Contacts of the helix formed by residues 468 - 480 (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 SER 468 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D ASN* 5.1 0.5 + - - -
467D VAL* 1.3 75.7 - - - +
469D ARG* 1.3 64.8 + - - +
470D ASN* 3.5 7.2 + - - +
471D GLU* 2.8 37.5 + - - +
472D LEU* 2.9 22.7 + - - +
517D MET* 4.3 4.0 - - - -
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Residues in contact with ARG 469 (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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468D SER* 1.3 72.2 - - - +
470D ASN* 1.3 63.5 + - - +
472D LEU* 3.1 5.8 + - - +
473D LEU* 2.8 51.9 + - + +
511D MET* 3.8 20.0 - - + +
517D MET* 2.3 66.9 + - + +
519D GLU 5.3 2.0 - - - +
560D ILE* 5.3 8.1 - - - +
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Residues in contact with ASN 470 (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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436D ASN* 4.4 12.3 - - - +
468D SER* 3.2 6.7 + - - +
469D ARG* 1.3 83.7 + - - +
471D GLU* 1.3 58.0 + - - +
473D LEU* 3.1 14.8 + - - +
474D ASP* 2.9 40.0 + - - +
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Residues in contact with GLU 471 (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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436D ASN* 3.8 36.9 - - + +
466D LEU 4.0 3.3 - - - +
467D VAL* 3.2 22.2 - - + +
468D SER* 2.8 41.0 + - - +
470D ASN* 1.3 76.7 - - - +
472D LEU* 1.3 57.2 + - - +
474D ASP* 3.4 2.6 + - - +
475D LYS* 3.1 26.9 + - - +
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Residues in contact with LEU 472 (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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467D VAL* 3.6 41.5 - - + -
468D SER 2.9 8.8 + - - +
469D ARG 3.6 7.0 - - - +
471D GLU* 1.3 75.2 - - - +
473D LEU* 1.3 65.5 + - - +
475D LYS* 3.4 16.7 + - + +
476D LEU* 3.0 23.9 + - - +
507D ILE* 4.2 20.2 - - + +
510D ASN* 6.5 0.2 - - + -
511D MET* 4.0 26.2 - - + -
515D LEU* 3.8 24.2 - - + -
517D MET* 4.2 9.6 - - - -
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Residues in contact with LEU 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 2.8 42.9 + - - +
470D ASN* 3.7 17.9 - - - +
472D LEU* 1.3 76.9 - - - +
474D ASP* 1.3 57.6 + - - +
476D LEU* 3.3 5.8 + - + +
477D THR* 2.8 36.2 + - - -
511D MET* 4.1 16.4 - - + -
560D ILE* 4.0 22.4 - - + +
564D CYS* 3.7 21.4 - - - -
567D ARG* 4.6 5.6 - - - +
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Residues in contact with ASP 474 (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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434D VAL* 3.4 28.9 - - + +
435D PRO* 3.3 9.2 - - - +
436D ASN* 3.0 42.6 + - + +
437D GLY* 5.5 0.9 - - - -
470D ASN* 2.9 22.3 + - - +
471D GLU 3.6 4.9 - - - +
473D LEU* 1.3 75.7 - - - +
475D LYS* 1.3 66.7 + - - +
477D THR* 3.2 2.9 + - - -
478D ALA* 2.9 23.8 + - - +
567D ARG* 2.9 24.8 + - - +
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Residues in contact with LYS 475 (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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436D ASN 5.6 1.2 + - - -
437D GLY* 5.8 3.8 - - - -
438D GLU* 6.0 7.2 - - + -
471D GLU 3.1 17.1 + - - +
472D LEU* 3.8 16.2 - - + +
474D ASP* 1.3 74.7 - - - +
476D LEU* 1.3 55.5 + - - +
478D ALA* 3.2 8.1 + - + +
479D LEU* 2.8 37.8 + - + +
503D ARG* 4.0 26.4 - - - +
507D ILE* 3.8 25.3 - - + +
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Residues in contact with LEU 476 (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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472D LEU 3.0 16.0 + - - +
473D LEU* 3.4 5.4 - - + +
475D LYS* 1.3 75.1 - - - +
477D THR* 1.3 65.9 + - - +
479D LEU* 3.1 18.0 + - - +
480D LEU* 3.1 46.1 + - + +
504D ALA* 3.6 31.6 - - + +
507D ILE* 3.9 23.5 - - + +
508D ALA* 4.1 7.4 - - + +
511D MET* 5.0 2.2 - - - -
560D ILE* 4.1 20.0 - - + -
561D VAL* 4.1 9.4 - - + -
564D CYS* 3.4 17.7 - - + -
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Residues in contact with THR 477 (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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430D VAL* 3.7 16.7 - - + +
434D VAL* 4.9 1.3 - - + -
473D LEU 2.8 19.2 + - - -
474D ASP* 3.6 7.2 - - - -
476D LEU* 1.3 76.2 - - - +
478D ALA* 1.3 65.0 + - - +
480D LEU* 3.2 12.2 + - - +
481D GLY 3.4 6.9 + - - -
564D CYS* 3.5 33.2 - - - +
567D ARG* 3.2 33.4 + - + +
568D ALA* 3.6 22.0 - - - +
571D ILE* 4.3 4.5 - - + -
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Residues in contact with ALA 478 (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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427D HIS* 3.1 17.3 + - + +
430D VAL* 3.5 17.7 - - + +
431D SER* 3.7 27.1 - - - +
434D VAL* 5.1 2.7 - - + -
437D GLY* 5.6 2.5 - - - -
474D ASP 2.9 13.4 + - - +
475D LYS* 3.5 11.9 - - + +
476D LEU 3.2 0.2 - - - -
477D THR* 1.3 77.0 - - - +
479D LEU* 1.3 57.1 + - - +
481D GLY* 2.8 20.6 + - - -
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Residues in contact with LEU 479 (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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427D HIS* 3.0 26.4 - - + +
448D ARG* 6.4 0.2 - - - +
475D LYS* 2.8 25.8 + - + +
476D LEU* 3.4 9.4 - - - +
478D ALA* 1.3 75.7 - - - +
480D LEU* 1.3 57.5 + - - +
482D GLY 4.4 0.2 + - - -
483D ARG 5.2 0.7 + - - -
500D ASP* 3.3 44.8 - - + +
503D ARG* 4.1 24.2 - - + -
504D ALA* 4.2 10.1 - - + +
507D ILE* 3.6 31.0 - - + -
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Residues in contact with LEU 480 (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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476D LEU* 3.1 36.9 + - + +
477D THR 3.8 7.2 - - - +
478D ALA 3.1 1.4 - - - -
479D LEU* 1.3 78.2 - - - +
481D GLY* 1.3 57.3 + - - +
482D GLY 3.4 1.1 - - - -
483D ARG* 3.3 11.6 + - + +
484D ALA* 2.8 29.8 + - - +
500D ASP* 5.0 2.5 - - + +
501D ILE* 4.8 11.0 - - + -
504D ALA* 4.2 17.0 - - + -
561D VAL* 3.7 18.2 - - + +
564D CYS* 3.9 1.8 - - + -
565D TYR* 3.7 45.8 - - + +
568D ALA* 4.4 1.6 - - + -
523E PRO* 4.6 13.0 - - + +
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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
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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