Contacts of the helix formed by residues 605 - 619 (chain D) in PDB entry 1WSU
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 SER 605 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599D ARG* 3.4 19.5 - - - +
604D SER* 1.3 78.8 + - - +
606D ARG* 1.3 67.2 + - - +
607D LYS* 3.5 21.3 - - - +
608D TYR* 2.8 17.8 + - - -
609D VAL* 2.8 19.9 + - - +
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Residues in contact with ARG 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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595D LEU* 3.7 28.6 - - + +
599D ARG* 3.1 30.3 - - - +
605D SER* 1.3 72.1 - - - +
607D LYS* 1.3 63.6 + - - +
608D TYR 2.9 1.0 + - - -
609D VAL* 4.5 0.9 - - - -
610D LEU* 3.0 69.0 + - + +
611D PRO* 3.0 1.4 - - - +
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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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538D GLU* 4.1 17.7 + - - -
569D GLU* 4.9 5.4 - - - +
570D PHE* 3.6 22.4 - - + -
605D SER* 3.5 14.7 + - - +
606D ARG* 1.3 79.2 - - - +
608D TYR* 1.3 95.1 + - + +
611D PRO* 3.2 16.1 - - - +
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Residues in contact with TYR 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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531D TRP 3.5 15.5 - - - +
532D GLN* 3.5 33.4 + - + +
533D PRO* 3.4 43.2 + - + -
538D GLU* 5.6 1.4 + - - -
570D PHE* 4.1 21.9 - + - -
572D TRP* 4.2 12.3 + - + +
604D SER* 3.9 13.0 - - - +
605D SER* 2.8 21.6 + - - -
607D LYS* 1.3 112.1 + - + +
609D VAL* 1.3 58.5 + - - +
611D PRO* 2.9 19.7 - - - +
612D LEU* 3.0 19.3 + - - +
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Residues in contact with VAL 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D TRP* 5.6 1.6 - - + -
595D LEU* 3.7 9.6 - - + -
598D ALA* 4.5 3.4 - - + +
599D ARG* 3.6 32.8 - - + +
602D LEU* 4.5 16.2 - - + -
604D SER* 3.2 33.2 - - - -
605D SER 2.8 17.6 + - - +
606D ARG* 4.5 0.4 - - - -
608D TYR* 1.3 69.1 - - + +
610D LEU* 1.3 66.2 + - - +
612D LEU* 3.7 7.2 - - + +
613D LEU* 2.8 47.8 + - + +
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Residues in contact with LEU 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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595D LEU* 4.0 26.7 - - + +
606D ARG* 3.0 58.9 + - + +
609D VAL* 1.3 78.7 - - - +
611D PRO* 1.3 64.0 - - + +
613D LEU* 3.3 1.9 + - + +
614D GLU* 2.6 55.9 + - - +
629D ARG* 5.4 4.0 - - - +
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Residues in contact with PRO 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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566D ILE* 3.2 22.5 - - + +
567D ASN* 4.9 11.0 - - + +
570D PHE* 4.4 16.2 - - + -
572D TRP* 6.0 0.4 - - - +
606D ARG 3.0 13.7 - - - +
607D LYS 3.2 15.3 - - - +
608D TYR 2.9 13.2 - - - +
610D LEU* 1.3 93.8 - - + +
612D LEU* 1.3 61.7 + - - +
614D GLU* 3.1 10.3 + - + +
615D TYR 3.0 18.7 + - - -
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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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566D ILE* 3.7 13.9 - - + +
572D TRP* 3.4 36.8 - - + -
577D LEU* 3.4 32.8 - - + -
580D ALA* 3.8 18.6 - - + -
584D ILE* 5.1 3.4 - - + -
602D LEU* 3.9 16.4 - - + -
608D TYR 3.0 16.1 + - - +
609D VAL* 3.7 7.0 - - + +
611D PRO* 1.3 76.1 - - - +
613D LEU* 1.3 60.3 + - + +
615D TYR* 3.2 3.5 + - + +
616D LEU* 2.8 51.0 + - + +
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Residues in contact with LEU 613 (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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584D ILE* 4.6 15.3 - - + -
593D PHE* 4.4 19.7 - - + -
595D LEU* 3.3 38.1 - - + -
598D ALA* 4.1 11.9 - - + -
609D VAL* 2.8 28.8 + - + +
610D LEU* 3.8 4.3 - - + +
612D LEU* 1.3 72.9 - - + +
614D GLU* 1.3 60.1 + - - +
616D LEU* 3.4 19.4 + - + +
617D ASP* 2.4 35.8 + - - +
622D THR* 4.0 3.5 + - - +
629D ARG* 3.0 27.6 + - + +
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Residues in contact with GLU 614 (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 ILE 6.0 0.7 - - - +
610D LEU* 2.6 52.7 + - - +
611D PRO* 3.3 11.8 - - + +
613D LEU* 1.3 76.2 - - - +
615D TYR* 1.3 63.4 + - - +
617D ASP* 3.3 9.8 + - - +
618D GLN* 3.1 21.4 + - - +
624D ARG* 5.4 3.1 + - - -
629D ARG* 3.3 22.7 + - - -
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Residues in contact with TYR 615 (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 VAL* 3.1 22.6 - - + +
565D LYS 3.6 23.8 - - - -
566D ILE* 3.7 28.2 + - + +
577D LEU* 3.5 31.1 - - + +
581D ARG* 5.7 1.1 - - - -
611D PRO 3.0 11.9 + - - +
612D LEU* 3.3 8.3 - - + +
614D GLU* 1.3 73.1 - - - +
616D LEU* 1.3 76.2 + - + +
617D ASP 3.0 4.5 - - - -
618D GLN* 3.0 32.0 + - - +
619D VAL* 3.0 46.7 + - + +
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Residues in contact with LEU 616 (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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577D LEU* 4.2 1.8 - - + -
581D ARG* 4.1 21.5 - - + +
584D ILE* 4.3 13.9 - - + -
612D LEU* 2.8 47.3 + - + +
613D LEU* 3.9 12.6 - - + +
615D TYR* 1.3 90.5 - - + +
617D ASP* 1.3 56.2 + - - +
619D VAL* 3.6 6.5 - - + -
620D LYS 3.6 0.5 + - - -
621D PHE* 2.8 64.2 + - + -
622D THR* 2.9 22.2 + - + +
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Residues in contact with ASP 617 (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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613D LEU 2.4 26.5 + - - +
614D GLU* 3.3 10.7 - - - +
615D TYR 3.0 0.6 - - - -
616D LEU* 1.3 77.1 - - - +
618D GLN* 1.3 60.6 + - - +
620D LYS* 3.0 28.8 + - - +
622D THR* 2.8 24.8 + - - +
623D ARG* 5.5 1.6 + - - -
624D ARG* 3.7 9.2 + - - -
629D ARG* 2.8 47.7 + - - -
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Residues in contact with GLN 618 (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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614D GLU 3.1 9.1 + - - +
615D TYR* 3.0 26.4 + - - +
617D ASP* 1.3 81.0 - - - +
619D VAL* 1.3 61.0 + - + +
620D LYS* 3.4 15.3 + - - +
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Residues in contact with VAL 619 (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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581D ARG* 5.9 4.9 - - - +
615D TYR* 3.0 56.3 + - + +
616D LEU* 3.6 19.5 - - + +
618D GLN* 1.3 81.5 - - + +
620D LYS* 1.3 68.9 + - - +
621D PHE* 3.4 10.7 + - + +
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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