Contacts of the helix formed by residues 598 - 609 (chain A) in PDB entry 4YJS
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 PRO 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ASP* 4.1 21.3 - - + +
472A ILE* 4.5 8.5 - - + -
566A PHE* 4.0 15.3 - - + -
596A GLY 3.5 8.0 - - - +
597A CYS* 1.3 92.8 - - - +
599A ARG* 1.3 66.5 + - - +
600A GLU* 3.3 2.5 - - - +
601A MET* 3.2 21.3 + - + +
602A TYR* 3.2 8.7 + - - +
629A TYR* 3.5 27.1 - - + +
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Residues in contact with ARG 599 (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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593A CYS* 3.8 24.8 - - - +
597A CYS 4.3 3.1 - - - +
598A PRO* 1.3 72.9 - - - +
600A GLU* 1.3 57.5 + - - +
602A TYR* 3.1 35.4 + - - +
603A ASP* 2.7 51.5 + - - +
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Residues in contact with GLU 600 (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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598A PRO* 4.2 1.2 - - - +
599A ARG* 1.3 83.8 + - + +
601A MET* 1.3 62.8 + - + +
603A ASP* 3.3 13.0 + - - +
604A LEU* 3.0 26.0 + - - +
629A TYR* 2.9 52.3 + - + -
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Residues in contact with MET 601 (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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472A ILE* 3.9 21.3 - - + -
562A MET* 3.8 10.4 - - + +
566A PHE* 3.8 21.1 - - + -
597A CYS* 3.9 13.9 - - - -
598A PRO* 3.2 14.4 + - + +
600A GLU* 1.3 81.7 - - + +
602A TYR* 1.3 65.1 + - - +
604A LEU* 3.3 15.5 + - + +
605A MET* 3.0 26.6 + - - +
625A ARG 5.0 2.0 - - - +
626A LEU* 3.5 33.2 - - + -
629A TYR* 3.6 37.7 - - + -
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Residues in contact with TYR 602 (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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590A ARG* 4.6 3.6 + - - +
591A MET 2.7 29.5 + - - -
592A GLY* 3.5 16.2 - - - -
593A CYS* 3.6 37.9 - - + -
594A PRO* 4.4 0.2 - - + -
597A CYS* 4.0 3.0 - - - -
598A PRO 3.2 7.2 + - - +
599A ARG* 3.1 36.6 + - - +
601A MET* 1.3 73.6 - - - +
603A ASP* 1.3 71.2 + - - +
605A MET* 3.1 22.1 + - - +
606A ASN* 3.1 48.8 + - - -
609A TRP* 4.3 8.5 - + - -
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Residues in contact with ASP 603 (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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599A ARG* 2.7 37.0 + - - +
600A GLU* 3.5 11.8 - - - +
601A MET 3.3 0.2 - - - -
602A TYR* 1.3 80.0 - - - +
604A LEU* 1.3 61.3 + - - +
606A ASN* 3.3 9.5 + - - +
607A LEU* 3.1 21.5 + - - +
625A ARG* 6.4 0.2 - - - +
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Residues in contact with LEU 604 (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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562A MET* 4.1 15.5 - - + -
600A GLU 3.0 14.0 + - - +
601A MET* 3.5 17.0 - - + +
602A TYR 3.1 0.2 - - - -
603A ASP* 1.3 74.7 - - - +
605A MET* 1.3 65.2 + - - +
607A LEU* 3.2 12.7 + - + +
608A CYS* 3.1 28.2 + - - -
617A PRO* 5.9 0.2 - - + -
622A VAL* 4.2 21.8 - - + +
625A ARG* 3.7 41.1 - - + +
626A LEU* 3.6 36.8 - - + -
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Residues in contact with MET 605 (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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559A GLY* 3.9 16.2 - - - +
562A MET* 3.9 11.0 - - + -
563A TRP* 3.7 43.1 - - - +
566A PHE* 3.8 17.0 - - + -
594A PRO* 4.3 4.5 - - + -
597A CYS* 3.6 31.0 - - - -
601A MET 3.0 18.1 + - - +
602A TYR* 3.1 24.0 + - - +
604A LEU* 1.3 75.2 - - - +
606A ASN* 1.3 58.6 + - - +
608A CYS* 3.3 9.3 + - - +
609A TRP* 3.0 47.9 + - + -
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Residues in contact with ASN 606 (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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590A ARG* 3.4 30.5 + - - +
602A TYR* 3.1 47.1 + - - +
603A ASP* 3.7 11.4 + - - +
604A LEU 3.2 0.4 - - - -
605A MET* 1.3 79.9 - - - +
607A LEU* 1.3 61.7 + - - +
609A TRP* 3.2 31.0 + - - +
610A THR* 3.5 2.4 + - - -
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Residues in contact with LEU 607 (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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603A ASP 3.1 13.6 + - - +
604A LEU* 3.2 13.9 + - + +
606A ASN* 1.3 72.9 - - - +
608A CYS* 1.3 63.2 + - - +
610A THR* 2.5 34.0 + - - +
615A ASN 5.3 3.1 - - - +
617A PRO* 3.4 34.2 - - + +
625A ARG* 3.7 44.0 - - - +
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Residues in contact with CYS 608 (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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555A VAL* 3.4 39.3 - - - +
556A TRP* 3.5 8.2 - - - -
558A PHE* 4.2 21.8 - - - -
559A GLY* 3.9 13.5 - - - -
562A MET* 5.0 0.7 - - - -
604A LEU* 3.1 24.0 + - - -
605A MET* 3.5 8.5 - - - +
607A LEU* 1.3 76.0 - - - +
609A TRP* 1.3 58.7 + - - +
610A THR 3.1 0.6 + - - -
616A ARG* 3.1 26.7 + - - -
617A PRO* 4.7 0.7 - - - -
622A VAL* 4.2 15.0 - - - -
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Residues in contact with TRP 609 (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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556A TRP* 3.4 43.8 - + + -
559A GLY* 3.5 20.1 - - - -
560A VAL* 3.4 26.7 - - + +
563A TRP* 4.0 16.6 - + + -
573A TYR* 4.9 4.5 - - - -
590A ARG* 3.2 46.1 + - + +
591A MET* 3.6 51.6 - - + -
602A TYR* 4.3 4.7 - + - -
605A MET* 3.0 34.8 + - + +
606A ASN* 3.2 28.9 + - - +
607A LEU 3.2 0.8 - - - -
608A CYS* 1.3 76.6 - - - +
610A THR* 1.3 61.5 + - - -
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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