Contacts of the helix formed by residues 577 - 583 (chain A) in PDB entry 3W3K
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 LEU 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A PHE* 4.5 5.6 - - + -
561A LEU* 5.4 0.4 - - + -
568A PHE* 3.8 28.5 - - + -
575A HIS 4.2 1.0 + - - -
576A HIS* 1.3 79.7 - - - +
578A GLU* 1.3 64.6 + - - +
579A PHE* 3.0 24.9 + - + -
580A ILE* 3.4 24.0 + - + +
591A LEU* 4.2 25.8 - - + -
596A ILE* 4.6 9.9 - - + -
599A LEU* 4.2 29.0 - - + +
602A LYS 5.7 2.2 + - - -
604A ASN 5.6 1.9 - - - +
605A LEU* 3.9 30.5 - - + +
615A PHE* 5.6 1.1 - - + -
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Residues in contact with GLU 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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547A ALA* 3.1 29.7 - - + +
576A HIS* 2.3 52.2 + - - +
577A LEU* 1.3 77.8 - - - +
579A PHE* 1.3 62.0 + - - +
580A ILE 3.1 1.0 + - - -
581A GLN* 3.1 33.1 + - - +
582A ASN* 4.6 1.0 + - - -
600A THR 4.0 9.0 - - - +
601A ASP* 4.9 1.4 - - - +
602A LYS* 3.5 48.0 + - + +
604A ASN 5.7 0.7 - - - -
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Residues in contact with PHE 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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544A PHE* 3.8 33.0 - + + -
546A ASN 4.2 4.9 - - - -
547A ALA 3.3 22.3 + - - +
549A ALA* 3.3 38.6 - - + +
550A LEU* 4.4 7.0 - - + -
551A THR* 4.1 2.4 - - + +
559A LEU* 4.3 20.6 - - + -
561A LEU* 4.1 7.9 - - + -
576A HIS 3.4 25.4 - - - -
577A LEU* 3.9 17.3 - - + -
578A GLU* 1.3 77.6 - - - +
580A ILE* 1.3 78.5 + - + +
581A GLN 3.1 1.1 + - - -
582A ASN* 3.2 20.7 + - - +
583A PHE* 3.5 21.2 - + - -
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Residues in contact with ILE 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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559A LEU* 6.0 0.4 - - + -
577A LEU* 3.5 22.2 - - + +
578A GLU 3.1 1.6 + - - +
579A PHE* 1.3 93.1 - - + +
581A GLN* 1.3 61.4 + - - +
583A PHE* 3.4 25.5 + - + +
586A LEU* 4.2 14.0 - - + +
589A LEU* 3.5 36.1 - - + -
591A LEU* 4.4 9.9 - - + -
605A LEU* 4.0 24.5 - - + -
606A GLU 3.7 15.9 - - - +
607A SER* 4.3 13.4 - - - -
610A LEU* 4.8 4.3 - - + -
638A LEU* 5.0 3.4 - - + -
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Residues in contact with GLN 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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578A GLU* 3.1 22.6 + - - +
580A ILE* 1.3 78.3 - - - +
582A ASN* 1.3 78.7 + - - +
583A PHE 3.2 7.6 + - - +
602A LYS* 3.5 23.8 + - - +
606A GLU* 3.1 34.7 + - + +
607A SER* 4.6 6.3 - - - +
608A LYS* 5.3 2.4 + - - +
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Residues in contact with ASN 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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547A ALA 4.7 4.4 + - - -
551A THR* 3.5 39.6 - - + +
578A GLU 4.6 0.2 + - - -
579A PHE* 3.2 12.1 + - - +
581A GLN* 1.3 97.4 - - - +
583A PHE* 1.3 65.1 + - + +
584A THR* 3.3 12.3 + - - +
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Residues in contact with PHE 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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549A ALA 4.3 1.3 - - - -
550A LEU* 3.2 46.0 - - + -
551A THR* 3.9 10.8 - - + -
553A LEU 3.6 20.9 - - - -
554A SER* 5.2 5.4 - - - +
556A LEU* 4.1 24.0 - - + +
559A LEU* 4.9 3.6 - - + -
579A PHE* 3.5 29.8 - + - -
580A ILE* 3.4 22.5 - - + +
581A GLN 3.2 9.1 - - - +
582A ASN* 1.3 78.4 - - + +
584A THR* 1.3 62.5 - - - +
585A ASN 4.5 0.4 - - - +
586A LEU* 3.6 36.6 - - + +
607A SER* 4.6 2.4 + - - -
608A LYS 5.4 1.0 + - - -
609A SER* 3.5 12.6 + - - -
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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