Contacts of the helix formed by residues 600 - 609 (chain D) in PDB entry 6V3O
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 GLY 600 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564D LEU* 4.0 5.7 - - - +
565D PHE 3.9 9.5 + - - -
598D MET* 5.7 0.4 - - - -
599D VAL* 1.3 73.4 - - - +
601D TYR* 1.3 64.0 + - - -
602D SER 4.0 0.2 - - - -
603D ASP* 4.1 24.5 - - - -
604D SER* 2.8 25.4 + - - -
617D LEU* 3.8 9.8 - - - +
640D GLY* 4.9 5.8 - - - -
641D ARG* 4.9 1.3 - - - -
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Residues in contact with TYR 601 (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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599D VAL* 4.1 11.7 - - + -
600D GLY* 1.3 73.7 - - - -
602D SER* 1.3 64.1 + - - +
603D ASP 3.1 1.1 - - - +
604D SER* 3.4 1.6 + - - -
605D GLY* 2.8 27.9 + - - -
610D ARG* 3.7 23.2 + - - +
613D ALA* 4.6 2.5 - - - +
614D ALA* 5.9 3.6 - - + -
617D LEU* 3.7 29.8 - - + -
621D GLN* 4.0 7.1 + - - -
639D HIS* 2.7 46.8 + - + -
640D GLY 3.7 10.3 - - - -
641D ARG* 3.4 10.6 + - - +
642D GLY 3.6 12.1 - - - +
643D GLY* 3.5 29.2 - - - -
644D THR* 4.5 11.3 + - + -
645D VAL* 4.3 5.0 - - + +
659D GLN* 4.6 6.1 + - - -
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Residues in contact with SER 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D TYR* 1.3 77.0 - - - +
603D ASP* 1.3 65.3 + - - +
605D GLY* 3.9 1.5 - - - -
606D LYS* 3.0 22.3 + - - +
610D ARG* 5.0 3.5 - - - +
641D ARG* 3.5 22.8 + - - -
642D GLY* 3.6 9.2 - - - -
774D ALA* 4.1 19.3 - - - +
777D TRP* 5.4 0.3 - - - -
778D ILE* 4.3 14.4 - - - +
970D GLY 2.3 33.8 + - - -
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Residues in contact with ASP 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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564D LEU* 4.1 8.7 - - - +
566D GLU* 3.5 38.2 - - + +
567D ARG* 3.7 14.1 + - - +
598D MET* 5.9 0.7 - - - +
600D GLY* 4.1 19.9 - - - -
601D TYR 4.0 0.4 - - - +
602D SER* 1.3 81.8 - - - +
604D SER* 1.3 63.0 + - - +
606D LYS* 3.2 15.5 + - - +
607D ASP 3.5 3.5 + - - -
641D ARG* 5.6 4.5 - - - +
774D ALA* 3.9 6.8 - - - +
1002D SO4 4.0 16.6 + - - -
1004D SO4 3.1 30.1 + - - -
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Residues in contact with SER 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D PHE 4.3 0.9 + - - -
566D GLU* 2.5 27.9 + - - -
568D LEU* 4.2 16.6 - - - +
571D LEU* 3.7 12.9 - - - +
600D GLY 2.8 20.4 + - - -
601D TYR 3.4 1.8 + - - -
603D ASP* 1.3 72.5 - - - +
605D GLY* 1.3 61.1 + - - +
607D ASP* 2.8 24.0 + - - +
608D ALA 3.2 10.0 + - - -
613D ALA* 3.8 19.0 - - - +
617D LEU* 5.2 0.7 - - - -
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Residues in contact with GLY 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 2.8 18.3 + - - -
602D SER* 3.9 1.8 - - - -
604D SER* 1.3 75.9 - - - +
606D LYS* 1.3 57.7 + - - +
609D GLY* 2.8 46.8 + - - -
610D ARG* 4.4 9.4 - - - -
613D ALA* 3.7 5.5 - - - +
728D TYR* 3.6 5.5 + - - -
777D TRP* 5.3 0.8 + - - -
789D PRO* 4.9 5.3 - - - +
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Residues in contact with LYS 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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567D ARG* 4.0 11.4 - - - +
602D SER 3.0 12.7 + - - +
603D ASP 3.4 9.0 - - - +
604D SER 3.1 0.2 - - - -
605D GLY* 1.3 76.5 - - - +
607D ASP* 1.3 60.9 + - - +
728D TYR* 2.9 24.0 + - - +
732D VAL* 5.4 1.6 - - - +
769D ILE* 3.1 23.7 + - + +
770D THR* 3.5 14.3 + - - +
772D LEU 2.7 30.0 + - - +
773D ARG 4.1 8.7 - - - +
774D ALA* 4.2 4.3 - - - +
777D TRP* 3.6 45.5 - - + +
1004D SO4 3.8 19.1 - - - -
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Residues in contact with ASP 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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567D ARG* 3.4 33.7 - - - +
568D LEU* 3.1 29.8 + - + +
569D ALA* 4.6 1.2 + - - +
603D ASP 3.5 1.0 + - - +
604D SER* 2.8 17.9 + - - +
606D LYS* 1.3 82.5 - - - +
608D ALA* 1.3 56.4 + - + +
609D GLY 4.0 0.2 - - - -
728D TYR* 3.9 4.4 - - - -
729D ARG* 3.1 52.8 + - - -
733D VAL* 5.7 1.0 - - - +
770D THR* 6.2 0.2 - - - +
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Residues in contact with ALA 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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568D LEU* 3.4 32.3 - - + -
604D SER 3.2 6.8 + - - +
607D ASP* 1.3 77.3 - - - +
609D GLY* 1.3 67.5 + - - +
612D SER* 3.5 7.4 + - - -
724D ALA* 4.6 0.9 - - - +
725D THR* 3.4 31.0 + - + +
728D TYR* 3.7 12.1 - - - +
729D ARG* 3.5 16.6 - - - +
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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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605D GLY* 2.8 24.3 + - - -
608D ALA* 1.3 77.5 - - - +
610D ARG* 1.3 65.5 + - - -
611D LEU 3.5 2.0 - - - -
612D SER 4.3 0.7 - - - -
613D ALA* 3.2 20.4 + - - +
724D ALA* 5.6 1.3 - - - -
728D TYR* 3.5 28.9 - - - -
789D PRO 5.1 0.7 - - - -
792D LEU 4.2 4.7 - - - -
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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