Contacts of the helix formed by residues 605 - 619 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532C GLN* 5.3 1.6 - - - +
599C ARG* 3.7 5.3 - - - +
604C SER* 1.3 83.5 - - - +
606C ARG* 1.3 55.5 + - - +
607C LYS* 2.6 17.7 + - - +
608C TYR* 2.8 31.0 + - - -
609C VAL* 2.9 14.1 + - - +
20G C 2.5 39.5 + - - -
21G C 3.6 13.7 - - - -
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Residues in contact with ARG 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595C LEU* 3.7 31.4 - - + +
596C ALA* 4.1 14.8 - - - +
599C ARG* 4.1 11.4 - - + +
605C SER* 1.3 69.6 - - - +
607C LYS* 1.3 61.5 + - - +
609C VAL* 3.9 8.3 - - - -
610C LEU* 3.1 28.5 + - - +
21G C 3.0 29.7 + - + +
22G G 2.9 76.4 + - - +
23G G 3.2 44.3 + - - -
24G U 3.8 12.8 + - - +
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Residues in contact with LYS 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535C SER* 6.3 0.4 - - - -
538C GLU* 4.4 10.7 + - - -
569C GLU* 5.9 0.4 - - - -
570C PHE* 4.5 15.1 - - + -
605C SER* 2.6 10.8 + - - +
606C ARG* 1.3 74.9 - - - +
608C TYR* 1.3 99.8 + - + +
610C LEU* 4.5 0.3 - - - +
611C PRO* 2.8 26.3 - - - +
19G G 2.8 34.3 + - - +
20G C 3.4 27.6 - - - +
21G C 4.4 1.2 + - - -
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Residues in contact with TYR 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C TRP 3.8 15.5 - - - +
532C GLN* 3.6 43.6 + - + +
533C PRO* 2.9 34.8 + - + -
534C PRO* 5.3 0.2 - - - +
538C GLU* 4.3 8.7 + - - -
570C PHE* 4.0 24.6 - + + -
572C TRP* 4.1 7.4 - - + -
604C SER* 4.5 2.9 - - - -
605C SER* 2.8 28.6 + - - +
607C LYS* 1.3 108.4 + - + +
609C VAL* 1.3 64.7 + - - +
610C LEU 3.3 0.7 - - - -
611C PRO* 3.3 10.6 - - - +
612C LEU* 3.5 15.4 + - - +
20G C 4.2 4.3 - - - -
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Residues in contact with VAL 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C TRP* 5.9 0.2 - - - -
595C LEU* 3.5 19.5 - - + -
598C ALA* 3.5 27.6 - - + -
599C ARG* 3.7 21.5 - - + +
602C LEU* 4.7 13.0 - - + -
604C SER* 3.6 23.6 - - - -
605C SER 2.9 18.5 + - - +
606C ARG* 4.4 0.9 - - - -
608C TYR* 1.3 76.7 - - - +
610C LEU* 1.3 64.1 + - - +
612C LEU* 3.8 5.7 - - + +
613C LEU* 3.1 27.5 + - + +
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Residues in contact with LEU 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595C LEU* 3.6 24.2 - - + +
606C ARG 3.1 19.8 + - - +
607C LYS 4.5 0.4 - - - +
609C VAL* 1.3 75.4 - - - +
611C PRO* 1.3 71.2 - - + +
613C LEU* 3.4 1.8 + - - +
614C GLU* 3.0 27.3 + - + +
629C ARG* 4.9 5.4 - - - +
23G G 3.5 43.1 - - + +
24G U 3.5 27.6 - - + +
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Residues in contact with PRO 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C ILE* 3.6 18.4 - - + +
567C ASN* 4.1 18.8 - - + +
569C GLU* 4.6 4.5 - - - +
570C PHE* 4.2 17.5 - - + -
607C LYS 2.8 29.8 - - - +
608C TYR 3.3 9.0 - - - +
610C LEU* 1.3 90.2 - - + +
612C LEU* 1.3 61.7 + - - +
614C GLU* 3.1 7.8 + - + +
615C TYR* 2.9 22.9 + - - +
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Residues in contact with LEU 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C ILE* 3.9 14.3 - - + +
572C TRP* 3.5 39.0 - - + -
577C LEU* 3.7 30.1 - - + -
580C ALA* 4.8 5.8 - - + -
584C ILE* 5.1 3.6 - - + -
602C LEU* 3.8 26.0 - - + -
608C TYR 3.5 14.8 + - - +
609C VAL* 3.8 6.7 - - - +
610C LEU 3.3 0.2 - - - -
611C PRO* 1.3 79.3 - - - +
613C LEU* 1.3 70.7 + - + +
615C TYR* 3.1 15.7 + - + +
616C LEU* 3.1 30.4 + - + +
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Residues in contact with LEU 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C ILE* 4.0 27.6 - - + -
593C PHE* 4.1 14.1 - - + -
595C LEU* 3.8 25.6 - - + +
598C ALA* 3.5 23.6 - - + -
609C VAL* 3.1 23.4 + - + +
610C LEU* 3.8 3.6 - - - +
612C LEU* 1.3 83.2 - - + +
614C GLU* 1.3 53.1 + - - +
616C LEU* 3.4 18.9 + - + +
617C ASP* 2.7 32.4 + - - +
622C THR* 5.8 0.2 - - - +
629C ARG* 2.7 35.1 + - + +
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Residues in contact with GLU 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C LEU* 3.0 16.8 + - + +
611C PRO* 3.1 11.4 + - + +
613C LEU* 1.3 74.7 - - - +
615C TYR* 1.3 65.2 + - - +
617C ASP* 3.1 36.4 + - - +
618C GLN* 3.2 12.3 + - - +
629C ARG* 3.7 7.2 + - - +
23G G 4.5 13.5 + - - +
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Residues in contact with TYR 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C VAL* 3.1 23.5 - - + +
565C LYS 3.3 24.9 - - - -
566C ILE* 3.8 32.8 - - + +
577C LEU* 3.9 23.8 - - + +
581C ARG* 5.0 3.8 + - - -
611C PRO 2.9 12.4 + - - +
612C LEU* 3.2 9.6 - - + +
614C GLU* 1.3 77.8 - - - +
616C LEU* 1.3 71.2 + - + +
618C GLN* 3.2 23.6 - - - +
619C VAL* 3.1 58.8 + - + +
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Residues in contact with LEU 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LEU* 4.8 5.2 - - + -
581C ARG* 4.1 17.7 - - + +
584C ILE* 4.3 14.1 - - + -
612C LEU* 3.1 26.4 + - + +
613C LEU* 3.6 25.4 - - + +
614C GLU 3.2 0.2 - - - -
615C TYR* 1.3 91.1 - - + +
617C ASP* 1.3 62.1 + - - +
618C GLN 3.1 1.8 - - - -
619C VAL* 3.9 2.5 - - - -
620C LYS 3.2 1.6 + - - -
621C PHE* 2.7 70.1 + - + -
622C THR* 3.2 18.1 + - + +
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Residues in contact with ASP 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C LEU 2.7 15.2 - - - +
614C GLU* 3.1 26.8 + - - +
616C LEU* 1.3 76.5 - - - +
618C GLN* 1.3 64.0 + - - +
620C LYS* 3.5 16.6 + - - +
622C THR* 3.2 24.5 + - - +
623C ARG* 3.5 12.6 - - - +
629C ARG* 2.8 38.3 + - - -
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Residues in contact with GLN 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C LYS 5.5 0.2 + - - -
566C ILE 5.2 3.1 - - - +
614C GLU 3.2 8.8 + - - +
615C TYR* 3.2 27.6 - - - +
617C ASP* 1.3 79.3 - - - +
619C VAL* 1.3 70.5 + - - +
620C LYS* 2.6 33.7 + - - +
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Residues in contact with VAL 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C ARG* 3.8 24.9 - - - +
615C TYR* 3.4 49.8 - - + +
616C LEU* 3.8 12.8 - - - +
618C GLN* 1.3 85.5 - - - +
620C LYS* 1.3 68.5 + - - +
621C PHE 3.5 3.1 + - - +
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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