Contacts of the helix formed by residues 480 - 491 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E LEU* 3.1 20.4 + - + +
477E THR 3.1 6.0 + - - +
479E LEU* 1.3 76.9 - - - +
481E GLY* 1.3 59.2 + - - +
482E GLY 3.4 0.9 - - - -
483E ARG* 3.4 12.5 + - + +
484E ALA* 2.9 27.4 + - - +
500E ASP* 4.9 5.2 - - + +
501E ILE* 4.9 8.1 - - + -
504E ALA* 4.0 20.0 - - + -
561E VAL* 3.7 40.6 - - + +
564E CYS* 3.8 9.0 - - + -
565E TYR* 3.7 29.3 - - + +
568E ALA* 4.2 2.8 - - + +
523F PRO* 4.5 18.6 - - + +
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Residues in contact with GLY 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E GLY* 4.1 10.8 - - - -
430E VAL* 4.0 21.8 - - - -
477E THR 3.1 6.9 + - - -
478E ALA 2.7 16.1 + - - -
480E LEU* 1.3 74.6 - - - +
482E GLY* 1.3 66.4 + - - +
484E ALA* 2.9 8.0 + - - +
485E ALA* 2.8 22.9 + - - +
568E ALA* 4.4 0.7 - - - -
572E ILE* 4.5 0.7 - - - +
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Residues in contact with GLY 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E HIS* 3.1 51.6 + - - -
426E GLY* 4.5 0.9 - - - -
427E HIS* 3.6 13.6 + - - +
480E LEU 3.4 0.8 - - - -
481E GLY* 1.3 76.0 - - - +
483E ARG* 1.3 60.2 + - - +
485E ALA* 3.1 4.5 + - - +
486E GLU* 3.1 22.2 + - - +
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Residues in contact with ARG 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E HIS* 4.1 3.2 + - - -
479E LEU 5.7 0.2 - - - +
480E LEU* 3.4 15.5 + - + +
481E GLY 3.1 0.4 - - - -
482E GLY* 1.3 73.5 - - - +
484E ALA* 1.3 67.1 - - - +
486E GLU* 3.3 8.6 + - - +
487E GLU* 3.0 22.2 + - - +
493E VAL* 2.8 43.2 - - - +
494E THR 3.5 14.5 + - - -
497E ALA* 3.7 27.0 - - + +
500E ASP* 5.1 1.7 + - + -
501E ILE* 3.9 18.5 - - + +
565E TYR* 3.5 24.3 + - + +
515F LEU* 3.1 16.3 + - - +
516F GLY* 2.3 38.6 + - - -
523F PRO* 4.8 9.4 - - + +
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Residues in contact with ALA 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480E LEU 2.9 14.2 + - - +
481E GLY 2.9 9.7 + - - +
483E ARG* 1.3 75.5 - - - +
485E ALA* 1.3 57.5 + - - +
487E GLU* 3.2 2.3 + - - +
488E VAL* 3.0 33.6 + - - +
565E TYR* 3.8 11.1 - - + -
568E ALA* 3.8 24.7 - - + -
569E LYS* 3.9 21.0 - - + +
572E ILE* 4.0 9.0 - - + -
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Residues in contact with ALA 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422E TYR* 3.4 27.8 - - + +
426E GLY* 4.1 1.8 - - - -
481E GLY 2.8 11.0 + - - +
482E GLY 3.4 9.0 - - - +
483E ARG 3.1 0.2 - - - -
484E ALA* 1.3 75.1 - - - +
486E GLU* 1.3 65.7 + - - +
489E VAL* 3.0 30.6 + - - +
572E ILE* 3.9 25.8 - - + -
579E LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E ILE* 3.9 23.9 - - + +
422E TYR* 5.3 0.8 - - - +
423E HIS* 3.1 30.0 + - + +
482E GLY 3.1 13.1 + - - +
483E ARG* 3.6 10.8 - - - +
485E ALA* 1.3 79.2 - - - +
487E GLU* 1.3 57.6 + - - +
490E PHE* 2.8 39.2 + - + +
492E ASP 3.2 14.7 - - - +
493E VAL* 3.7 7.1 - - + -
494E THR* 2.6 53.2 + - - +
496E GLY* 4.5 0.9 - - - -
497E ALA* 4.5 5.9 + - - +
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Residues in contact with GLU 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E ARG* 3.0 16.3 + - - +
484E ALA* 3.8 3.1 - - - +
486E GLU* 1.3 79.3 - - - +
488E VAL* 1.3 59.2 + - - +
491E GLY* 2.7 40.5 + - - +
492E ASP 3.8 9.6 - - - +
493E VAL* 5.3 9.1 - - + +
565E TYR* 2.4 38.7 + - + +
569E LYS* 4.0 18.8 + - + -
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Residues in contact with VAL 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484E ALA 3.0 19.0 + - - +
485E ALA 4.2 0.2 - - - +
487E GLU* 1.3 78.5 - - + +
489E VAL* 1.3 63.1 + - + +
491E GLY 4.5 1.0 + - - -
569E LYS* 4.2 22.4 - - + +
572E ILE* 4.0 20.2 - - + -
573E ARG* 3.6 48.9 - - + +
576E ARG* 3.9 21.2 + - - +
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Residues in contact with VAL 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418E ARG* 5.3 3.8 - - - +
422E TYR* 3.7 33.0 - - + +
485E ALA 3.0 20.2 + - - +
488E VAL* 1.3 81.4 - - + +
490E PHE* 1.3 87.8 + - + +
576E ARG* 3.5 40.0 + - - +
579E LEU* 4.2 8.3 - - + -
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Residues in contact with PHE 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E ARG* 3.9 30.5 - - + -
419E ILE* 3.9 40.4 - - + -
422E TYR* 4.1 27.6 - + + -
486E GLU* 2.8 30.0 + - + +
489E VAL* 1.3 95.4 - - + +
491E GLY* 1.3 53.7 + - - +
492E ASP* 2.6 29.7 + - + +
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Residues in contact with GLY 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E GLU 3.5 0.4 + - - -
487E GLU* 2.7 39.9 + - - +
488E VAL 4.4 1.0 + - - -
489E VAL 3.7 0.8 - - - -
490E PHE* 1.3 68.8 - - - +
492E ASP* 1.3 58.4 + - - +
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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