Contacts of the helix formed by residues 602 - 609 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598D GLU* 5.0 3.6 - - - +
600D ARG 4.8 0.2 - - - +
601D TYR* 1.3 94.7 - - + +
603D LYS* 1.3 61.3 + - - +
604D ALA* 3.6 5.2 - - + +
605D MET* 4.6 11.6 + - + +
606D LEU* 3.3 22.3 + - - +
647D TRP* 5.0 15.3 - - + -
666D VAL* 5.6 2.2 - - + -
675D TYR* 3.5 47.3 - - + +
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Residues in contact with LYS 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D ILE* 5.4 7.4 - - + -
595D ASN* 4.1 19.8 + - - +
598D GLU* 3.8 32.4 + - + +
602D PRO* 1.3 74.6 - - - +
604D ALA* 1.3 60.4 + - - +
605D MET 3.4 0.9 - - - -
606D LEU* 3.4 8.1 + - + -
607D LYS* 2.9 55.7 + - + +
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Residues in contact with ALA 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D PRO* 3.6 2.1 - - + +
603D LYS* 1.3 77.4 - - - +
605D MET* 1.3 58.4 + - - +
607D LYS* 3.3 6.9 + - - +
608D GLU* 2.9 30.8 + - - +
637D LEU* 4.0 12.3 - - + +
641D GLU* 5.9 1.6 - - - +
647D TRP* 3.6 32.1 - - + +
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Residues in contact with MET 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D TYR* 4.8 23.1 - - + -
602D PRO* 4.6 12.1 + - + +
603D LYS 3.4 0.2 - - - -
604D ALA* 1.3 78.8 - - - +
606D LEU* 1.3 65.9 + - + +
608D GLU* 4.0 5.1 - - - +
609D LEU* 2.9 53.6 + - + +
629D TRP* 6.5 0.7 - - - -
633D LEU* 4.6 17.0 - - + -
637D LEU* 4.6 10.5 - - + +
647D TRP* 5.0 7.7 - - + -
664D VAL* 4.6 22.0 - - + -
675D TYR* 5.3 13.0 - - + -
677D LEU* 5.2 14.1 - - + -
681D PHE* 4.8 15.9 - - + -
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Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D ILE* 4.1 39.7 - - + +
597D MET* 4.3 28.0 - - + +
598D GLU* 4.7 4.7 - - + -
601D TYR* 4.4 22.9 - - + +
602D PRO 3.3 21.8 - - - +
603D LYS* 3.4 9.3 + - - +
604D ALA 3.3 0.6 - - - -
605D MET* 1.3 89.7 - - + +
607D LYS* 1.3 61.5 + - - +
609D LEU* 4.0 17.7 + - + +
610D ILE* 4.1 10.0 - - - +
681D PHE* 5.4 7.2 - - + -
690D ILE* 4.6 18.4 - - + +
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Residues in contact with LYS 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591D GLN* 5.5 6.7 - - - +
594D ILE* 5.7 5.6 - - + -
603D LYS* 2.9 47.6 + - + +
604D ALA* 3.8 4.9 - - - +
606D LEU* 1.3 78.6 - - + +
608D GLU* 1.3 62.9 + - - +
610D ILE* 3.2 34.2 - - + +
611D TYR* 4.6 4.5 + - - -
720D GLU* 4.5 23.2 + - - -
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Residues in contact with GLU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D ALA 2.9 17.5 + - - +
605D MET 4.0 2.9 - - - +
607D LYS* 1.3 72.3 - - - +
609D LEU* 1.3 58.1 + - - +
610D ILE 2.9 10.4 + - - -
611D TYR* 3.0 19.3 + - - +
612D GLN* 2.8 55.0 + - + +
633D LEU* 3.8 12.8 - - + -
636D GLU* 3.1 29.2 - - + +
637D LEU* 4.0 17.1 - - + +
640D LYS* 4.5 8.5 - - - +
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Residues in contact with LEU 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605D MET* 2.9 40.3 + - + +
606D LEU* 4.3 17.0 - - + +
607D LYS 3.4 0.6 - - - -
608D GLU* 1.3 75.7 - - - +
610D ILE* 1.3 61.8 + - - +
611D TYR 3.3 0.2 - - - -
612D GLN* 3.9 30.5 - - + +
613D PRO 5.4 2.8 - - - +
629D TRP* 4.2 24.5 - - + -
633D LEU* 4.8 8.3 - - + -
681D PHE* 5.4 5.2 - - + -
687D TYR* 4.3 27.4 - - + +
690D ILE* 4.4 20.7 - - + +
691D CYS* 6.0 0.7 - - - -
694D GLY* 4.9 2.8 - - - -
698D ARG* 4.2 2.9 + - - -
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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