Contacts of the helix formed by residues 574 - 588 (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 ARG 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A VAL 5.2 2.0 + - - -
561A GLY* 3.3 36.5 + - - +
562A VAL 3.0 19.8 + - - +
563A LEU 5.0 1.0 + - - -
564A VAL* 3.9 33.4 - - + +
572A TRP 3.3 2.0 + - - -
573A HIS* 1.3 73.5 - - + +
575A GLN* 1.3 65.3 + - - +
577A LEU* 3.4 5.3 + - + +
578A GLY* 3.0 24.1 + - - -
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Residues in contact with GLN 575 (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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527A ARG* 4.3 4.7 - - - +
573A HIS* 2.9 22.7 + - + +
574A ARG* 1.3 83.7 - - - +
576A ALA* 1.3 66.1 + - - +
578A GLY* 3.2 2.7 + - - +
579A GLU* 3.0 28.5 + - + +
575B GLN* 2.5 32.6 - - + +
579B GLU* 3.3 31.6 - - + +
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Residues in contact with ALA 576 (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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527A ARG* 5.7 0.9 - - - +
530A ARG* 3.7 44.2 - - + +
531A TRP* 2.9 27.6 + - + +
572A TRP* 4.3 2.9 - - + -
573A HIS* 3.0 24.9 + - + +
575A GLN* 1.3 77.7 - - - +
577A LEU* 1.3 57.4 + - - +
579A GLU* 3.3 4.0 + - - +
580A ALA* 2.9 15.1 + - - +
579B GLU* 4.8 4.3 + - - +
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Residues in contact with LEU 577 (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* 3.9 35.4 - - + -
566A ILE* 4.4 5.6 - - + -
572A TRP* 3.9 15.4 - - + -
573A HIS 3.0 11.3 + - - +
574A ARG* 3.5 10.1 - - + +
576A ALA* 1.3 74.2 - - - +
578A GLY* 1.3 61.0 + - - +
580A ALA* 3.1 3.2 + - - +
581A ARG* 2.9 41.7 + - + +
612A LEU* 3.6 31.2 - - + -
615A TYR* 4.0 23.6 - - + +
616A LEU* 4.4 7.6 - - + -
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Residues in contact with GLY 578 (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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574A ARG 3.0 14.7 + - - -
575A GLN* 3.2 4.2 + - - -
577A LEU* 1.3 76.7 - - - +
579A GLU* 1.3 62.6 + - - +
581A ARG* 3.3 14.3 + - - +
582A GLU* 3.2 23.7 + - - +
575B GLN* 5.8 1.3 - - - -
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Residues in contact with GLU 579 (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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530A ARG* 3.0 22.5 + - - +
531A TRP* 3.9 14.8 - - + +
575A GLN* 3.0 20.1 + - + +
576A ALA* 3.6 7.9 - - - +
578A GLY* 1.3 72.8 - - - +
580A ALA* 1.3 66.8 + - - +
582A GLU* 3.1 6.7 + - - +
583A VAL* 3.0 24.1 + - - +
527B ARG* 2.6 44.0 + - - +
530B ARG* 5.2 0.2 - - - -
573B HIS* 4.5 2.6 - - - -
575B GLN* 2.7 49.7 + - + +
576B ALA* 4.5 1.9 + - - +
579B GLU* 5.1 4.3 - - - +
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Residues in contact with ALA 580 (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* 3.7 19.3 - - + +
572A TRP* 3.9 17.9 - - + -
576A ALA 2.9 13.6 + - - +
577A LEU* 3.5 7.9 - - - +
579A GLU* 1.3 76.6 - - - +
581A ARG* 1.3 57.1 + - - +
583A VAL* 3.2 2.4 + - - +
584A ILE* 2.9 34.9 + - - +
602A LEU* 4.1 10.0 - - + +
612A LEU* 4.1 16.6 - - + -
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Residues in contact with ARG 581 (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* 2.9 33.6 + - + +
578A GLY* 3.5 13.9 - - - +
579A GLU 3.1 0.2 - - - -
580A ALA* 1.3 79.5 - - + +
582A GLU* 1.3 59.5 + - - +
584A ILE* 3.4 3.4 + - - -
585A LYS* 2.8 32.7 + - - +
615A TYR* 5.4 2.6 + - - -
616A LEU* 4.0 25.3 - - + +
619A VAL* 4.2 10.9 - - - +
621A PHE* 3.3 51.4 - - + +
634A ASN* 2.9 28.3 + - - -
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Residues in contact with GLU 582 (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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578A GLY 3.2 13.4 + - - +
579A GLU 3.1 9.5 + - - +
581A ARG* 1.3 76.1 - - - +
583A VAL* 1.3 65.0 + - - +
585A LYS* 3.3 33.8 + - - +
586A ASN* 3.1 33.6 + - - +
520B LYS* 5.7 2.6 + - - -
524B ASP* 4.9 0.9 - - - -
527B ARG* 3.4 37.5 - - - +
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Residues in contact with VAL 583 (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* 3.7 24.9 - - + -
579A GLU 3.0 15.3 + - - +
580A ALA 3.6 5.8 - - - +
582A GLU* 1.3 75.6 - - - +
584A ILE* 1.3 63.9 + - + +
586A ASN* 3.2 5.5 + - - +
587A LEU* 3.0 19.3 + - + +
601A ALA* 3.7 35.4 - - + +
602A LEU* 3.8 13.0 - - + -
524B ASP* 4.0 19.6 - - + +
527B ARG* 3.9 16.6 - - + -
528B VAL* 4.3 6.7 - - + -
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Residues in contact with ILE 584 (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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580A ALA 2.9 18.4 + - - +
581A ARG* 3.8 4.7 - - - +
583A VAL* 1.3 80.4 - - + +
585A LYS* 1.3 62.6 + - - +
587A LEU* 3.2 10.8 + - + +
588A ALA* 2.9 22.0 + - - +
593A PHE* 3.9 23.7 - - + -
598A ALA* 5.1 5.8 - - + -
602A LEU* 4.4 15.7 - - + -
612A LEU* 3.8 17.9 - - + -
613A LEU* 3.6 27.4 - - + -
616A LEU* 3.7 16.4 - - + -
621A PHE* 4.2 9.2 - - + -
622A THR* 4.4 3.6 - - + -
631A VAL* 4.0 15.5 - - + -
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Residues in contact with LYS 585 (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* 2.8 17.7 + - - +
582A GLU* 3.5 36.1 + - - +
584A ILE* 1.3 76.5 - - - +
586A ASN* 1.3 68.9 + - - +
588A ALA* 3.2 12.5 + - - +
589A SER* 3.3 13.0 + - - +
621A PHE* 4.0 21.0 - - + -
631A VAL* 4.4 18.3 - - + +
633A GLY 4.7 1.6 - - - +
634A ASN* 2.8 36.1 + - + +
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Residues in contact with ASN 586 (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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582A GLU* 3.1 16.7 + - - +
583A VAL 3.6 4.5 - - - +
585A LYS* 1.3 84.5 - - - +
587A LEU* 1.3 63.7 + - - +
589A SER* 3.3 23.3 + - - -
590A THR* 4.6 3.8 + - - +
520B LYS* 3.9 43.6 - - + +
521B ASP* 6.0 0.9 - - - +
523B GLU* 5.5 1.4 - - - +
524B ASP* 3.3 36.8 - - - +
527B ARG* 4.8 6.2 + - - -
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Residues in contact with LEU 587 (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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583A VAL 3.0 13.8 + - - +
584A ILE* 3.2 11.6 + - + +
586A ASN* 1.3 76.9 - - - +
588A ALA* 1.3 62.2 + - - +
589A SER 3.2 0.9 + - - -
590A THR* 3.7 17.5 + - - +
591A GLY 4.1 3.6 - - - +
593A PHE* 3.8 31.5 - - + +
597A GLU* 3.8 21.1 - - + +
598A ALA* 3.7 32.1 - - + +
601A ALA* 4.1 15.9 - - + -
524B ASP* 5.3 0.2 + - - -
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Residues in contact with ALA 588 (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 2.9 10.4 + - - +
585A LYS 3.6 4.9 - - - +
586A ASN 3.2 0.4 - - - -
587A LEU* 1.3 76.6 - - - +
589A SER* 1.3 62.5 + - - +
590A THR 3.3 0.7 - - - -
591A GLY* 3.3 22.3 + - - +
593A PHE* 4.2 13.5 - - + -
630A VAL* 5.4 2.3 - - + +
631A VAL* 3.4 43.9 + - + +
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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