEU* 2.9 43.5 + - - +
580B ARG* 3.6 11.3 + - - +
582B PHE* 1.3 76.2 - - - +
584B TRP* 1.3 62.0 + - - +
586B ARG* 4.0 4.5 - - - +
587B ALA* 3.2 26.2 + - - +
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Residues in contact with TRP 584 (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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580B ARG 3.0 16.8 + - - +
581B GLU 3.7 3.4 - - - +
582B PHE 3.3 0.2 - - - -
583B GLN* 1.3 75.1 - - - +
585B LEU* 1.3 78.4 + - + +
587B ALA* 3.3 2.6 + - - -
588B ASN* 3.0 58.4 + - + +
603B LYS 5.3 0.9 - - - -
606B GLU* 3.7 33.6 + - + -
607B TRP* 3.6 41.3 - + + -
610B ARG* 3.4 48.2 - - - +
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Residues in contact with LEU 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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581B GLU* 2.9 28.3 + - + +
582B PHE* 3.4 5.8 + - - +
584B TRP* 1.3 92.9 - - + +
586B ARG* 1.3 61.4 + - - +
589B SER* 3.4 7.6 + - - -
607B TRP* 2.9 55.9 + - + +
610B ARG* 4.2 4.9 - - + +
611B ALA* 3.8 30.3 - - + +
614B PHE* 3.8 34.5 - - + -
658B VAL* 4.3 17.3 - - + -
661B LEU* 4.2 1.5 - - + +
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Residues in contact with ARG 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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691A ARG 5.5 0.2 + - - -
692A LEU* 3.4 57.7 + - - +
582B PHE* 3.0 28.5 + - + +
583B GLN* 4.0 4.4 - - - +
585B LEU* 1.3 75.8 - - - +
587B ALA* 1.3 63.5 + - - +
589B SER* 3.1 19.9 - - - -
657B PHE* 3.7 27.8 - - + -
661B LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 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 GLN 3.2 16.5 + - - +
584B TRP* 3.3 4.0 + - - +
586B ARG* 1.3 81.3 - - - +
588B ASN* 1.3 62.6 + - - +
589B SER 3.4 1.8 + - - -
590B SER* 5.1 4.9 + - - -
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Residues in contact with ASN 588 (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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584B TRP* 3.0 67.1 + - + +
587B ALA* 1.3 80.9 - - - +
589B SER* 1.3 63.1 + - - +
590B SER* 3.4 3.8 - - - -
591B VAL* 3.3 25.7 - - + +
603B LYS* 5.8 2.3 + - - -
607B TRP* 3.5 22.7 - - + -
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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