Contacts of the helix formed by residues 578 - 587 (chain L) in PDB entry 5L6W
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 SER 578 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576L PRO 3.6 0.2 + - - -
577L PRO* 1.3 76.5 + - - +
579L PHE* 1.3 64.1 + - - +
580L PHE 3.3 2.0 - - - -
581L PRO* 3.2 11.9 - - - +
582L ILE* 2.9 37.1 + - - +
607L LEU* 3.8 16.3 - - - +
617L LEU* 5.1 2.5 - - - -
621L LEU* 4.0 41.2 - - - +
624L LEU* 4.9 1.8 - - - -
625L ASP* 2.8 23.1 + - - -
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Residues in contact with PHE 579 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434L TRP* 3.8 28.3 - + - -
437L ARG 4.3 3.6 - - - -
438L VAL* 3.8 32.8 - - + -
441L ALA* 4.1 8.5 - - + -
539L LEU* 4.0 22.2 - - + -
542L ILE* 4.4 10.5 - - + -
543L ILE* 3.8 25.4 - - + -
575L CYS* 4.0 2.2 - - - -
576L PRO* 3.3 17.4 + - + +
577L PRO 3.2 5.7 + - - -
578L SER* 1.3 76.8 + - - +
580L PHE* 1.3 61.8 + - - +
582L ILE* 3.5 5.7 - - + +
583L THR* 3.0 22.2 + - - -
604L LEU* 4.0 23.1 - - + -
607L LEU* 3.9 21.1 - - + -
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Residues in contact with PHE 580 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543L ILE* 4.1 7.9 - - + -
561L LEU* 4.6 9.6 - - + -
563L VAL* 4.1 11.0 - - + -
566L PHE* 3.2 45.1 - + + -
567L LEU* 3.7 23.8 - - + -
571L CYS* 4.6 8.7 - - - -
575L CYS* 4.2 16.6 - - - -
576L PRO 4.2 0.6 + - - +
579L PHE* 1.3 76.0 - - - +
581L PRO* 1.3 77.2 - - + +
582L ILE 3.1 2.2 - - - -
583L THR* 2.8 25.3 + - + -
584L VAL* 2.9 37.3 + - + -
628L PHE* 3.7 25.6 - + - -
629L TRP* 5.1 3.8 - + + -
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Residues in contact with PRO 581 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576L PRO 5.4 0.7 - - - +
578L SER* 3.3 14.1 - - - +
580L PHE* 1.3 97.9 - - + +
582L ILE* 1.3 56.7 + - - +
584L VAL* 3.5 6.3 + - + +
585L ARG* 2.9 30.1 + - - +
624L LEU* 3.9 20.1 - - + +
625L ASP* 3.6 23.8 - - - +
628L PHE* 3.8 42.0 - - + +
629L TRP* 4.5 4.9 - - + +
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Residues in contact with ILE 582 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539L LEU* 4.2 14.8 - - + -
578L SER* 2.9 36.3 + - - +
579L PHE* 3.5 6.7 - - - +
581L PRO* 1.3 74.7 - - - +
583L THR* 1.3 60.0 + - - +
585L ARG* 3.3 7.6 + - - +
586L CYS* 2.9 27.9 + - - -
595L PRO* 5.2 0.3 - - - +
600L LEU* 3.8 25.5 - - + +
603L TRP* 4.0 29.2 - - + -
604L LEU* 4.3 21.8 - - + -
607L LEU* 5.2 1.6 - - + -
621L LEU* 4.2 5.4 - - + -
624L LEU* 3.9 19.7 - - + -
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Residues in contact with THR 583 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536L GLY 3.5 24.2 - - - +
539L LEU* 3.5 22.3 - - + +
540L CYS* 3.5 22.9 - - - +
543L ILE* 3.3 15.7 - - + +
561L LEU* 4.5 5.6 - - + -
579L PHE 3.0 14.4 + - - -
580L PHE* 2.8 17.5 + - + -
582L ILE* 1.3 76.7 - - - +
584L VAL* 1.3 54.5 + - - +
586L CYS* 2.8 24.6 + - - +
587L CYS* 3.0 13.3 + - - -
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Residues in contact with VAL 584 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561L LEU* 4.4 6.7 - - + -
563L VAL* 4.1 20.6 - - + -
580L PHE* 2.9 47.2 + - + +
581L PRO 3.7 8.1 - - - +
583L THR* 1.3 75.4 - - - +
585L ARG* 1.3 65.6 + - - +
587L CYS* 3.2 15.7 + - - +
588L ASP* 3.2 13.2 + - - +
628L PHE* 4.0 26.9 - - + -
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Residues in contact with ARG 585 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581L PRO 2.9 17.5 + - - +
582L ILE* 3.6 8.1 - - - +
583L THR 3.2 0.4 - - - -
584L VAL* 1.3 78.2 - - - +
586L CYS* 1.3 62.4 + - - +
587L CYS 3.3 0.5 + - - -
588L ASP* 3.4 26.5 + - - +
593L LYS* 3.8 18.8 - - - +
594L ARG* 3.7 11.1 - - - +
595L PRO* 4.0 14.8 - - + -
603L TRP* 5.5 3.4 - - + -
624L LEU* 4.8 18.6 - - + -
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Residues in contact with CYS 586 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532L VAL* 3.7 25.1 - - + +
533L PHE* 3.3 21.3 + - - -
535L PHE* 3.9 15.5 - - - -
536L GLY* 3.7 17.7 - - - -
539L LEU* 4.6 2.2 - - - -
582L ILE* 2.9 20.6 + - - -
583L THR 2.8 13.2 + - - +
585L ARG* 1.3 72.6 - - - +
587L CYS* 1.3 58.1 + - - +
588L ASP 3.4 0.4 - - - -
594L ARG* 3.3 14.9 - - - -
595L PRO* 4.2 4.0 - - - -
600L LEU* 3.6 28.7 - - - -
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Residues in contact with CYS 587 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533L PHE* 3.4 25.4 - - + -
536L GLY* 3.5 36.1 - - - -
537L ILE* 4.0 18.2 - - - -
540L CYS* 4.5 0.4 - - - -
560L GLY* 4.7 7.8 - - - -
561L LEU* 4.1 34.0 + - + -
583L THR 3.0 12.3 + - - +
584L VAL* 3.2 5.6 + - - +
586L CYS* 1.3 76.9 - - - +
588L ASP* 1.3 65.7 + - - +
589L LEU* 3.5 1.4 + - - -
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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