Contacts of the helix formed by residues 604 - 609 (chain D) in PDB entry 5LS6
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 CYS 604 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579D GLU* 3.3 11.2 - - - -
590D ALA* 4.3 15.0 - - + -
599D VAL* 4.1 12.3 - - - -
601D CYS* 3.8 27.1 - - - -
603D ASN* 1.3 78.6 - - - +
605D SER* 1.3 65.1 + - - +
606D ILE 3.4 0.2 + - - -
607D GLN* 3.2 28.3 + - - +
608D ARG* 3.0 46.2 + - + +
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Residues in contact with SER 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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579D GLU* 3.4 6.8 + - - -
602D LYS* 4.4 13.5 + - - -
603D ASN* 4.4 0.7 + - - -
604D CYS* 1.3 78.3 + - - +
606D ILE* 1.3 57.0 + - - +
608D ARG* 3.7 1.0 - - - -
609D GLY* 3.0 23.2 + - - -
610D SER* 3.1 22.5 + - - -
637D PHE* 3.5 41.8 - - - +
711D PHE* 5.8 0.7 - - - -
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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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579D GLU* 3.1 24.1 + - + +
605D SER* 1.3 74.9 - - - +
607D GLN* 1.3 65.9 + - - +
609D GLY* 3.2 11.8 + - - -
637D PHE* 3.5 26.7 - - + -
640D GLU* 4.0 12.4 - - + +
700D MET* 4.5 19.7 - - + -
702D VAL* 4.5 4.7 - - + -
707D ARG* 3.4 63.3 + - + +
708D ILE 4.7 0.2 - - - -
709D GLY* 4.1 22.2 - - - +
711D PHE* 4.7 1.8 - - + -
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Residues in contact with GLN 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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579D GLU* 3.2 12.8 + - - +
580D CYS* 2.7 36.9 + - - +
582D PRO* 4.0 15.3 - - - +
590D ALA* 4.5 4.2 - - - +
604D CYS* 3.2 33.7 - - - +
606D ILE* 1.3 79.0 - - - +
608D ARG* 1.3 61.5 + - + +
609D GLY 3.5 0.5 + - - -
702D VAL* 3.7 15.7 - - + +
703D ASN* 4.3 7.0 - - - +
707D ARG* 3.6 16.6 + - - +
627F ILE* 3.9 40.5 - - + +
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Residues in contact with ARG 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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589D GLY 3.9 4.4 + - - -
590D ALA 3.1 30.3 + - - -
592D ASP 3.4 12.5 + - - -
593D HIS 3.5 18.8 + - - -
594D TRP* 3.3 32.3 + - - -
596D SER 3.6 14.1 + - - -
597D LYS* 3.6 46.0 + - + +
599D VAL* 4.0 18.6 - - - +
604D CYS* 3.0 33.6 + - + +
605D SER* 4.0 0.7 - - - +
607D GLN* 1.3 79.8 + - + +
609D GLY* 1.3 62.4 + - - +
610D SER* 3.6 10.9 + - - +
627F ILE* 3.9 13.7 - - + -
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Residues in contact with GLY 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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117D GLN* 6.2 0.4 - - - -
118D GLN* 6.3 1.6 - - - -
605D SER 3.0 7.2 + - - -
606D ILE* 3.2 11.2 + - - -
607D GLN 3.4 0.6 + - - -
608D ARG* 1.3 77.9 - - - +
610D SER* 1.3 60.3 + - - +
611D LYS* 3.2 29.2 + - - -
637D PHE* 5.5 2.7 - - - -
640D GLU* 6.3 2.2 - - - -
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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