Contacts of the helix formed by residues 574 - 589 (chain B) 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 ARG 574 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B GLY* 3.1 33.4 + - - +
562B VAL* 2.9 22.8 + - - +
563B LEU 5.7 0.2 + - - -
564B VAL* 4.4 28.3 - - + +
572B TRP 3.4 2.7 + - - -
573B HIS* 1.3 75.5 - - + +
575B GLN* 1.3 63.9 + - + +
577B LEU* 3.4 5.7 + - - +
578B GLY* 3.1 18.5 + - - -
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Residues in contact with GLN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLN* 2.5 38.4 - - + +
578A GLY* 5.8 1.5 - - - -
579A GLU* 2.7 39.7 + - + +
527B ARG* 3.8 8.5 - - - +
573B HIS* 3.0 17.5 + - + +
574B ARG* 1.3 79.5 - - + +
576B ALA* 1.3 64.7 + - - +
578B GLY* 3.4 2.3 + - - +
579B GLU* 3.1 24.7 + - + +
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A GLU* 4.5 2.2 + - - +
527B ARG* 5.9 0.2 - - - -
530B ARG* 3.7 52.3 - - + +
531B TRP* 2.8 26.9 + - + +
572B TRP* 4.1 2.9 - - + -
573B HIS* 3.1 22.0 + - + +
575B GLN* 1.3 76.2 - - - +
577B LEU* 1.3 61.0 + - - +
579B GLU* 3.6 2.0 + - - -
580B ALA* 3.1 12.5 + - - +
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B VAL* 3.9 37.9 - - + -
566B ILE* 4.4 6.1 - - + -
572B TRP* 3.9 15.6 - - + -
573B HIS 3.1 11.8 + - - +
574B ARG* 3.6 8.5 - - - +
576B ALA* 1.3 76.6 - - - +
578B GLY* 1.3 65.8 + - - +
580B ALA* 3.2 2.9 + - - +
581B ARG* 3.0 37.5 + - - +
612B LEU* 3.7 29.2 - - + -
615B TYR* 4.1 25.6 - - + +
616B LEU* 4.5 7.4 - - + -
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Residues in contact with GLY 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B ARG 3.1 11.9 + - - -
575B GLN* 3.4 3.7 + - - -
577B LEU* 1.3 79.3 - - - +
579B GLU* 1.3 60.6 + - - +
581B ARG* 3.3 14.9 + - - +
582B GLU* 3.1 25.5 + - - +
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Residues in contact with GLU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 2.6 46.1 + - - +
530A ARG* 4.6 5.0 + - - +
573A HIS* 4.1 2.9 - - - -
575A GLN* 3.3 32.0 - - + +
576A ALA* 4.8 4.3 + - - +
579A GLU* 5.1 4.9 - - - +
530B ARG* 2.9 25.4 + - - +
531B TRP* 4.0 9.2 - - + -
575B GLN* 3.1 19.8 + - + +
576B ALA* 4.0 4.9 - - - +
578B GLY* 1.3 74.7 - - - +
580B ALA* 1.3 66.8 + - - +
582B GLU* 3.1 8.8 + - - +
583B VAL* 3.0 25.8 + - - +
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Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B TRP* 3.7 18.4 - - - +
572B TRP* 3.8 16.6 - - + -
576B ALA 3.1 19.1 + - - +
577B LEU* 3.2 4.5 + - - +
579B GLU* 1.3 76.6 - - - +
581B ARG* 1.3 57.8 + - - +
583B VAL* 3.1 3.8 + - - +
584B ILE* 2.9 34.2 + - - +
602B LEU* 4.0 14.8 - - + +
612B LEU* 4.1 14.1 - - + -
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Residues in contact with ARG 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B LEU* 3.0 34.7 + - + +
578B GLY* 3.4 12.7 - - - +
580B ALA* 1.3 78.3 - - - +
582B GLU* 1.3 52.8 + - - +
584B ILE* 3.2 4.8 + - - +
585B LYS* 2.8 40.5 + - - +
612B LEU* 5.7 0.2 - - + -
615B TYR* 5.5 2.4 - - - -
616B LEU* 3.9 27.7 - - + +
619B VAL* 4.5 10.7 - - - +
621B PHE* 3.2 56.5 - - + +
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Residues in contact with GLU 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A ASP* 4.8 1.6 - - - +
527A ARG* 3.3 37.2 - - - +
578B GLY 3.1 14.9 + - - +
579B GLU* 3.1 10.4 + - - +
581B ARG* 1.3 76.2 - - - +
583B VAL* 1.3 63.6 + - - +
585B LYS* 3.3 31.0 + - + +
586B ASN* 3.2 33.2 + - - +
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Residues in contact with VAL 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ASP* 3.9 19.0 - - + +
527A ARG* 3.8 24.9 - - + -
528A VAL* 4.3 4.9 - - + -
531B TRP* 3.8 15.7 - - + -
579B GLU 3.0 15.0 + - - +
580B ALA 3.1 7.2 + - - +
582B GLU* 1.3 78.2 - - - +
584B ILE* 1.3 61.1 + - + +
586B ASN* 3.5 2.6 + - - +
587B LEU* 3.1 20.3 + - - +
601B ALA* 3.6 35.2 - - + +
602B LEU* 3.8 13.5 - - + -
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Residues in contact with ILE 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B ALA 2.9 20.8 + - - +
581B ARG* 3.2 5.6 + - - +
583B VAL* 1.3 75.7 - - + +
585B LYS* 1.3 66.5 + - - +
587B LEU* 3.1 13.0 + - + +
588B ALA* 2.9 21.5 + - - +
593B PHE* 3.6 31.0 - - + -
598B ALA* 5.2 3.1 - - + -
602B LEU* 4.7 13.5 - - + -
612B LEU* 3.9 16.2 - - + -
613B LEU* 3.7 17.3 - - + -
616B LEU* 3.5 27.8 - - + -
621B PHE* 4.2 7.6 - - + -
622B THR* 4.3 3.1 - - + -
631B VAL* 4.2 11.0 - - + -
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Residues in contact with LYS 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A LYS* 6.3 0.2 - - - -
581B ARG* 2.8 24.9 + - - +
582B GLU* 3.5 33.0 + - - +
583B VAL 3.3 0.2 - - - -
584B ILE* 1.3 74.7 - - - +
586B ASN* 1.3 71.7 + - - +
588B ALA* 3.2 2.4 + - - +
589B SER* 3.1 21.2 + - - -
621B PHE* 3.9 22.1 - - + -
631B VAL* 4.2 19.6 - - + +
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Residues in contact with ASN 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LYS* 5.2 5.7 + - - -
520A LYS* 3.0 46.3 - - + +
521A ASP* 5.9 1.8 - - - +
523A GLU* 5.6 3.6 - - - +
524A ASP* 2.9 32.8 - - - +
527A ARG* 6.0 0.2 + - - -
582B GLU* 3.2 20.0 + - - +
583B VAL 4.0 3.4 - - - +
585B LYS* 1.3 88.3 - - - +
587B LEU* 1.3 60.7 + - - +
589B SER* 3.0 25.5 + - - -
590B THR* 4.9 2.4 - - - +
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B VAL 3.1 17.3 + - - +
584B ILE* 3.1 10.7 + - + +
586B ASN* 1.3 79.0 - - - +
588B ALA* 1.3 61.5 + - - +
589B SER 3.5 0.5 + - - -
590B THR* 3.9 14.2 + - - -
591B GLY 4.1 3.6 - - - +
593B PHE* 3.8 37.4 - - + +
597B GLU* 4.0 16.6 - - + +
598B ALA* 3.8 28.9 - - + +
601B ALA* 4.2 15.5 - - + -
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Residues in contact with ALA 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B ILE 2.9 15.3 + - - +
585B LYS 3.2 2.2 + - - +
587B LEU* 1.3 73.2 - - - +
589B SER* 1.3 64.7 + - - +
590B THR 3.0 4.0 + - - -
591B GLY* 3.1 22.9 + - - +
593B PHE* 3.6 23.3 - - + -
630B VAL* 4.9 2.5 - - - -
631B VAL* 3.8 28.7 - - + +
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Residues in contact with SER 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LYS* 5.6 2.8 - - - +
585B LYS* 3.1 11.1 + - - -
586B ASN* 3.0 22.5 + - - -
588B ALA* 1.3 77.9 - - - +
590B THR* 1.3 71.5 + - - +
591B GLY 3.5 1.1 + - - -
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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
------------------------------------------------------------
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