Contacts of the helix formed by residues 575 - 590 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B VAL* 4.4 12.3 - - + +
433B VAL* 3.9 29.6 - - + +
571B ILE* 2.9 35.7 + - + +
572B ILE 3.2 4.3 - - - -
574B LYS* 1.3 112.6 + - + +
576B ARG* 1.3 66.2 + - - +
577B LYS 3.2 2.2 - - - -
578B GLN* 3.4 28.3 - - + +
579B LEU* 3.0 22.3 + - - +
605B PHE* 3.4 30.3 - + - -
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Residues in contact with ARG 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B TYR* 5.0 1.2 + - - -
488B VAL* 4.3 12.7 + - - +
489B VAL* 3.6 49.8 + - - +
572B ILE* 2.9 12.7 + - - +
573B ARG* 3.4 16.9 + - - +
574B LYS 3.5 0.8 + - - -
575B TYR* 1.3 77.7 - - - +
577B LYS* 1.3 58.1 + - - +
579B LEU* 3.1 10.8 + - - +
580B ASP* 2.7 58.0 + - - +
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B TYR* 3.2 0.6 - - - +
576B ARG* 1.3 80.2 - - - +
578B GLN* 1.3 75.2 + - - +
580B ASP* 2.9 17.8 + - - +
581B ASN* 3.0 29.4 + - - +
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Residues in contact with GLN 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B VAL* 4.8 1.8 - - + -
574B LYS 4.5 1.7 - - - +
575B TYR* 3.4 50.4 - - + +
577B LYS* 1.3 81.2 - - - +
579B LEU* 1.3 64.4 + - - +
581B ASN* 3.2 3.5 + - - +
582B ILE* 2.9 30.8 + - + +
604B GLU* 2.9 59.5 + - + +
605B PHE* 3.8 17.1 - - + -
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Residues in contact with LEU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B TYR* 3.6 31.6 - - + +
425B ALA* 3.6 41.5 - - + +
426B GLY* 3.8 8.5 - - - +
429B VAL* 4.1 15.3 - - + +
485B ALA* 4.3 5.6 - - + -
489B VAL* 3.9 10.1 - - + -
572B ILE* 3.9 27.8 - - + +
575B TYR 3.0 15.2 + - - +
576B ARG* 3.2 14.6 - - - +
578B GLN* 1.3 78.5 - - - +
580B ASP* 1.3 63.7 + - - +
582B ILE* 3.2 3.5 + - - +
583B VAL* 3.1 24.6 + - - +
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Residues in contact with ASP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B TYR* 2.6 41.4 + - - +
576B ARG* 2.7 48.8 + - - +
577B LYS* 3.5 10.0 - - - +
579B LEU* 1.3 74.0 - - - +
581B ASN* 1.3 63.6 + - - +
583B VAL* 3.3 2.9 + - - +
584B GLU* 3.0 25.2 + - - +
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Residues in contact with ASN 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B LYS* 3.0 33.6 + - - +
578B GLN* 3.2 4.4 + - - +
580B ASP* 1.3 74.8 - - - +
582B ILE* 1.3 66.1 + - + +
584B GLU* 3.5 18.4 + - - +
585B ILE* 3.2 32.3 + - + +
604B GLU* 3.1 36.1 + - - +
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Residues in contact with ILE 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ALA* 4.2 15.7 - - + +
428B ALA* 4.9 7.6 - - + -
429B VAL* 4.4 19.7 - - + -
443B ILE* 4.2 19.3 - - + -
578B GLN 2.9 18.8 + - - +
579B LEU* 3.7 3.8 - - - +
581B ASN* 1.3 76.3 - - - +
583B VAL* 1.3 63.7 + - - +
585B ILE* 3.3 9.8 + - - +
586B LEU* 2.9 22.2 + - + +
592B ILE* 4.1 10.0 - - + +
600B ILE* 4.4 17.7 - - + -
601B LEU* 4.1 26.5 - - + -
604B GLU* 4.9 7.2 - - + -
605B PHE* 5.1 4.7 - - + -
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Residues in contact with VAL 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG 4.9 0.4 - - - +
421B ALA* 3.6 22.2 - - + +
422B TYR* 3.6 52.0 - - + +
425B ALA* 3.6 19.5 - - + -
579B LEU 3.1 14.7 + - - +
580B ASP 3.7 5.6 - - - +
582B ILE* 1.3 76.3 - - - +
584B GLU* 1.3 65.2 + - - +
586B LEU* 2.9 7.3 + - - +
587B LEU* 2.8 38.4 + - + +
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Residues in contact with GLU 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B ASP 3.0 16.3 + - - +
581B ASN* 3.5 20.3 - - - +
583B VAL* 1.3 79.5 - - - +
585B ILE* 1.3 66.3 + - + +
587B LEU* 3.4 9.0 + - - +
588B GLU* 3.4 25.4 + - - +
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Residues in contact with ILE 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B ASN* 3.2 23.3 + - + +
582B ILE* 3.7 7.6 - - - +
583B VAL 3.2 0.6 - - - -
584B GLU* 1.3 80.9 - - + +
586B LEU* 1.3 58.5 + - - +
588B GLU* 2.9 25.1 + - + +
589B LYS* 3.1 23.5 + - + +
592B ILE* 3.3 29.4 - - + -
596B GLU* 4.9 2.2 - - - +
600B ILE* 4.6 26.7 - - + -
604B GLU* 5.9 1.3 - - - +
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ALA* 3.7 38.6 - - + +
424B GLU* 4.5 3.8 - - + -
425B ALA* 5.0 3.1 - - + +
443B ILE* 4.0 33.0 - - + +
444B SER* 4.3 0.7 - - - -
445B ILE* 4.2 14.2 - - + +
582B ILE* 2.9 19.2 + - + +
583B VAL* 2.9 6.4 + - - +
585B ILE* 1.3 77.7 - - - +
587B LEU* 1.3 56.7 + - - +
590B GLU* 2.5 57.0 + - - +
592B ILE* 3.5 29.2 - - + -
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LYS* 3.4 48.7 + - + +
418B ARG* 4.3 16.8 - - + -
421B ALA* 3.6 24.2 - - + -
445B ILE* 4.3 11.4 - - + -
583B VAL* 2.8 36.6 + - + +
584B GLU* 3.9 8.1 - - - +
586B LEU* 1.3 72.6 - - - +
588B GLU* 1.3 62.8 + - - +
590B GLU* 4.4 2.6 + - - +
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Residues in contact with GLU 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B MET* 3.8 14.6 - - - +
360B LYS* 5.4 4.0 - - - -
584B GLU* 3.4 18.6 + - - +
585B ILE* 2.9 14.1 + - + +
587B LEU* 1.3 82.4 - - - +
589B LYS* 1.3 67.5 + - + +
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Residues in contact with LYS 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ASP* 6.0 0.3 - - - +
333B MET* 2.7 25.7 - - + +
585B ILE* 3.1 21.5 + - + +
588B GLU* 1.3 85.8 - - + +
590B GLU* 1.3 66.9 + - - +
591B THR* 3.0 27.9 + - - +
592B ILE* 4.9 3.6 - - + -
596B GLU* 3.5 30.7 + - - +
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Residues in contact with GLU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 3.8 1.5 - - + -
333B MET* 3.0 30.2 + - + +
336B ARG* 2.5 25.0 + - - -
360B LYS* 4.7 3.1 - - - +
363B PRO* 3.8 10.3 - - - +
417B LYS* 4.1 14.6 + - - +
444B SER* 3.0 6.6 + - - -
445B ILE* 2.8 54.1 + - + -
446B ILE* 2.9 27.3 - - + +
586B LEU* 2.5 29.4 + - - +
587B LEU 5.3 0.4 - - - +
588B GLU 3.7 0.6 - - - -
589B LYS* 1.3 74.9 - - - +
591B THR* 1.3 58.0 + - - +
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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