Contacts of the helix formed by residues 605 - 619 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A GLN* 6.2 0.2 - - - -
599A ARG* 3.7 2.2 - - - -
604A SER* 1.3 82.4 + - - +
606A ARG* 1.3 65.0 + - - +
607A LYS* 3.9 4.2 + - - +
608A TYR* 2.9 19.6 + - - -
609A VAL* 2.9 24.8 + - - +
20E C 2.7 36.9 + - - -
21E C 3.5 20.0 - - - -
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Residues in contact with ARG 606 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A LEU* 3.2 34.7 - - + +
596A ALA* 4.4 3.8 - - - +
599A ARG* 4.1 9.1 - - + +
605A SER* 1.3 70.1 - - - +
607A LYS* 1.3 64.0 + - - +
609A VAL* 4.4 6.3 - - - +
610A LEU* 3.0 29.8 + - + +
21E C 3.0 30.4 + - + +
22E G 2.9 61.2 + - - +
23E G 3.2 43.9 + - - -
24E U 2.7 30.5 + - - +
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Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A GLU* 5.2 6.5 + - - -
569A GLU* 4.9 4.7 - - - -
570A PHE* 4.0 26.6 - - + -
605A SER* 3.2 3.9 + - - +
606A ARG* 1.3 78.1 - - - +
608A TYR* 1.3 95.4 + - + +
611A PRO* 3.2 21.7 - - - +
19E G 2.8 37.6 + - - +
20E C 3.5 27.1 + - - +
21E C 4.6 1.0 + - - -
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Residues in contact with TYR 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A TRP 3.6 7.2 - - - +
532A GLN* 3.6 44.8 + - + +
533A PRO* 3.4 30.4 + - + -
534A PRO* 5.8 0.2 - - - +
538A GLU* 5.0 6.1 + - - -
570A PHE* 3.7 26.8 - + - -
572A TRP* 3.7 21.8 + - + -
604A SER* 3.4 15.7 - - - +
605A SER* 2.9 26.4 + - - +
607A LYS* 1.3 101.1 + - + +
609A VAL* 1.3 64.8 + - - +
611A PRO* 3.8 7.8 - - - +
612A LEU 3.8 4.0 + - - -
20E C 3.9 11.0 - - - -
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A TRP* 5.6 0.9 - - + -
595A LEU* 3.5 22.7 - - + -
598A ALA* 3.9 17.0 - - + -
599A ARG* 3.9 17.9 - - - +
602A LEU* 4.2 14.8 - - + -
604A SER* 3.5 25.1 - - - -
605A SER 2.9 20.7 + - - +
606A ARG* 4.3 0.9 - - - +
608A TYR* 1.3 76.6 - - - +
610A LEU* 1.3 67.2 + - - +
611A PRO 3.3 0.4 - - - -
612A LEU* 3.0 16.1 + - + +
613A LEU* 3.0 25.1 + - + +
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Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A LEU* 3.9 20.2 - - + +
606A ARG* 3.0 14.9 + - + +
609A VAL* 1.3 75.6 - - - +
611A PRO* 1.3 66.0 - - + +
613A LEU* 3.1 3.8 + - + -
614A GLU* 2.9 46.4 + - + +
629A ARG* 4.6 4.5 - - - +
23E G 3.5 52.3 - - + +
24E U 3.9 25.1 - - + +
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Residues in contact with PRO 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A ILE* 3.0 25.8 - - + +
567A ASN* 3.8 26.0 - - - +
570A PHE* 4.5 13.5 - - + -
572A TRP* 6.0 1.1 - - - +
607A LYS* 3.2 27.8 - - - +
608A TYR 3.8 5.8 - - - +
609A VAL 3.6 2.7 - - - -
610A LEU* 1.3 95.7 - - + +
612A LEU* 1.3 59.7 + - - +
614A GLU* 3.9 14.4 - - - +
615A TYR* 3.2 13.9 + - - +
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Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A ILE* 4.0 11.1 - - + +
572A TRP* 3.7 39.5 - - + -
577A LEU* 3.6 32.1 - - + -
580A ALA* 4.1 8.7 - - + -
581A ARG* 6.0 0.2 - - + -
584A ILE* 3.8 25.4 - - + -
602A LEU* 4.0 16.8 - - + -
608A TYR 3.8 3.6 + - - +
609A VAL* 3.0 11.4 + - - +
611A PRO* 1.3 77.0 - - - +
613A LEU* 1.3 61.9 + - + +
615A TYR* 3.2 4.0 + - - +
616A LEU* 2.8 44.0 + - + +
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A ILE* 3.6 31.0 - - + -
593A PHE* 4.0 22.7 - - + -
595A LEU* 3.8 33.7 - - + -
598A ALA* 3.9 11.9 - - + -
609A VAL* 3.0 21.2 + - + +
610A LEU* 3.8 6.3 - - + +
612A LEU* 1.3 75.5 - - + +
614A GLU* 1.3 59.7 + - - +
616A LEU* 3.2 9.3 + - + +
617A ASP* 2.9 34.0 + - - +
622A THR* 4.1 1.1 + - + -
629A ARG* 3.6 33.0 - - - +
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Residues in contact with GLU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ASN* 5.6 1.7 + - - -
610A LEU* 2.9 44.3 + - + +
611A PRO* 3.9 14.6 - - - +
613A LEU* 1.3 75.9 - - - +
615A TYR* 1.3 63.0 + - - +
617A ASP* 3.4 10.7 + - - +
618A GLN* 3.1 22.5 + - - +
629A ARG* 4.3 7.0 - - - +
23E G 4.4 12.9 + - - +
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Residues in contact with TYR 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A VAL* 3.6 20.1 - - + +
565A LYS 3.7 24.7 - - - -
566A ILE* 3.5 30.7 - - + +
577A LEU* 4.0 20.3 - - + +
581A ARG* 5.4 2.1 + - - -
611A PRO 3.2 15.6 + - - +
612A LEU* 3.2 7.8 + - + +
613A LEU 3.1 0.2 - - - -
614A GLU* 1.3 77.6 - - - +
616A LEU* 1.3 85.2 + - + +
618A GLN* 3.2 10.7 + - + +
619A VAL* 3.1 50.2 + - + +
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Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 4.4 4.9 - - + -
581A ARG* 4.0 37.2 - - + +
584A ILE* 3.7 30.1 - - + -
612A LEU* 2.8 29.7 + - + +
613A LEU* 3.2 10.5 + - + +
615A TYR* 1.3 94.5 - - + +
617A ASP* 1.3 62.2 + - - +
619A VAL* 3.5 3.3 + - + +
620A LYS 3.1 3.1 + - - -
621A PHE* 2.9 46.6 + - + +
622A THR* 3.4 17.4 + - + +
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Residues in contact with ASP 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU 2.9 9.5 + - - +
614A GLU* 3.7 8.8 - - - +
616A LEU* 1.3 76.3 - - - +
618A GLN* 1.3 60.0 + - - +
620A LYS* 2.9 23.6 + - - +
622A THR* 2.5 40.6 + - - +
623A ARG* 5.1 0.7 - - - -
624A ARG* 3.7 16.7 + - - +
629A ARG* 2.6 44.7 + - - -
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Residues in contact with GLN 618 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A GLU 3.1 11.9 + - - +
615A TYR* 3.2 15.7 + - + +
617A ASP* 1.3 81.5 - - - +
619A VAL* 1.3 62.2 + - + +
620A LYS* 3.1 9.8 + - - +
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Residues in contact with VAL 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A ARG* 4.2 12.1 - - - +
615A TYR* 3.1 51.7 + - + +
616A LEU* 3.7 14.8 - - - +
617A ASP 3.3 0.2 - - - -
618A GLN* 1.3 79.2 - - + +
620A LYS* 1.3 70.0 + - - +
621A PHE* 4.1 12.1 - - + +
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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