Contacts of the helix formed by residues 580 - 595 (chain A) in PDB entry 4CEK
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 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A CYS 3.4 1.0 + - - +
579A VAL* 1.3 80.1 - - + +
581A ARG* 1.3 64.6 + - - +
582A ASP* 4.0 13.1 + - - +
583A LEU* 2.8 46.8 + - - +
584A ILE* 3.1 24.9 + - - +
621A PHE* 3.7 12.1 - - - -
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Residues in contact with ARG 581 (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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466A ASN* 3.5 34.2 + - - +
467A PHE* 4.4 21.5 - - + +
470A ASN* 3.4 27.7 + - - +
580A ASN* 1.3 73.9 - - - +
582A ASP* 1.3 72.3 + - - +
584A ILE* 3.5 7.5 + - - +
585A ASP* 3.2 32.1 + - - +
621A PHE* 3.9 3.8 - - - -
624A ARG* 3.5 31.2 - - - +
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Residues in contact with ASP 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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580A ASN* 3.3 12.7 + - - +
581A ARG* 1.3 84.8 - - - +
583A LEU* 1.3 67.5 + - - +
585A ASP* 3.8 6.5 - - - +
586A LYS* 3.1 41.7 + - - +
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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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577A ASN 3.3 26.7 - - - +
578A CYS* 3.8 21.6 - - + -
579A VAL* 3.8 8.5 - - + +
580A ASN* 2.8 33.9 + - - +
582A ASP* 1.3 75.4 - - - +
584A ILE* 1.3 60.0 + - - +
586A LYS* 3.4 18.6 + - + +
587A ALA* 3.2 21.3 + - - +
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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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575A LEU* 4.2 19.3 - - + -
578A CYS* 3.5 27.1 - - + +
580A ASN 3.1 15.3 + - - +
581A ARG* 3.6 11.9 - - - +
583A LEU* 1.3 72.8 - - - +
585A ASP* 1.3 75.9 + - - +
587A ALA* 3.3 4.2 + - + +
588A ALA* 3.2 20.4 + - - +
621A PHE* 3.5 37.9 - - + +
622A TYR* 4.4 9.0 - - + -
624A ARG* 4.0 22.4 - - + -
625A LEU* 3.9 17.0 - - + +
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Residues in contact with ASP 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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472A ILE* 3.7 33.5 - - + +
474A LEU* 5.5 0.5 - - - +
581A ARG* 3.2 19.8 + - - +
582A ASP* 3.8 5.5 - - - +
584A ILE* 1.3 77.0 - - - +
586A LYS* 1.3 63.7 + - - +
588A ALA* 3.2 10.4 + - - +
589A MET* 3.1 27.9 + - + +
624A ARG* 2.8 44.0 + - - +
628A THR* 4.3 11.2 + - - +
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Residues in contact with LYS 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 ASP* 3.1 33.2 + - - +
583A LEU* 3.6 20.3 - - + +
584A ILE 3.3 0.2 - - - -
585A ASP* 1.3 74.8 - - - +
587A ALA* 1.3 57.7 + - - +
589A MET* 3.0 22.0 + - + +
590A ASP* 2.8 31.0 + - - +
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Residues in contact with ALA 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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571A PHE* 3.3 34.7 - - + -
574A GLN* 4.2 4.5 - - - +
575A LEU* 4.4 9.0 - - + -
578A CYS* 4.1 18.4 - - - -
583A LEU 3.2 10.0 + - - +
584A ILE* 3.4 10.8 - - - +
585A ASP 3.3 0.2 - - - -
586A LYS* 1.3 79.5 - - - +
588A ALA* 1.3 56.6 - - - +
590A ASP* 3.5 2.4 + - - -
591A PHE* 2.9 25.5 + - - +
625A LEU* 4.3 4.0 - - + -
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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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474A LEU* 4.3 4.7 - - + -
584A ILE 3.2 8.9 + - - +
585A ASP* 3.4 10.8 - - - +
586A LYS 3.2 0.4 - - - -
587A ALA* 1.3 73.5 - - - +
589A MET* 1.3 59.4 + - - +
591A PHE* 4.0 2.4 - - - +
592A CYS* 3.0 32.6 + - - +
625A LEU* 3.5 24.3 - - + +
628A THR* 4.1 26.9 - - + -
629A LEU* 4.0 13.5 - - + +
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Residues in contact with MET 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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472A ILE* 4.2 27.4 - - + -
474A LEU* 3.7 21.8 - - + -
477A PHE* 3.9 24.0 - - + -
585A ASP* 3.1 24.9 + - + +
586A LYS* 3.0 25.6 + - + +
588A ALA* 1.3 74.6 - - - +
590A ASP* 1.3 63.9 + - - +
592A CYS* 3.3 5.2 + - - +
593A MET* 3.1 31.4 + - + +
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Residues in contact with ASP 590 (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 ILE* 5.3 3.4 - - - +
571A PHE* 3.6 21.9 - - + -
586A LYS 2.8 15.6 + - - +
587A ALA* 3.7 6.3 - - - +
589A MET* 1.3 77.9 - - - +
591A PHE* 1.3 62.0 + - - +
593A MET* 5.0 0.4 - - - -
594A ASN* 2.7 57.5 + - - +
595A MET* 4.0 5.8 - - - +
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Residues in contact with PHE 591 (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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568A VAL* 5.2 3.4 - - + -
571A PHE* 3.7 28.2 - + + -
572A LEU* 5.4 0.9 - - + -
587A ALA 2.9 17.6 + - - +
588A ALA* 4.0 5.6 - - - +
590A ASP* 1.3 77.1 - - - +
592A CYS* 1.3 64.5 + - - +
593A MET 3.2 1.4 + - - -
595A MET* 3.2 53.6 + - + -
596A ASN* 3.2 15.6 + - - -
600A ASN* 3.7 32.5 - - + -
601A ARG* 4.2 9.6 - - + -
604A LEU* 4.1 26.0 - - + -
625A LEU* 5.9 0.4 - - + -
629A LEU* 4.5 6.3 - - + -
633A MET* 3.9 33.0 - - + -
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Residues in contact with CYS 592 (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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474A LEU* 3.8 21.5 - - + -
477A PHE* 5.1 9.9 - - + -
478A VAL 5.6 1.0 - - - +
480A ALA* 4.7 12.3 - - - +
588A ALA 3.0 19.2 + - - +
589A MET* 3.8 4.7 - - - +
591A PHE* 1.3 82.5 - - - +
593A MET* 1.3 62.3 + - + +
596A ASN* 4.1 13.4 - - - +
629A LEU* 4.4 2.5 - - + -
632A CYS* 3.6 31.0 - - - -
633A MET* 4.1 13.9 - - - -
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Residues in contact with MET 593 (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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477A PHE* 4.2 42.0 - - + -
478A VAL* 4.4 22.2 - - + -
480A ALA* 5.4 9.3 - - + +
589A MET* 3.1 19.2 + - + +
592A CYS* 1.3 81.5 - - - +
594A ASN* 1.3 74.5 + - - +
595A MET 3.8 0.4 - - - -
596A ASN* 5.4 0.4 - - - -
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Residues in contact with ASN 594 (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 LEU* 3.4 20.1 - - - +
567A ILE* 4.5 10.5 - - + +
590A ASP* 2.7 38.1 + - - +
593A MET* 1.3 92.3 - - - +
595A MET* 1.3 66.6 + - + +
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Residues in contact with MET 595 (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 LEU* 4.3 2.9 - - - -
567A ILE* 3.8 18.4 - - + +
568A VAL* 2.9 59.0 - - + +
571A PHE* 3.5 38.4 - - + -
590A ASP* 4.0 9.0 - - - +
591A PHE* 3.2 28.1 + - + +
594A ASN* 1.3 90.0 - - + +
596A ASN* 1.3 67.3 + - - +
597A THR* 4.3 1.6 - - - -
600A ASN* 2.7 37.7 + - - +
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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