Contacts of the helix formed by residues 559 - 575 (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 SER 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560A THR* 1.3 59.7 + - - +
561A GLY* 3.2 7.0 - - - +
562A SER* 2.8 38.1 + - - +
563A HIS* 3.3 12.8 + - - +
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Residues in contact with THR 560 (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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559A SER* 1.3 77.7 + - - +
561A GLY* 1.3 56.8 + - - +
563A HIS* 3.9 11.6 + - + +
564A LEU* 3.3 22.2 + - - +
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Residues in contact with GLY 561 (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 SER* 3.2 2.2 - - - +
560A THR* 1.3 77.4 - - - +
562A SER* 1.3 55.3 + - - +
563A HIS 3.2 1.6 - - - -
564A LEU* 3.7 11.5 - - - +
565A LYS* 2.7 35.5 + - - +
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Residues in contact with SER 562 (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 SER* 2.8 42.9 + - - +
561A GLY* 1.3 75.2 - - - +
563A HIS* 1.3 60.2 + - - +
565A LYS* 4.1 9.4 - - - +
566A LEU* 3.3 21.0 + - - +
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Residues in contact with HIS 563 (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 SER 3.3 12.6 + - - +
560A THR* 4.2 11.7 + - + +
561A GLY 3.2 0.6 - - - -
562A SER* 1.3 78.7 + - - +
564A LEU* 1.3 67.8 + - - +
566A LEU* 3.1 15.6 + - + +
567A ILE* 3.1 44.8 + - + +
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Residues in contact with LEU 564 (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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560A THR 3.3 19.3 + - - +
561A GLY* 3.7 9.0 - - - +
563A HIS* 1.3 78.9 + - - +
565A LYS* 1.3 66.8 + - - +
567A ILE* 3.2 14.8 + - + +
568A VAL* 3.0 26.9 + - + +
594A ASN 3.4 26.2 - - - +
595A MET* 4.3 2.7 - - - -
597A THR* 4.2 16.6 - - + +
600A ASN* 3.8 26.9 - - - +
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Residues in contact with LYS 565 (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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548A GLN* 3.6 34.4 + - - +
561A GLY 2.7 22.3 + - - +
562A SER* 4.1 9.2 - - - +
564A LEU* 1.3 72.7 - - - +
566A LEU* 1.3 65.0 + - - +
568A VAL* 3.2 7.9 + - - -
569A ASP* 2.9 51.9 + - - +
600A ASN* 5.6 2.7 - - - -
603A LYS* 5.0 8.3 - - - +
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Residues in contact with LEU 566 (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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562A SER 3.3 12.5 + - - +
563A HIS* 3.1 19.1 + - + +
565A LYS* 1.3 81.6 - - - +
567A ILE* 1.3 63.2 + - + +
569A ASP* 3.4 8.4 + - + +
570A ALA* 3.1 22.0 + - + +
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Residues in contact with ILE 567 (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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563A HIS* 3.1 40.9 + - + +
564A LEU* 3.2 16.5 + - + +
566A LEU* 1.3 78.2 - - + +
568A VAL* 1.3 62.6 + - + +
570A ALA* 3.3 8.5 - - - +
571A PHE* 2.9 27.2 + - - +
590A ASP* 5.3 4.0 - - - +
594A ASN* 4.5 16.2 - - + +
595A MET* 3.8 28.7 - - + -
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Residues in contact with VAL 568 (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* 3.0 21.1 + - + +
565A LYS* 3.6 5.6 - - - +
567A ILE* 1.3 75.0 - - + +
569A ASP* 1.3 64.3 + - - +
571A PHE* 3.4 0.3 - - - +
572A LEU* 2.8 49.4 + - + +
591A PHE* 5.2 3.1 - - + -
595A MET* 2.9 31.2 - - + -
600A ASN* 3.1 44.2 - - + +
603A LYS* 5.0 8.7 - - + -
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Residues in contact with ASP 569 (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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548A GLN 5.2 1.6 - - - +
565A LYS* 2.9 49.7 + - - +
566A LEU* 3.9 10.2 - - + +
568A VAL* 1.3 75.1 - - - +
570A ALA* 1.3 62.7 + - - +
572A LEU* 4.1 7.3 - - - +
573A GLN* 3.0 39.6 + - - +
603A LYS* 3.6 24.5 - - - -
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Residues in contact with ALA 570 (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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566A LEU* 3.1 15.8 + - + +
567A ILE* 3.3 12.6 - - - +
569A ASP* 1.3 77.0 - - - +
571A PHE* 1.3 63.4 + - - +
573A GLN* 3.3 8.9 + - - +
574A GLN* 3.2 23.1 + - - +
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Residues in contact with PHE 571 (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 2.9 17.3 + - - +
568A VAL 3.4 4.5 - - - +
570A ALA* 1.3 77.0 - - - +
572A LEU* 1.3 77.4 + - + +
574A GLN* 2.3 49.3 + - - +
575A LEU* 3.3 21.7 + - + +
587A ALA* 3.3 45.3 - - + -
590A ASP* 3.6 25.1 - - + +
591A PHE* 3.7 24.7 - + + -
595A MET* 3.5 22.7 - - + -
604A LEU* 4.6 5.2 - - + -
625A LEU* 5.4 2.9 - - + -
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Residues in contact with LEU 572 (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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545A LEU* 4.9 6.5 - - + -
568A VAL* 2.8 33.2 + - + +
569A ASP* 4.2 10.1 - - - +
571A PHE* 1.3 89.1 - - + +
573A GLN* 1.3 65.5 + - + +
574A GLN 3.0 1.6 + - - -
575A LEU* 3.2 23.0 + - + +
576A PRO* 3.5 4.9 - - - +
591A PHE* 5.4 1.1 - - + -
603A LYS* 4.0 34.5 - - + +
604A LEU* 4.0 33.0 - - + +
607A ALA* 4.2 19.2 - - + +
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Residues in contact with GLN 573 (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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569A ASP* 3.0 31.8 + - - +
570A ALA* 3.7 7.4 + - - +
571A PHE 3.3 0.6 - - - -
572A LEU* 1.3 76.6 - - + +
574A GLN* 1.3 56.9 + - - +
576A PRO* 3.6 14.5 - - - +
577A ASN* 5.1 4.0 + - - -
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Residues in contact with GLN 574 (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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570A ALA 3.2 10.4 + - - +
571A PHE* 2.3 60.7 + - - +
573A GLN* 1.3 76.5 - - - +
575A LEU* 1.3 66.4 + - - +
576A PRO* 3.2 4.0 - - - -
577A ASN* 2.8 39.5 + - + +
578A CYS* 3.1 24.8 + - - -
587A ALA* 4.2 9.0 - - - +
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Residues in contact with LEU 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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571A PHE* 4.1 14.6 - - + +
572A LEU* 3.2 21.5 + - + +
574A GLN* 1.3 83.0 - - - +
576A PRO* 1.3 62.3 - - + +
578A CYS* 2.9 28.4 + - - +
584A ILE* 4.2 14.1 - - + -
587A ALA* 4.4 15.3 - - + -
604A LEU* 3.7 29.6 - - + -
607A ALA* 5.0 6.3 - - + -
608A LEU* 3.8 16.2 - - + -
618A LEU* 4.4 0.7 - - - +
622A TYR* 3.4 23.4 + - + +
625A LEU* 3.9 19.1 - - + -
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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
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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