Contacts of the helix formed by residues 604 - 612 (chain D) in PDB entry 4PE5
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 LYS 604 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602D ILE 3.1 4.0 + - - -
603D GLY* 1.3 72.5 - - - -
605D ALA* 1.3 58.7 + - - +
606D ILE 3.3 1.3 - - - -
607D TRP* 3.5 9.8 + - + +
608D LEU* 3.0 28.6 + - - +
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Residues in contact with ALA 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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566D LEU 6.1 0.2 - - - -
602D ILE* 3.5 24.0 + - + +
603D GLY 3.3 0.4 - - - -
604D LYS* 1.3 77.2 - - - +
606D ILE* 1.3 58.6 + - - +
608D LEU* 3.4 6.0 + - - +
609D LEU* 2.9 30.1 + - - +
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Residues in contact with ILE 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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566D LEU* 5.5 10.9 - - + +
602D ILE* 4.7 13.5 - - + +
603D GLY 4.2 9.7 + - - +
604D LYS 3.3 0.4 - - - -
605D ALA* 1.3 80.2 - - - +
607D TRP* 1.3 57.1 - - - +
609D LEU* 3.8 5.5 - - - +
610D TRP* 2.9 32.7 + - - +
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Residues in contact with TRP 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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634C MET* 6.5 0.9 - - - -
603D GLY 4.4 3.7 + - - +
604D LYS* 3.5 15.5 + - + +
605D ALA 3.3 0.2 - - - -
606D ILE* 1.3 78.0 - - - +
608D LEU* 1.3 58.6 + - - +
610D TRP* 4.6 3.4 - - - +
611D GLY* 2.9 25.9 + - - +
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Residues in contact with LEU 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 LYS 3.0 18.1 + - - +
605D ALA* 3.7 7.4 - - - +
607D TRP* 1.3 77.1 - - - +
609D LEU* 1.3 61.9 + - - +
611D GLY* 4.1 1.1 - - - -
612D LEU* 3.3 24.6 + - - +
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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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566D LEU* 4.9 23.1 - - + +
605D ALA 2.9 18.4 + - - +
606D ILE* 3.9 5.8 - - - +
608D LEU* 1.3 77.2 - - - +
610D TRP* 1.3 61.9 + - - +
612D LEU* 3.6 6.0 + - - +
613D VAL* 3.5 18.0 + - - +
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Residues in contact with TRP 610 (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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634C MET* 5.7 9.2 - - + -
637C ALA* 6.1 1.0 - - - +
566D LEU* 6.1 4.7 - - + -
606D ILE 2.9 18.4 + - - +
607D TRP* 4.6 2.9 - - - +
609D LEU* 1.3 75.3 - - - +
611D GLY* 1.3 64.1 + - - +
612D LEU 3.3 0.4 - - - -
613D VAL* 3.3 20.9 + - + +
614D PHE* 4.1 6.1 + - - +
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Residues in contact with GLY 611 (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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637C ALA* 6.2 4.3 - - - -
607D TRP 2.9 21.4 + - - -
608D LEU* 4.1 1.3 - - - -
609D LEU 3.3 0.2 - - - -
610D TRP* 1.3 79.1 - - - +
612D LEU* 1.3 56.3 + - - +
613D VAL 3.2 1.0 + - - -
614D PHE* 3.8 14.7 + - - +
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Residues in contact with LEU 612 (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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608D LEU 3.3 19.2 + - - +
609D LEU* 4.1 6.1 - - - +
610D TRP 3.3 0.4 - - - -
611D GLY* 1.3 74.9 - - - +
613D VAL* 1.3 60.5 + - - +
614D PHE 3.3 7.2 + - - +
632D VAL 5.7 1.6 - - - +
635D TRP* 5.8 1.8 - - + +
636D ALA* 4.5 21.3 - - + +
639D ALA* 3.3 16.9 - - + +
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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