Contacts of the helix formed by residues 575 - 590 (chain D) in PDB entry 2CEA
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 TYR 575 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429D VAL* 4.2 15.2 - - + +
433D VAL* 3.8 30.3 - - + +
571D ILE* 2.9 36.0 + - + +
572D ILE* 3.3 4.3 - - - -
574D LYS* 1.3 115.8 + - + +
576D ARG* 1.3 64.6 + - - +
577D LYS 3.3 2.5 - - - -
578D GLN* 3.3 35.7 + - + +
579D LEU* 3.1 21.3 + - - +
605D PHE* 4.1 16.2 - + + -
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Residues in contact with ARG 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TYR* 5.1 1.2 + - - -
488D VAL* 4.4 15.1 + - - +
489D VAL* 3.7 38.2 + - - +
572D ILE* 2.9 12.3 + - - +
573D ARG* 3.4 17.9 + - - +
574D LYS 3.5 1.2 + - - -
575D TYR* 1.3 77.2 - - - +
577D LYS* 1.3 65.4 + - + +
579D LEU* 3.0 18.5 + - - +
580D ASP* 2.9 49.6 + - - +
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Residues in contact with LYS 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D TYR* 3.3 1.0 - - - +
576D ARG* 1.3 78.0 - - + +
578D GLN* 1.3 66.1 + - + +
580D ASP* 3.0 12.3 + - - +
581D ASN* 2.9 36.7 + - - +
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Residues in contact with GLN 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D VAL* 4.8 0.9 - - + -
575D TYR* 3.7 32.8 - - + +
577D LYS* 1.3 80.4 - - + +
579D LEU* 1.3 61.5 + - - +
581D ASN* 3.5 13.3 + - - +
582D ILE* 3.1 32.8 + - - +
604D GLU* 2.8 39.2 + - + +
605D PHE* 3.2 39.4 - - + +
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Residues in contact with LEU 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TYR* 3.9 27.1 - - + +
425D ALA* 3.3 44.2 - - + +
426D GLY* 3.9 4.7 - - - +
429D VAL* 4.2 14.0 - - + +
485D ALA* 4.2 4.5 - - + -
489D VAL* 4.4 2.2 - - + -
572D ILE* 3.7 36.3 - - + +
575D TYR 3.1 12.4 + - - +
576D ARG* 3.0 19.0 + - - +
578D GLN* 1.3 74.4 - - - +
580D ASP* 1.3 66.0 + - - +
582D ILE* 3.2 3.7 + - - +
583D VAL* 3.1 28.3 + - + +
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Residues in contact with ASP 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TYR* 2.8 35.1 + - - +
576D ARG* 2.9 51.6 + - - +
577D LYS* 3.5 9.6 - - - +
579D LEU* 1.3 75.3 - - - +
581D ASN* 1.3 65.4 + - - +
583D VAL* 3.2 5.0 + - - +
584D GLU* 3.0 22.2 + - - +
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Residues in contact with ASN 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D LYS* 2.9 21.8 + - - +
578D GLN* 3.6 9.3 - - - +
580D ASP* 1.3 77.1 - - - +
582D ILE* 1.3 62.7 + - - +
584D GLU* 3.1 16.9 + - - +
585D ILE* 3.2 18.9 + - + +
604D GLU* 2.8 39.5 + - - +
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Residues in contact with ILE 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D ALA* 4.1 14.4 - - + +
428D ALA* 5.4 2.5 - - + -
429D VAL* 3.9 25.6 - - + -
443D ILE* 3.9 26.7 - - + -
578D GLN 3.1 20.2 + - - +
579D LEU* 3.2 4.0 + - - +
581D ASN* 1.3 76.7 - - - +
583D VAL* 1.3 57.9 + - - +
585D ILE* 3.4 8.4 + - - +
586D LEU* 2.8 30.7 + - + +
592D ILE* 4.5 6.2 - - + +
597D LEU* 6.1 0.7 - - + -
600D ILE* 4.1 20.4 - - + -
601D LEU* 4.1 21.5 - - + -
604D GLU* 4.2 6.1 - - + -
605D PHE* 4.4 7.0 - - + -
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Residues in contact with VAL 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ARG* 4.7 0.9 - - + +
421D ALA* 3.7 25.4 - - + +
422D TYR* 3.8 43.1 - - + +
425D ALA* 3.6 21.1 - - + -
579D LEU 3.1 15.6 + - - +
580D ASP 3.5 6.5 - - - +
581D ASN 3.1 0.2 - - - -
582D ILE* 1.3 74.7 - - - +
584D GLU* 1.3 59.9 + - - +
586D LEU* 3.5 5.5 - - - +
587D LEU* 2.8 44.7 + - + +
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Residues in contact with GLU 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D ASP 3.0 11.9 + - - +
581D ASN* 3.1 12.0 + - - +
583D VAL* 1.3 78.7 - - - +
585D ILE* 1.3 69.9 - - + +
587D LEU* 3.4 14.6 + - - +
588D GLU* 3.4 24.6 + - - +
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Residues in contact with ILE 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ASN* 3.2 18.2 + - + +
582D ILE* 3.8 5.6 - - - +
584D GLU* 1.3 81.7 - - + +
586D LEU* 1.3 66.3 + - - +
588D GLU* 3.1 16.8 + - + +
589D LYS* 3.1 33.9 + - + +
592D ILE* 4.1 4.9 - - + -
600D ILE* 3.9 46.4 - - + -
603D GLU* 5.9 2.9 - - - +
604D GLU* 4.8 6.1 - - - +
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Residues in contact with LEU 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D ALA* 4.2 25.6 - - + +
424D GLU* 4.3 6.5 - - + -
425D ALA 4.6 1.8 - - - +
443D ILE* 2.9 42.8 - - + -
444D SER* 4.6 0.4 - - - -
445D ILE* 4.1 13.4 - - + +
582D ILE* 2.8 21.9 + - + +
583D VAL* 3.5 6.5 - - - +
585D ILE* 1.3 78.0 - - - +
587D LEU* 1.3 55.9 + - - +
588D GLU 3.0 0.2 - - - -
590D GLU* 2.6 54.7 + - - +
591D THR* 4.4 0.9 - - - -
592D ILE* 3.6 24.7 - - + +
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Residues in contact with LEU 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LYS* 3.8 56.6 + - + +
418D ARG* 4.3 18.2 - - + -
421D ALA* 4.0 8.1 - - + -
445D ILE* 4.1 12.1 - - + -
583D VAL* 2.8 38.6 + - + +
584D GLU* 3.7 8.7 - - - +
585D ILE 3.3 0.2 - - - -
586D LEU* 1.3 72.3 - - - +
588D GLU* 1.3 59.9 + - - +
590D GLU* 4.4 2.7 + - - +
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Residues in contact with GLU 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D MET* 5.9 2.4 - - - +
360D LYS* 5.2 7.8 + - - +
584D GLU* 3.4 24.9 + - - +
585D ILE* 3.1 11.1 + - + +
586D LEU 3.0 0.8 - - - -
587D LEU* 1.3 82.0 - - - +
589D LYS* 1.3 66.2 + - + +
590D GLU* 3.5 1.1 - - - +
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Residues in contact with LYS 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D ASP* 5.4 0.9 - - - +
333D MET* 5.5 4.8 + - - +
585D ILE* 3.1 32.2 + - + +
588D GLU* 1.3 81.6 - - + +
590D GLU* 1.3 62.9 + - - +
591D THR* 2.6 34.9 + - - +
592D ILE* 4.5 8.4 - - + +
596D GLU* 3.2 46.2 - - - +
600D ILE* 5.4 2.6 - - - +
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Residues in contact with GLU 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D ASP* 3.5 3.1 - - + -
333D MET* 2.5 44.2 + - + +
336D ARG* 2.9 28.1 + - - -
363D PRO* 3.7 13.7 - - - +
417D LYS* 4.3 13.4 + - - +
444D SER* 3.4 2.4 - - - -
445D ILE* 2.9 46.4 + - + +
446D ILE* 4.2 17.4 + - + +
586D LEU* 2.6 28.1 + - - +
587D LEU 4.4 2.4 - - - +
588D GLU 3.5 2.3 - - - +
589D LYS* 1.3 74.6 - - - +
591D THR* 1.3 60.5 + - - +
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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