Contacts of the helix formed by residues 578 - 587 (chain B) in PDB entry 3S95
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576B PRO 3.3 1.0 + - - -
577B PRO* 1.3 75.8 + - - +
579B PHE* 1.3 58.0 + - - +
580B PHE 3.4 2.5 - - - -
581B PRO* 3.4 8.0 - - - +
582B ILE* 2.8 42.7 + - - +
607B LEU* 4.0 7.3 - - - +
617B LEU* 4.4 5.2 - - - +
621B LEU* 3.9 46.1 - - - +
624B LEU* 5.0 1.8 - - - -
625B ASP* 2.8 25.3 + - - -
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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
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434B TRP* 3.9 21.8 - + - -
437B ARG 4.4 3.4 - - - -
438B VAL* 4.0 25.8 - - + -
441B ALA* 4.3 4.0 - - + -
539B LEU* 4.0 25.6 - - + -
542B ILE* 4.5 10.1 - - + -
543B ILE* 3.6 30.7 - - + -
575B CYS* 3.9 2.9 - - - -
576B PRO* 3.2 24.8 + - + +
577B PRO 3.2 4.6 + - - -
578B SER* 1.3 77.1 + - - +
580B PHE* 1.3 60.5 + - - +
582B ILE* 3.5 5.9 + - + +
583B THR* 2.9 26.6 + - - -
604B LEU* 3.8 25.1 - - + -
607B LEU* 3.8 23.1 - - + -
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Residues in contact with PHE 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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543B ILE* 4.2 6.1 - - + -
561B LEU* 4.3 11.9 - - + -
563B VAL* 4.0 10.5 - - + -
566B PHE* 3.3 45.5 - + - -
567B LEU* 3.6 31.6 - - + -
571B CYS* 4.5 7.2 - - - -
575B CYS* 4.1 18.1 - - - -
576B PRO 4.5 0.6 + - - -
579B PHE* 1.3 76.7 - - - +
581B PRO* 1.4 69.8 - - + +
583B THR* 3.0 16.3 + - + -
584B VAL* 2.9 48.8 + - + +
628B PHE* 3.9 20.2 - + - -
629B TRP* 4.9 4.0 - + + -
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Residues in contact with PRO 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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576B PRO 5.6 0.2 - - - +
578B SER* 3.4 14.6 - - - +
579B PHE 4.0 0.2 - - - +
580B PHE* 1.4 95.8 - - + +
582B ILE* 1.3 62.3 + - - +
584B VAL* 3.4 7.6 + - + +
585B ARG* 3.0 22.3 + - - +
624B LEU* 3.8 32.7 - - + +
625B ASP* 3.4 24.2 - - - +
628B PHE* 3.8 31.8 - - + -
629B TRP* 4.3 5.2 - - + +
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Residues in contact with ILE 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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539B LEU* 4.1 14.1 - - + -
578B SER* 2.8 40.1 + - - +
579B PHE* 3.6 9.2 - - + +
580B PHE 3.2 0.2 - - - -
581B PRO* 1.3 72.9 - - - +
583B THR* 1.3 63.8 + - - +
585B ARG* 3.2 5.8 + - - +
586B CYS* 3.0 21.7 + - - -
595B PRO* 5.2 0.2 - - - +
600B LEU* 3.5 29.4 - - + -
603B TRP* 3.9 18.6 - - + -
604B LEU* 4.1 24.5 - - + -
607B LEU* 4.5 4.3 - - + -
621B LEU* 4.0 11.2 - - + -
624B LEU* 3.5 20.8 - - + +
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Residues in contact with THR 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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536B GLY 3.5 12.8 - - - +
539B LEU* 3.2 25.6 - - + +
540B CYS* 3.5 35.0 - - - +
543B ILE* 3.2 17.1 - - + +
561B LEU* 4.8 0.7 - - + -
579B PHE* 2.9 13.5 + - - -
580B PHE* 3.0 20.3 + - + -
582B ILE* 1.3 77.6 - - - +
584B VAL* 1.3 61.9 - - - +
586B CYS* 3.1 4.8 + - - +
587B CYS* 3.0 24.0 + - - -
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Residues in contact with VAL 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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561B LEU* 4.4 3.8 - - + -
563B VAL* 4.1 21.5 - - + -
580B PHE* 2.9 54.0 + - + +
581B PRO 3.8 4.7 - - - +
583B THR* 1.3 75.8 - - - +
585B ARG* 1.3 62.6 + - - +
587B CYS* 3.2 16.3 + - - +
588B ASP* 3.4 11.8 + - - +
628B PHE* 3.9 29.2 - - + -
637B SER 4.6 4.3 - - - +
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Residues in contact with ARG 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 PRO 3.0 13.8 + - - +
582B ILE* 3.5 10.1 - - - +
584B VAL* 1.3 75.0 - - - +
586B CYS* 1.3 64.5 + - - +
588B ASP* 3.2 31.6 + - - +
593B LYS* 3.2 50.8 + - - +
594B ARG* 3.7 8.5 - - - +
595B PRO* 3.9 15.3 - - + -
603B TRP* 5.1 4.5 - - + -
624B LEU* 4.3 24.0 - - + +
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Residues in contact with CYS 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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532B VAL* 3.6 25.4 - - - +
533B PHE* 3.4 10.6 - - - -
535B PHE* 4.0 10.5 - - - -
536B GLY* 3.6 10.3 - - - -
539B LEU* 4.2 6.1 - - - -
582B ILE 3.0 17.9 + - - -
583B THR 3.1 7.6 + - - +
585B ARG* 1.3 75.8 - - - +
587B CYS* 1.3 59.0 + - - +
588B ASP 3.3 0.2 - - - -
594B ARG* 3.1 24.8 - - - -
595B PRO* 4.1 4.9 - - - -
600B LEU* 3.6 40.6 - - - -
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Residues in contact with CYS 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B PHE* 3.4 25.3 - - + -
536B GLY* 3.6 29.8 - - - -
537B ILE* 4.0 17.9 - - - -
540B CYS* 4.5 2.2 - - - -
560B GLY* 4.8 4.0 - - - -
561B LEU* 4.2 30.8 + - + -
583B THR 3.0 20.0 + - - +
584B VAL 3.7 7.4 - - - +
585B ARG 3.1 0.8 - - - -
586B CYS* 1.3 75.6 - - - +
588B ASP* 1.3 66.0 + - - +
589B LEU* 3.3 5.5 + - - +
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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