Contacts of the helix formed by residues 480 - 491 (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 LEU 480 (chain D).
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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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Residues in contact with GLY 481 (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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426D GLY* 3.7 12.9 - - - -
430D VAL* 3.9 24.2 - - - -
477D THR 3.4 2.3 + - - -
478D ALA 2.8 15.7 + - - -
479D LEU 3.2 0.2 - - - -
480D LEU* 1.3 75.8 - - - +
482D GLY* 1.3 65.0 + - - +
484D ALA* 3.7 6.0 - - - +
485D ALA* 3.0 24.3 + - - +
568D ALA* 4.5 0.4 - - - -
572D ILE* 4.0 1.9 - - - +
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Residues in contact with GLY 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D HIS* 3.1 48.4 - - - -
427D HIS* 3.8 14.2 - - - +
480D LEU 3.4 0.2 - - - -
481D GLY* 1.3 75.8 - - - +
483D ARG* 1.3 62.6 + - - +
485D ALA* 3.2 4.2 + - - +
486D GLU* 3.1 25.3 + - - +
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Residues in contact with ARG 483 (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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423D HIS* 3.7 3.6 + - - -
479D LEU 5.2 1.2 + - - +
480D LEU* 3.3 14.5 + - + +
481D GLY 3.2 0.4 - - - -
482D GLY* 1.3 76.9 - - - +
484D ALA* 1.3 64.4 + - - +
486D GLU* 3.2 8.7 + - - +
487D GLU* 3.0 21.2 + - - +
493D VAL* 3.3 40.9 - - - +
494D THR 4.0 12.3 + - - -
497D ALA* 3.7 27.2 - - + +
500D ASP* 6.3 0.2 - - + -
501D ILE* 3.6 19.5 - - + +
565D TYR* 3.6 26.5 + - + -
515E LEU 3.3 13.7 + - - -
516E GLY* 2.3 38.8 + - - -
523E PRO* 4.3 13.4 - - + +
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Residues in contact with ALA 484 (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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480D LEU 2.8 17.2 + - - +
481D GLY* 3.7 4.9 - - - +
483D ARG* 1.3 78.4 - - - +
485D ALA* 1.3 61.9 + - - +
487D GLU* 3.4 0.7 + - - +
488D VAL* 3.0 31.0 + - - +
565D TYR* 3.9 11.4 - - + -
568D ALA* 3.7 26.5 - - + -
569D LYS* 3.7 22.4 - - + +
572D ILE* 4.2 4.3 - - + -
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Residues in contact with ALA 485 (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* 3.7 28.0 - - + +
426D GLY* 4.1 0.9 - - - -
481D GLY 3.0 12.9 + - - +
482D GLY 3.2 2.4 + - - +
484D ALA* 1.3 73.6 - - - +
486D GLU* 1.3 65.6 + - - +
489D VAL* 2.9 30.6 + - - +
572D ILE* 3.4 31.4 - - + +
579D LEU* 4.2 10.5 - - + -
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Residues in contact with GLU 486 (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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419D ILE* 4.1 21.3 - - + +
423D HIS* 2.5 44.2 + - + +
482D GLY 3.1 9.1 + - - +
483D ARG* 3.6 12.2 - - - +
485D ALA* 1.3 75.2 - - - +
487D GLU* 1.3 62.9 + - - +
490D PHE* 3.0 35.3 + - + +
492D ASP 3.1 17.1 - - - +
493D VAL* 4.1 3.8 - - + +
494D THR* 2.6 44.3 + - + +
496D GLY* 4.9 1.7 - - - -
497D ALA* 4.7 4.8 + - - +
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Residues in contact with GLU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ARG* 3.0 11.6 + - - +
484D ALA 3.8 3.6 - - - +
485D ALA 3.2 0.2 - - - -
486D GLU* 1.3 77.3 - - - +
488D VAL* 1.3 59.6 + - - +
491D GLY* 2.9 38.5 + - - +
492D ASP 3.8 8.5 + - - -
493D VAL* 4.1 11.2 - - + +
565D TYR* 1.9 49.4 + - - +
569D LYS* 4.2 20.9 + - + -
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Residues in contact with VAL 488 (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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484D ALA 3.0 17.7 + - - +
485D ALA 4.0 2.0 - - - +
487D GLU* 1.3 79.0 - - + +
489D VAL* 1.3 63.0 + - + +
491D GLY 4.5 1.0 + - - -
569D LYS* 4.0 38.4 - - + +
572D ILE* 4.1 17.3 - - + -
573D ARG* 3.8 31.9 - - + +
576D ARG* 4.4 17.4 + - - +
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Residues in contact with VAL 489 (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* 3.7 34.1 - - + +
485D ALA 2.9 18.4 + - - +
488D VAL* 1.3 83.3 - - + +
490D PHE* 1.3 90.9 + - + +
576D ARG* 3.7 35.2 + - - +
579D LEU* 4.4 7.9 - - + -
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Residues in contact with PHE 490 (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* 3.4 37.9 - - - -
419D ILE* 4.1 34.1 - - + -
422D TYR* 3.8 34.8 - + + -
486D GLU* 3.0 25.7 + - + +
489D VAL* 1.3 97.9 - - + +
491D GLY* 1.3 58.9 + - - +
492D ASP* 3.1 18.1 + - + +
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Residues in contact with GLY 491 (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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486D GLU 3.6 0.6 + - - -
487D GLU* 2.9 29.9 + - - +
488D VAL 4.5 1.2 + - - -
489D VAL 3.7 0.6 - - - -
490D PHE* 1.3 75.7 - - - +
492D ASP* 1.3 57.7 + - - +
493D VAL* 5.4 0.2 - - - +
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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