Contacts of the helix formed by residues 574 - 586 (chain B) in PDB entry 1MZC
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 GLN 574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572B VAL* 3.6 34.2 + - - +
573B LEU* 1.3 66.9 - - - +
575B ARG* 1.3 63.9 + - - +
576B GLU 3.4 2.7 - - - -
577B LYS* 3.1 48.4 + - + +
578B HIS* 3.0 31.4 + - + +
844B GLN* 2.8 26.9 - - + +
845B CYS 5.6 2.0 - - - +
846B PRO* 6.0 1.1 - - + -
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Residues in contact with ARG 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LEU* 2.8 29.5 + - + +
574B GLN* 1.3 69.6 - - - +
576B GLU* 1.3 64.7 + - + +
578B HIS* 3.2 10.7 + - - +
579B PHE* 2.8 29.5 + - - +
614B LEU* 3.1 47.0 + - + +
615B ASP* 5.3 2.2 - - - +
616B GLU* 5.0 6.2 + - - +
891B GLU* 2.5 34.6 + - - +
892B ASN* 4.2 1.6 + - - +
893B ALA 2.7 32.1 + - - -
894B LEU* 4.0 12.2 - - - +
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Residues in contact with GLU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLN 3.4 0.6 - - - -
575B ARG* 1.3 82.7 - - + +
577B LYS* 1.3 64.4 + - + +
579B PHE* 3.4 13.3 + - - +
580B HIS* 3.0 50.4 + - + +
616B GLU* 3.5 20.6 - - - +
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLN* 3.1 47.9 + - + +
576B GLU* 1.3 75.1 - - + +
578B HIS* 1.3 66.1 + - - +
580B HIS* 3.4 5.9 + - - +
581B TYR* 3.1 23.0 + - - +
845B CYS 4.9 0.4 - - - +
846B PRO* 2.9 34.7 + - - +
847B ALA 4.3 5.3 - - - +
848B GLY* 3.6 18.4 - - - +
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Residues in contact with HIS 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LEU* 3.9 14.4 - - + +
574B GLN* 3.0 28.8 + - + -
575B ARG* 3.6 7.6 - - - +
577B LYS* 1.3 75.4 - - - +
579B PHE* 1.3 64.2 + - - +
581B TYR* 3.3 2.8 + - - +
582B LEU* 2.9 33.1 + - + +
614B LEU* 4.1 14.8 - - + -
844B GLN* 2.9 34.3 + - + -
845B CYS 4.5 2.0 - - - -
848B GLY* 3.7 4.7 - - - -
849B GLY* 2.8 49.6 + - - +
850B LEU* 3.6 20.9 - - + +
863B THR* 5.5 0.9 - - + -
867B LEU* 5.0 4.3 - - + -
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Residues in contact with PHE 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ARG 2.8 16.8 + - - +
576B GLU* 3.6 21.1 - - - +
578B HIS* 1.3 76.5 - - - +
580B HIS* 1.3 82.7 + + - +
582B LEU* 3.3 8.1 + - - +
583B LYS* 2.9 52.6 + - + +
611B LEU* 3.7 17.5 - - + -
614B LEU* 4.4 2.6 - - + +
616B GLU* 3.5 43.1 - - + +
617B PRO* 5.3 6.7 - - + -
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Residues in contact with HIS 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B GLU* 3.0 43.5 + - + +
577B LYS* 4.0 5.8 - - - +
579B PHE* 1.3 96.3 - + - +
581B TYR* 1.3 63.8 + - - +
583B LYS* 3.6 13.9 + - + +
584B ARG* 3.2 24.1 + - - +
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Residues in contact with TYR 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 LYS 3.1 13.7 + - - +
578B HIS 3.5 8.7 - - - +
580B HIS* 1.3 77.2 - - - +
582B LEU* 1.3 69.4 + - + +
584B ARG* 3.5 5.0 + - + +
585B GLY 3.2 16.5 + - - -
593B TYR* 4.0 2.1 + - - -
847B ALA 4.8 1.1 - - - +
848B GLY* 4.1 9.9 - - - -
849B GLY* 3.4 20.4 - - - -
858B ARG* 3.4 43.7 + - + +
859B ASP* 3.2 31.9 + - - -
860B PHE* 3.5 38.8 + + - -
863B THR* 3.5 22.0 - - + -
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Residues in contact with LEU 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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578B HIS* 2.9 22.1 + - + +
579B PHE 3.7 3.1 - - - +
581B TYR* 1.3 76.3 - - + +
583B LYS* 1.3 65.9 + - - +
585B GLY* 3.1 11.4 + - - -
586B LEU* 3.1 9.7 + - - +
606B TRP 4.8 0.4 - - - +
607B ILE* 3.5 27.5 - - + +
610B SER* 3.5 36.8 - - - +
611B LEU* 3.9 19.5 - - + -
614B LEU* 3.7 23.3 - - + -
860B PHE* 4.0 22.4 - - + +
863B THR* 3.9 19.7 - - + -
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Residues in contact with LYS 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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579B PHE* 2.9 50.2 + - + +
580B HIS* 3.9 13.6 + - - +
582B LEU* 1.3 73.1 - - - +
584B ARG* 1.3 65.4 + - - +
586B LEU* 3.4 17.2 + - - +
587B ARG* 4.1 11.0 + - + +
611B LEU* 4.8 7.1 - - + +
619B PRO* 6.6 0.4 - - - -
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Residues in contact with ARG 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 HIS 3.2 15.0 + - - +
581B TYR* 3.7 5.6 - - - +
582B LEU 3.2 0.8 - - - -
583B LYS* 1.3 81.2 - - - +
585B GLY* 1.3 63.3 + - - +
586B LEU 3.2 1.0 + - - -
587B ARG* 3.2 14.5 + - - +
588B GLN* 3.4 42.2 + - - +
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Residues in contact with GLY 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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88A VAL* 3.8 9.7 - - - +
581B TYR 3.2 4.9 + - - -
582B LEU 3.1 5.3 + - - -
584B ARG* 1.3 80.3 - - - +
586B LEU* 1.3 60.7 + - - +
587B ARG 3.2 1.1 + - - -
588B GLN 3.7 10.8 - - - +
589B LEU* 3.6 18.1 - - - +
607B ILE* 3.5 12.7 - - - +
860B PHE* 3.7 25.6 - - - -
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.4 12.6 - - + +
88A VAL* 2.9 28.5 + - + -
582B LEU 3.1 10.3 + - - +
583B LYS* 3.6 13.2 - - - +
584B ARG 3.1 1.0 - - - -
585B GLY* 1.3 76.6 - - - +
587B ARG* 1.3 61.7 + - + +
604B CYS* 4.6 8.5 - - - -
607B ILE* 3.7 19.9 - - + +
608B LEU* 4.1 21.1 - - + -
611B LEU* 4.4 15.7 - - + -
618B ILE* 5.8 0.9 - - + -
619B PRO* 6.5 0.2 - - + -
622B VAL* 3.4 33.9 - - + -
626B VAL* 4.4 17.3 - - + -
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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