Contacts of the helix formed by residues 602 - 609 (chain B) in PDB entry 6RKU
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 602 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598B GLU* 5.0 3.8 - - - +
601B TYR* 1.3 93.6 - - + +
603B LYS* 1.3 63.2 + - - +
604B ALA* 4.5 4.5 - - + +
605B MET* 4.6 11.7 + - + +
606B LEU* 3.3 22.6 + - - +
647B TRP* 5.0 16.2 - - + -
666B VAL* 5.6 2.2 - - + -
675B TYR* 3.5 48.0 - - + +
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Residues in contact with LYS 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ILE* 5.4 7.2 - - + -
595B ASN* 4.1 19.6 + - - +
598B GLU* 3.8 31.3 + - + +
602B PRO* 1.3 74.2 - - - +
604B ALA* 1.3 60.8 + - - +
605B MET 3.4 0.4 - - - -
606B LEU* 3.4 8.4 + - + -
607B LYS* 2.9 55.0 + - + +
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Residues in contact with ALA 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B PRO* 3.6 2.0 - - + +
603B LYS* 1.3 78.3 - - - +
605B MET* 1.3 58.7 + - - +
607B LYS* 3.3 6.8 + - - +
608B GLU* 2.9 30.3 + - - +
637B LEU* 4.0 12.3 - - + +
641B GLU* 5.9 1.1 - - - +
647B TRP* 3.6 33.2 - - + +
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Residues in contact with MET 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B TYR* 4.8 23.6 - - + -
602B PRO* 4.6 12.3 + - + +
603B LYS 3.4 0.4 - - - -
604B ALA* 1.3 79.6 - - - +
606B LEU* 1.3 66.8 + - + +
608B GLU* 4.0 4.7 - - - +
609B LEU* 2.9 52.5 + - + +
629B TRP* 6.5 0.9 - - - -
633B LEU* 4.6 17.5 - - + -
637B LEU* 4.6 10.3 - - + +
647B TRP* 5.0 7.8 - - + -
664B VAL* 4.6 22.2 - - + -
675B TYR* 5.3 13.2 - - + -
677B LEU* 5.2 14.1 - - + -
681B PHE* 4.8 15.3 - - + -
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ILE* 4.1 40.0 - - + +
597B MET* 4.3 27.8 - - + -
598B GLU* 4.7 5.2 - - + -
601B TYR* 4.4 23.8 - - + +
602B PRO 3.3 22.0 + - - +
603B LYS* 3.4 9.3 + - - +
604B ALA 3.3 0.4 - - - -
605B MET* 1.3 90.1 - - + +
607B LYS* 1.3 61.6 + - - +
609B LEU* 4.0 16.8 + - + +
610B ILE* 4.1 10.0 - - - +
681B PHE* 5.4 7.0 - - + -
690B ILE* 4.6 18.6 - - + +
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Residues in contact with LYS 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B GLN* 5.5 6.7 - - - +
594B ILE* 5.7 5.8 - - + -
603B LYS* 2.9 47.0 + - + +
604B ALA* 3.8 5.6 - - - +
606B LEU* 1.3 77.7 - - + +
608B GLU* 1.3 62.7 + - - +
610B ILE* 3.2 33.5 - - + +
611B TYR* 4.6 4.3 + - - -
720B GLU* 4.5 22.8 + - - -
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B ALA 2.9 17.7 + - - +
605B MET 3.2 3.1 + - - +
607B LYS* 1.3 72.1 - - - +
609B LEU* 1.3 58.2 + - - +
610B ILE 2.9 10.4 + - - -
611B TYR* 3.0 19.9 + - - +
612B GLN* 2.8 54.6 + - + +
633B LEU* 3.8 12.1 - - + -
636B GLU* 3.1 29.9 - - + +
637B LEU* 4.0 17.2 - - + +
640B LYS* 4.5 8.8 - - - +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B MET* 2.9 41.3 + - + +
606B LEU* 4.3 17.0 - - + +
607B LYS 3.4 0.6 - - - -
608B GLU* 1.3 75.7 - - - +
610B ILE* 1.3 62.3 + - - +
611B TYR 3.3 0.2 - - - -
612B GLN* 3.9 30.0 - - + +
613B PRO 5.4 2.9 - - - +
629B TRP* 4.2 24.2 - - + +
633B LEU* 4.8 8.1 - - + -
681B PHE* 5.4 6.3 - - + -
687B TYR* 4.3 26.9 - - + +
690B ILE* 4.4 21.2 - - + +
691B CYS* 6.0 1.0 - - - -
694B GLY* 4.9 2.9 - - - -
698B ARG* 4.2 3.1 + - - -
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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