Contacts of the strand formed by residues 609 - 618 (chain A) in PDB entry 1YC0
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 VAL 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A CYS 3.7 10.8 - - - +
395A GLY 3.6 2.9 - - - -
396A ARG* 4.2 17.5 - - + +
521A CYS* 3.5 31.4 - - - -
605A GLU* 3.2 4.4 - - - +
606A LYS 3.0 26.0 + - - +
607A ASN* 3.2 11.8 - - + +
608A GLY* 1.3 83.2 - - - +
610A ALA* 1.3 62.6 + - - +
611A TYR* 3.2 32.2 - - + +
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Residues in contact with ALA 610 (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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395A GLY* 2.9 14.2 + - - +
397A ARG* 4.6 9.2 - - - +
421A TRP* 3.5 39.0 - - + -
520A ILE* 3.9 6.5 - - + -
521A CYS* 3.3 28.2 + - - +
603A ALA* 4.6 6.3 - - + -
604A CYS 3.8 4.5 - - - -
605A GLU* 4.2 6.1 + - + +
609A VAL* 1.3 72.9 - - - +
611A TYR* 1.3 59.4 + - - +
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Residues in contact with TYR 611 (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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520A ILE* 3.8 4.7 - - - -
521A CYS* 3.3 19.2 - - + -
522A LEU 3.5 23.3 - - - -
523A PRO* 3.8 17.0 - - + -
524A GLU 5.6 0.2 - - - -
529A PHE* 4.4 20.9 - + + -
603A ALA* 3.3 4.9 - - - -
604A CYS* 2.8 40.5 + - - +
606A LYS* 3.9 23.0 + - + -
609A VAL* 3.2 52.2 - - + +
610A ALA* 1.3 74.4 - - - +
612A LEU* 1.3 61.1 + - - +
613A TYR* 3.0 5.5 + - - -
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Residues in contact with LEU 612 (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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435A SER* 3.7 15.0 - - - +
437A VAL* 3.8 26.9 - - + -
443A VAL* 4.0 19.3 - - + -
520A ILE* 3.8 12.4 - - + +
521A CYS 2.7 17.0 + - - +
522A LEU* 4.0 13.5 - - + -
523A PRO* 3.1 20.7 - - - +
601A PRO* 3.4 26.5 - - + -
602A LEU 4.4 0.9 - - - -
611A TYR* 1.3 67.9 - - - +
613A TYR* 1.3 58.3 + - - +
614A GLY 3.3 24.7 - - - +
615A ILE* 4.6 4.3 - - + -
634A VAL* 3.2 19.3 - - + +
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Residues in contact with TYR 613 (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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523A PRO* 4.6 13.0 - - + -
527A SER 3.9 9.0 - - - -
528A THR* 3.5 24.2 - - + +
529A PHE* 3.1 53.1 + + + -
561A LEU* 3.7 25.8 - - + -
582A LEU* 3.7 28.1 - - + +
602A LEU* 3.3 5.5 + - + +
604A CYS* 3.7 32.8 - - + -
611A TYR 3.0 9.1 + - - +
612A LEU* 1.3 73.5 - - - +
614A GLY* 1.3 58.1 + - - +
632A THR 3.8 1.2 - - - +
633A ARG* 4.6 9.2 + - + -
634A VAL* 3.4 19.8 + - - +
635A ALA* 4.3 6.6 + - + -
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Residues in contact with GLY 614 (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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582A LEU* 5.0 0.7 - - - -
602A LEU* 2.9 43.9 + - - +
612A LEU* 3.3 15.3 - - - +
613A TYR* 1.3 78.9 - - - +
615A ILE* 1.3 64.4 + - - -
631A TYR* 4.3 2.5 - - - -
632A THR 3.1 12.8 - - - -
634A VAL* 3.6 1.6 - - - -
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Residues in contact with ILE 615 (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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443A VAL* 3.4 32.5 - - + +
444A SER 3.6 10.1 - - - +
445A ALA* 3.9 13.7 - - + +
497A ASP 4.0 9.0 - - - +
498A LEU* 3.8 17.5 - - + -
599A GLY* 3.6 32.5 - - - +
600A GLY 3.6 3.6 - - - +
612A LEU* 4.6 5.6 - - + -
614A GLY* 1.3 77.9 - - - +
616A ILE* 1.3 73.1 + - - +
617A SER* 3.0 4.5 + - - -
631A TYR* 3.3 6.2 - - - +
632A THR* 3.1 33.1 + - - +
634A VAL* 3.5 13.5 - - + -
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Residues in contact with ILE 616 (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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408A ILE* 5.0 0.2 - - + -
445A ALA* 4.0 2.6 - - - +
537A ILE* 4.3 13.0 - - + -
538A ALA 3.9 16.2 - - - +
593A ALA* 3.7 23.6 - - + -
597A ASP* 3.3 44.0 - - + +
598A SER* 3.5 5.6 + - - +
599A GLY 2.9 22.6 + - - +
600A GLY* 2.8 31.4 + - - +
601A PRO 4.2 6.7 - - - +
614A GLY 4.3 0.2 - - - -
615A ILE* 1.3 71.8 - - - +
617A SER* 1.3 60.2 + - - +
631A TYR* 3.6 26.1 - - + -
260I ARG* 4.3 11.4 - - - +
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Residues in contact with SER 617 (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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447A HIS* 3.3 16.2 - - - -
494A SER 3.9 1.2 + - - -
497A ASP* 2.6 28.3 + - - +
598A SER* 3.5 1.2 + - - -
615A ILE 3.0 9.7 + - - -
616A ILE* 1.3 78.0 - - - +
618A TRP* 1.3 81.1 + - - +
630A VAL 3.3 14.1 + - - -
631A TYR* 4.1 1.1 - - - -
632A THR* 4.0 14.4 - - - -
259I CYS* 3.6 0.2 - - - -
260I ARG* 3.2 22.6 + - - +
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Residues in contact with TRP 618 (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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494A SER* 3.9 13.2 + - - -
573A TYR* 3.6 40.4 - + - -
576A ASP* 4.1 18.8 - - + -
577A ILE* 3.9 4.7 - - + -
581A MET* 3.6 29.7 - - + +
617A SER* 1.3 105.1 - - - +
619A GLY* 1.3 79.7 + - - +
620A ASP* 5.5 0.7 - - + -
630A VAL* 2.9 61.1 + - + +
258I ARG* 3.1 64.6 - - + +
259I CYS* 3.9 4.9 - - - -
260I ARG* 3.6 17.0 + - - +
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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