Contacts of the helix formed by residues 576 - 589 (chain A) in PDB entry 3SHW
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 ASN 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A GLU* 2.9 24.8 + - - +
554A LEU* 5.7 0.8 - - - +
555A GLY* 3.1 27.5 + - - +
557A TRP* 3.2 35.2 - - + +
574A ILE 3.8 0.2 + - - -
575A PRO* 1.3 74.7 - - - +
577A LYS* 1.3 68.2 + - - +
578A ASN* 3.9 15.3 - - - +
579A ARG* 3.0 22.7 + - - +
580A ALA* 2.8 21.0 + - - +
633A TYR* 3.8 1.8 - - - -
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Residues in contact with LYS 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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481A GLU* 5.3 2.5 - - - +
557A TRP* 3.6 27.8 - - + -
576A ASN* 1.3 72.5 - - - +
578A ASN* 1.3 52.7 + - - +
580A ALA* 3.3 1.7 + - - +
581A GLU* 2.8 70.6 + - + +
631A PRO* 3.5 12.5 - - - +
633A TYR* 3.1 47.7 + - + +
635A ARG* 6.6 0.2 - - - -
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Residues in contact with ASN 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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481A GLU* 6.0 0.2 - - - +
576A ASN* 3.1 16.0 - - - +
577A LYS* 1.3 81.7 - - - +
579A ARG* 1.3 62.3 + - - +
581A GLU* 3.4 7.2 + - - +
582A GLN* 3.2 21.0 + - - +
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Residues in contact with ARG 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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527A TYR* 4.2 3.6 + - - -
530A GLU* 2.5 44.2 + - - +
555A GLY* 4.8 11.2 + - - -
575A PRO* 4.2 17.2 - - + +
576A ASN* 3.0 18.5 + - - +
578A ASN* 1.3 74.1 - - - +
580A ALA* 1.3 60.1 + - - +
582A GLN* 3.2 12.9 + - + +
583A LEU* 2.8 54.7 + - + +
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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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525A PHE* 3.8 18.2 - - + -
575A PRO* 4.1 6.1 - - + +
576A ASN 2.8 18.2 + - - +
577A LYS 3.5 4.5 - - - +
579A ARG* 1.3 77.8 - - - +
581A GLU* 1.3 51.1 + - - +
583A LEU* 3.2 4.7 + - - +
584A ALA* 2.7 36.7 + - - +
632A ALA* 3.6 7.1 - - + +
633A TYR* 3.5 34.8 - - + +
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Residues in contact with GLU 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 LYS* 2.8 57.9 + - + +
578A ASN* 3.6 7.4 - - - +
580A ALA* 1.3 72.4 - - - +
582A GLN* 1.3 56.6 + - - +
584A ALA* 3.4 3.8 + - - +
585A SER* 2.9 30.7 + - - -
631A PRO* 4.2 7.8 - - - +
632A ALA* 3.3 22.2 + - + +
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Residues in contact with GLN 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 ASN* 3.2 11.2 + - - +
579A ARG* 3.2 19.3 + - + +
581A GLU* 1.3 78.5 - - - +
583A LEU* 1.3 65.8 + - + +
585A SER* 2.7 28.5 + - - -
586A VAL* 3.0 29.8 + - + +
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Residues in contact with LEU 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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525A PHE* 4.0 11.7 - - + -
527A TYR* 3.9 32.8 - - + -
530A GLU* 4.4 4.3 - - - +
575A PRO* 3.9 15.7 - - + -
579A ARG* 2.8 47.5 + - + +
580A ALA* 3.6 4.7 - - - +
582A GLN* 1.3 75.8 - - + +
584A ALA* 1.3 61.6 + - - +
586A VAL* 3.6 8.1 + - + +
587A GLN* 3.3 24.6 + - - +
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Residues in contact with ALA 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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524A HIS 5.4 0.4 - - - +
525A PHE* 3.7 27.5 - - + -
580A ALA 2.7 21.7 + - - +
581A GLU* 3.8 4.9 - - - +
583A LEU* 1.3 71.8 - - - +
585A SER* 1.3 61.7 + - - +
587A GLN* 3.7 3.0 - - - +
588A TYR* 3.2 34.7 + - + -
632A ALA* 3.7 22.9 - - + +
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Residues in contact with SER 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 GLU 2.9 13.7 + - - -
582A GLN* 2.7 29.6 + - - -
584A ALA* 1.3 75.2 - - - +
586A VAL* 1.3 66.1 + - - +
587A GLN 3.1 2.3 + - - -
588A TYR* 3.3 5.4 + - - +
589A THR* 3.1 30.5 + - - +
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Residues in contact with VAL 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 GLN* 3.0 36.4 + - + +
583A LEU* 3.6 8.7 + - + +
585A SER* 1.3 84.3 + - - +
587A GLN* 1.3 61.6 + - - +
589A THR* 4.1 16.3 + - - -
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Residues in contact with GLN 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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525A PHE* 4.0 15.5 - - + +
526A GLU* 3.1 58.8 + - - +
539A LYS* 4.9 4.0 + - - +
583A LEU 3.3 14.7 + - - +
584A ALA 3.7 7.9 - - - +
585A SER 3.1 0.4 - - - -
586A VAL* 1.3 78.2 - - - +
588A TYR* 1.3 68.8 + - + +
589A THR 4.5 1.9 - - - -
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Residues in contact with TYR 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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524A HIS 4.6 16.9 + - - -
525A PHE* 5.7 2.0 - - + -
539A LYS* 5.2 8.5 + - - -
584A ALA* 3.2 25.6 + - + +
585A SER* 3.3 9.2 + - - +
587A GLN* 1.3 85.5 - - + +
589A THR* 1.3 66.5 + - + +
627A GLN 5.4 7.9 - - - -
628A THR* 2.9 36.6 + - - -
630A PHE* 5.1 11.6 + - - +
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Residues in contact with THR 589 (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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585A SER* 3.1 19.2 + - - +
586A VAL* 4.1 15.1 + - - -
587A GLN 4.5 2.0 - - - -
588A TYR* 1.3 84.7 - - + +
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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