Contacts of the helix formed by residues 602 - 607 (chain O) in PDB entry 6RQT
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 TYR 602 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333O ASP* 4.9 1.7 + - - +
336O LEU* 3.4 66.0 - - + -
337O THR* 3.8 3.1 - - - +
340O SER* 3.9 16.6 + - - -
383O TYR* 3.9 35.9 + + + +
386O PHE* 5.8 0.3 - - - -
387O HIS* 4.1 9.4 - - - +
597O LEU* 4.2 18.2 - - + -
599O LEU* 4.5 14.4 - - + +
601O ASN* 1.3 75.3 - - - +
603O LYS* 1.3 56.8 + - - +
604O ILE 3.1 4.7 - - - -
605O LEU* 3.0 40.8 + - + +
606O MET* 3.3 36.3 + - + +
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Residues in contact with LYS 603 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597O LEU* 3.7 33.7 + - + +
599O LEU 3.6 24.3 + - - +
600O LYS* 4.3 9.8 - - - +
601O ASN 3.5 1.0 - - - +
602O TYR* 1.3 75.9 - - - +
604O ILE* 1.3 63.3 + - - +
605O LEU 3.2 0.2 - - - -
606O MET 3.8 2.0 - - - +
607O LYS* 3.0 52.1 + - + +
610O TYR* 4.1 28.7 - - - -
612O GLU* 4.9 8.2 + - - -
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Residues in contact with ILE 604 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337O THR* 5.4 8.7 - - + -
600O LYS 4.5 3.8 + - - +
601O ASN* 3.3 43.3 - - + +
603O LYS* 1.3 79.3 - - - +
605O LEU* 1.3 70.9 + - + +
607O LYS* 4.5 10.3 - - - +
608O GLU* 5.2 1.2 + - - +
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Residues in contact with LEU 605 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336O LEU 4.2 5.2 - - - +
337O THR* 4.2 13.0 - - + +
340O SER* 3.9 13.0 - - - +
341O THR* 3.4 29.8 - - + +
344O GLU* 4.3 4.5 - - - +
387O HIS* 3.2 39.6 + - + +
602O TYR* 3.0 38.8 + - + +
604O ILE* 1.3 87.9 - - + +
606O MET* 1.3 58.8 + - - +
607O LYS 3.5 0.4 - - - -
608O GLU* 3.5 20.7 - - - +
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Residues in contact with MET 606 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386O PHE* 3.6 46.9 - - + +
387O HIS* 2.7 40.4 - - - +
390O GLN* 3.7 13.0 - - - +
597O LEU* 3.9 22.6 - - + +
602O TYR* 3.3 34.8 + - + +
603O LYS* 3.5 3.7 + - - +
605O LEU* 1.3 77.1 - - - +
607O LYS* 1.3 57.8 + - - +
608O GLU* 3.1 5.4 - - - +
609O TYR* 4.7 10.8 - - + +
610O TYR* 3.2 26.0 + - + +
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Residues in contact with LYS 607 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603O LYS* 3.0 45.3 + - + +
604O ILE* 4.5 9.0 - - - +
605O LEU 3.5 0.4 - - - -
606O MET* 1.3 77.3 - - - +
608O GLU* 1.3 65.3 + - - +
609O TYR 3.6 0.4 - - - -
610O TYR* 3.7 20.7 - - + +
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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