Contacts of the helix formed by residues 602 - 608 (chain A) in PDB entry 5YDJ
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 ASP 602 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TRP* 6.1 0.3 - - - -
483A ASN* 4.3 0.2 - - - +
583A TYR* 3.8 25.3 + - + +
585A HIS 4.5 4.8 - - - +
586A ARG* 5.3 2.1 - - - -
587A SER* 5.8 1.4 + - - +
590A ASN* 4.5 16.6 + - - -
592A TRP* 6.0 1.4 - - - -
597A GLY 3.9 3.5 - - - +
598A VAL* 3.4 9.5 - - + +
599A MET* 2.8 46.7 + - - +
600A HIS 4.5 1.2 - - - +
601A GLY* 1.3 78.0 - - - +
603A GLU* 1.3 64.6 + - - +
604A ILE 3.2 0.7 + - - -
605A ASN* 3.4 23.2 + - - +
606A TYR* 3.9 3.5 - - + -
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Residues in contact with GLU 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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359A GLU* 3.2 26.3 - - - +
385A GLN* 3.3 25.0 - - - +
386A SER* 3.6 13.9 + - - -
483A ASN* 2.9 26.3 + - - +
581A TYR* 4.0 12.6 - - + +
583A TYR* 3.6 34.9 - - + -
601A GLY* 3.1 7.7 + - - -
602A ASP* 1.3 82.2 + - - +
604A ILE* 1.3 64.9 + - - +
606A TYR* 3.1 6.6 + - - +
607A VAL* 3.0 28.2 + - + +
629A ILE* 4.1 1.2 - - + +
633A TRP* 5.8 1.6 - - + -
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Residues in contact with ILE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TRP* 3.8 22.0 - - + -
275A TRP* 4.5 1.3 - - + -
290A VAL* 4.1 12.5 - - + +
291A TYR* 3.7 30.7 - - + +
359A GLU* 3.6 45.1 - - + +
360A SEB 5.6 0.4 - - + -
385A GLN* 3.9 8.3 - - - +
601A GLY* 3.4 19.1 - - - +
602A ASP 3.2 0.4 - - - -
603A GLU* 1.3 77.2 - - - +
605A ASN* 1.3 64.9 + - - +
607A VAL* 3.3 8.9 - - - +
608A PHE* 3.2 40.5 + - + +
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Residues in contact with ASN 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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244A MET* 4.2 22.1 - - - +
245A TRP* 4.8 4.0 - - - -
290A VAL* 4.5 12.8 - - - +
587A SER* 5.5 1.1 + - - +
601A GLY 3.7 10.9 - - - +
602A ASP* 3.5 17.6 - - - +
603A GLU 3.2 0.6 - - - -
604A ILE* 1.3 78.5 - - - +
606A TYR* 1.3 65.1 + - + +
608A PHE* 4.3 0.3 - - - +
609A GLY 3.6 1.4 + - - -
610A GLU* 2.8 60.9 + - - +
611A PRO* 3.4 1.6 - - - +
618A TYR* 3.4 18.8 + - - +
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Residues in contact with TYR 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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583A TYR* 3.1 24.7 - - + +
585A HIS* 3.0 21.8 + + - -
587A SER* 3.0 27.7 + - - -
602A ASP 3.9 9.9 - - - -
603A GLU 3.1 4.9 + - - +
605A ASN* 1.3 82.6 - - + +
607A VAL* 1.3 63.6 + - - +
608A PHE 3.3 1.8 - - - -
609A GLY 3.5 2.0 + - - -
611A PRO* 4.0 4.9 - - + -
618A TYR* 3.6 13.9 - + - -
622A GLU* 3.3 43.7 + - + +
625A PHE* 3.6 23.3 - + - -
626A SER* 2.8 34.3 + - - +
629A ILE* 3.4 21.6 - - + +
630A MET* 3.5 7.6 - - - +
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Residues in contact with VAL 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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296A LEU* 3.6 19.6 - - - +
357A PHE* 5.1 3.8 - - + -
385A GLN* 3.8 17.9 - - - +
603A GLU* 3.0 17.7 + - + +
604A ILE* 3.3 22.4 - - - +
606A TYR* 1.3 75.7 - - - +
608A PHE* 1.3 75.2 + - + +
609A GLY 3.4 0.2 - - - -
629A ILE* 3.5 21.3 - - + -
630A MET* 3.4 19.2 - - - +
633A TRP* 3.5 42.5 - - + +
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Residues in contact with PHE 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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275A TRP* 3.4 55.4 - + - -
290A VAL 3.3 25.8 - - - +
291A TYR* 3.8 16.4 - + - -
292A ASP* 3.4 34.1 - - + +
293A HIS* 4.0 20.0 - + - -
295A ALA* 3.4 12.4 - - - +
296A LEU* 4.3 17.6 + - + -
304A VAL* 4.6 1.3 - - + -
357A PHE* 3.7 20.6 - + - -
604A ILE* 3.2 26.3 + - + +
605A ASN 4.8 1.6 - - - +
607A VAL* 1.3 81.7 - - + +
609A GLY* 1.3 62.2 + - - +
610A GLU* 3.5 2.0 + - + +
630A MET* 4.6 1.1 - - - -
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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