Contacts of the helix formed by residues 570 - 587 (chain A) in PDB entry 1CEZ
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 ILE 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A CYS* 4.2 18.2 - - + -
543A ILE* 3.7 25.6 - - + -
558A ALA* 3.8 33.1 + - + +
559A VAL* 4.6 2.5 - - + -
568A GLN 4.1 0.2 + - - -
569A ASP* 1.3 71.7 + - - +
571A TYR* 1.3 84.2 + - + +
573A ILE* 3.9 8.5 - - - -
574A VAL* 3.0 46.9 + - + +
688A THR* 4.3 5.8 - - + -
689A VAL* 3.5 31.6 - - + -
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Residues in contact with TYR 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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539A SER 5.9 1.3 - - - -
540A CYS* 3.5 28.3 - - + +
569A ASP* 2.9 23.2 + - - +
570A ILE* 1.3 95.4 - - + +
572A GLY* 1.3 61.6 + - - +
574A VAL* 3.7 3.0 + - + +
575A ALA* 3.2 13.0 + - - +
627A ARG* 3.8 15.7 - - + -
630A THR* 3.0 21.1 + - - -
631A LYS* 3.2 72.0 + - + -
634A VAL* 4.4 18.8 - - + -
635A MET* 4.0 22.7 - - + +
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Residues in contact with GLY 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ASP* 2.7 26.5 + - - -
571A TYR* 1.3 75.7 - - - +
573A ILE* 1.3 58.9 + - - -
575A ALA* 3.3 7.7 + - - +
576A LYS* 3.0 27.0 + - - +
627A ARG* 4.3 8.7 - - - -
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Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A ALA* 4.6 15.3 - - + -
568A GLN* 5.8 4.5 - - + +
569A ASP 2.9 26.9 + - - +
570A ILE* 3.9 6.1 - - - +
572A GLY* 1.3 73.2 - - - +
574A VAL* 1.3 66.9 + - - +
576A LYS* 3.3 27.0 - - - +
577A LYS* 3.0 43.2 + - - +
688A THR* 3.4 32.1 - - + -
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 3.0 36.3 + - + +
571A TYR* 4.1 5.2 - - + +
572A GLY 3.3 0.2 - - - -
573A ILE* 1.3 77.4 - - - +
575A ALA* 1.3 56.9 + - - +
577A LYS* 3.2 7.9 + - - +
578A VAL* 2.9 32.8 + - + +
630A THR* 4.7 5.6 - - - +
634A VAL* 4.6 12.8 - - + -
681A ILE* 4.3 4.7 - - + +
684A SER* 3.5 21.7 + - - -
685A VAL* 3.6 29.4 - - + -
688A THR* 4.1 17.7 - - + +
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Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A TYR 3.2 15.4 + - - +
572A GLY* 3.3 11.9 - - - +
574A VAL* 1.3 74.8 - - - +
576A LYS* 1.3 64.4 + - - +
578A VAL* 3.2 3.8 + - - +
579A ASN* 2.9 34.8 + - - +
626A THR* 4.2 2.9 - - - -
627A ARG 4.1 15.7 - - - +
630A THR* 3.6 26.2 + - + -
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Residues in contact with LYS 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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572A GLY 3.0 12.1 + - - +
573A ILE* 3.3 41.0 - - + +
575A ALA* 1.3 75.5 - - - +
577A LYS* 1.3 87.4 + - + +
579A ASN* 3.4 8.1 + - - +
580A GLU* 3.1 32.8 + - - +
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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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573A ILE* 3.0 32.9 + - - +
574A VAL 3.4 8.3 - - - +
575A ALA 3.1 0.6 - - - -
576A LYS* 1.3 96.7 - - + +
578A VAL* 1.3 64.7 + - - +
580A GLU* 3.2 30.3 + - + +
581A ILE* 3.4 16.8 - - + +
684A SER* 3.8 11.9 - - - +
687A VAL* 4.3 18.5 - - + +
688A THR* 3.5 30.3 - - - +
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Residues in contact with VAL 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 2.9 20.4 + - + +
575A ALA* 3.2 9.8 + - - +
577A LYS* 1.3 74.4 - - - +
579A ASN* 1.3 59.6 + - - +
581A ILE* 3.1 9.4 + - - +
582A LEU* 3.0 29.6 + - + +
625A VAL* 3.7 24.2 - - + -
630A THR* 5.1 3.8 - - + -
677A MET* 4.0 12.6 - - - -
680A LEU* 3.7 25.7 - - + +
681A ILE* 4.1 17.0 - - + +
684A SER* 3.1 25.1 - - - +
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Residues in contact with ASN 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ALA* 2.9 29.6 + - - +
576A LYS* 3.7 8.6 - - - +
578A VAL* 1.3 74.1 - - - +
580A GLU* 1.3 60.7 + - - +
581A ILE 3.0 1.6 - - - -
582A LEU* 3.1 7.8 + - - +
583A GLN* 2.8 35.5 + - + +
621A LEU* 4.3 14.7 - - - +
624A GLY 3.8 14.2 - - - +
625A VAL* 3.0 31.6 + - - +
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Residues in contact with GLU 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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576A LYS* 3.1 22.6 + - - +
577A LYS* 3.2 33.4 + - - +
579A ASN* 1.3 76.5 - - - +
581A ILE* 1.3 60.8 + - + +
583A GLN* 3.9 9.9 - - - +
584A ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 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* 3.4 16.6 - - + +
578A VAL* 3.1 7.4 + - - +
579A ASN 3.0 0.8 - - - -
580A GLU* 1.3 79.1 - - + +
582A LEU* 1.3 62.4 + - - +
584A ALA* 3.2 8.7 + - + +
585A ASP* 2.9 37.7 + - - +
680A LEU* 3.7 33.7 - - + +
683A GLU* 3.4 28.9 - - + +
684A SER* 4.2 15.0 - - - +
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Residues in contact with LEU 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 VAL* 3.0 26.3 + - + +
579A ASN* 3.1 11.9 + - - +
581A ILE* 1.3 75.1 - - - +
583A GLN* 1.3 60.4 + - - +
585A ASP 3.2 0.2 + - - -
586A ALA* 2.8 32.0 + - - +
617A ALA* 3.5 35.2 - - - +
620A TRP* 3.9 12.6 - - + -
621A LEU* 3.8 24.0 - - + +
625A VAL* 3.9 30.1 - - + -
676A TYR* 3.6 22.9 - - + +
677A MET* 4.3 0.9 - - + -
680A LEU* 3.8 7.4 - - + -
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Residues in contact with GLN 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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579A ASN* 2.8 23.6 + - + +
580A GLU* 4.1 8.1 - - - +
582A LEU* 1.3 77.1 - - - +
584A ALA* 1.3 60.2 + - - +
586A ALA* 3.5 6.7 + - - +
587A ILE* 3.3 33.2 + - + +
621A LEU* 3.6 29.7 - - - +
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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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580A GLU 3.2 17.6 + - - +
581A ILE* 3.2 14.8 + - + +
582A LEU 3.0 0.2 - - - -
583A GLN* 1.3 79.9 - - - +
585A ASP* 1.3 62.5 + - - +
587A ILE* 3.6 3.5 + - - +
588A ASN* 3.3 27.2 + - - +
589A GLY 4.7 0.2 + - - -
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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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581A ILE* 2.9 25.3 + - - +
584A ALA* 1.3 76.5 - - - +
586A ALA* 1.3 61.5 + - - +
587A ILE 3.2 2.5 - - - -
588A ASN 2.4 28.1 - - - +
589A GLY* 4.7 4.2 - - - -
613A THR* 3.6 24.0 + - - +
614A LYS* 3.3 10.4 - - - -
617A ALA* 3.5 20.0 - - + -
676A TYR* 2.6 26.3 + - - +
680A LEU* 4.9 0.7 - - - +
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Residues in contact with ALA 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 LEU 2.8 17.2 + - - +
583A GLN* 3.8 9.4 - - - +
584A ALA 3.3 0.2 - - - -
585A ASP* 1.3 78.1 - - - +
587A ILE* 1.3 67.1 + - + +
614A LYS* 3.8 21.2 - - - +
617A ALA* 3.8 7.1 - - + +
618A GLY* 5.1 3.1 - - - +
621A LEU* 3.7 24.0 - - + -
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Residues in contact with ILE 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLN* 3.3 20.7 + - + +
584A ALA* 4.0 3.4 - - - +
586A ALA* 1.3 85.2 - - + +
588A ASN* 1.3 80.1 + - - +
614A LYS* 3.8 15.9 + - - -
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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
------------------------------------------------------------
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