Contacts of the helix formed by residues 578 - 587 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A PRO 3.3 1.0 + - - -
577A PRO* 1.3 77.4 + - - +
579A PHE* 1.3 57.6 + - - +
580A PHE 3.4 2.0 - - - -
581A PRO* 3.4 8.2 - - - +
582A ILE* 2.9 37.6 + - - +
607A LEU* 4.0 6.9 - - - +
617A LEU* 4.5 3.7 - - - +
621A LEU* 3.7 52.1 - - - +
624A LEU* 5.0 2.2 - - - -
625A ASP* 2.9 24.9 + - - -
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Residues in contact with PHE 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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434A TRP* 3.9 22.2 - + - -
437A ARG* 4.3 5.2 - - + -
438A VAL* 3.9 24.7 - - + -
441A ALA* 4.2 4.0 - - + -
539A LEU* 3.8 30.1 - - + -
542A ILE* 4.5 9.2 - - + -
543A ILE* 3.6 29.2 - - + -
575A CYS* 4.0 2.7 - - - -
576A PRO* 3.2 25.6 + - + +
577A PRO 3.2 4.0 + - - -
578A SER* 1.3 76.0 - - - +
580A PHE* 1.3 61.7 + - - +
582A ILE* 3.4 5.4 + - + +
583A THR* 2.9 26.6 + - - -
604A LEU* 3.8 21.3 - - + -
607A LEU* 3.8 23.1 - - + -
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Residues in contact with PHE 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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540A CYS* 5.3 0.2 - - - -
543A ILE* 4.2 5.8 - - + -
561A LEU* 4.3 12.1 - - + -
563A VAL* 3.9 18.6 - - + -
566A PHE* 3.3 42.6 - + - -
567A LEU* 3.5 33.0 - - + -
571A CYS* 4.6 8.3 - - - -
575A CYS* 4.1 15.8 - - - -
576A PRO 4.5 0.8 + - - -
579A PHE* 1.3 74.5 - - - +
581A PRO* 1.4 69.7 - - + +
583A THR* 2.9 18.4 + - + -
584A VAL* 2.8 53.0 + - + +
628A PHE* 3.9 13.9 - + - -
629A TRP* 4.9 4.0 - + + -
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Residues in contact with PRO 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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578A SER 3.4 14.1 - - - +
579A PHE 4.0 0.2 - - - +
580A PHE* 1.4 95.3 - - + +
582A ILE* 1.3 61.8 + - - +
584A VAL* 3.3 8.3 + - + +
585A ARG* 3.0 24.6 + - - +
624A LEU* 3.9 22.4 - - + +
625A ASP* 3.4 26.0 - - - +
628A PHE* 3.8 38.9 - - + +
629A TRP* 4.3 5.6 - - + +
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Residues in contact with ILE 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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539A LEU* 4.1 14.6 - - + -
578A SER* 2.9 31.8 + - - +
579A PHE* 3.6 10.8 - - + +
581A PRO* 1.3 71.8 - - - +
583A THR* 1.3 65.5 + - - +
585A ARG* 3.2 6.5 + - - +
586A CYS* 3.0 21.7 + - - -
595A PRO* 5.4 0.2 - - - +
600A LEU* 3.5 29.4 - - + -
603A TRP* 3.8 17.9 - - + -
604A LEU* 3.9 26.0 - - + -
607A LEU* 4.6 4.0 - - + -
621A LEU* 4.0 17.0 - - + -
624A LEU* 3.5 20.4 - - + -
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Residues in contact with THR 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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536A GLY 3.5 22.4 - - - +
539A LEU* 3.3 24.6 - - + +
540A CYS* 3.5 24.7 - - - +
543A ILE* 3.2 15.8 - - + +
561A LEU* 4.7 0.7 - - + -
579A PHE* 2.9 12.2 + - - -
580A PHE* 2.9 22.3 + - + -
582A ILE* 1.3 76.7 - - - +
584A VAL* 1.3 62.5 - - - +
586A CYS* 3.1 4.4 + - - +
587A CYS* 3.0 24.3 + - - -
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Residues in contact with VAL 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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561A LEU* 4.3 8.3 - - + -
563A VAL* 4.1 20.2 - - + -
580A PHE* 2.8 58.5 + - + +
581A PRO 3.8 3.8 - - - +
583A THR* 1.3 72.4 - - - +
585A ARG* 1.3 63.2 + - - +
587A CYS* 3.2 13.4 + - - +
588A ASP* 3.4 11.4 + - - +
628A PHE* 3.8 29.6 - - + -
637A SER 4.6 5.4 - - - +
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Residues in contact with ARG 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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6A GOL 3.1 36.1 + - - +
581A PRO 3.0 17.0 + - - +
582A ILE* 3.2 7.2 + - - +
584A VAL* 1.3 77.7 - - - +
586A CYS* 1.3 61.9 + - - +
588A ASP* 3.2 31.2 + - - +
593A LYS* 3.1 45.7 + - - +
594A ARG* 3.6 8.7 - - - +
595A PRO* 3.8 12.6 - - + -
603A TRP* 5.0 1.6 - - + -
624A LEU* 4.2 19.9 - - + +
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Residues in contact with CYS 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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532A VAL* 3.6 25.9 - - + +
533A PHE* 3.4 11.5 - - - -
535A PHE* 3.9 11.9 - - - -
536A GLY* 3.6 10.3 - - - -
539A LEU* 4.3 2.5 - - - -
582A ILE* 3.0 21.3 + - - -
583A THR 3.1 7.4 + - - +
585A ARG* 1.3 76.1 - - - +
587A CYS* 1.3 57.8 + - - +
588A ASP 3.3 0.2 - - - -
594A ARG* 3.2 23.7 - - - -
595A PRO* 4.2 4.3 - - - -
600A LEU* 3.6 40.4 - - - -
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Residues in contact with CYS 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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533A PHE* 3.4 23.9 - - + -
536A GLY* 3.6 30.1 - - - -
537A ILE* 4.0 17.5 - - - -
540A CYS* 4.5 1.6 - - - -
560A GLY* 4.8 2.6 - - - -
561A LEU* 4.0 36.9 + - + -
583A THR 3.0 16.9 + - - +
584A VAL 3.2 9.3 + - - +
586A CYS* 1.3 76.3 - - - +
588A ASP* 1.3 64.4 + - - +
589A LEU* 3.3 2.1 + - - +
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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