Contacts of the helix formed by residues 480 - 491 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476F LEU* 3.3 29.4 + - + +
477F THR* 3.2 7.1 + - - +
478F ALA 3.1 0.8 - - - -
479F LEU* 1.3 79.2 - - - +
481F GLY* 1.3 58.6 + - - +
482F GLY 3.4 1.1 - - - -
483F ARG* 3.3 13.0 + - + +
484F ALA* 2.8 28.3 + - - +
500F ASP* 4.9 2.0 - - + +
501F ILE* 4.4 23.6 - - + +
504F ALA* 4.1 17.9 - - + -
561F VAL* 3.7 34.8 - - + +
564F CYS* 4.1 2.7 - - + -
565F TYR* 3.9 33.8 - - + +
568F ALA* 4.4 1.3 - - + -
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Residues in contact with GLY 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F GLY* 3.7 12.1 - - - -
430F VAL* 3.8 25.6 - - - -
477F THR 3.2 3.9 + - - -
478F ALA 2.9 14.9 + - - -
479F LEU 3.2 0.2 - - - -
480F LEU* 1.3 75.0 - - - +
482F GLY* 1.3 60.4 + - - +
484F ALA* 3.1 6.8 - - - +
485F ALA* 2.9 29.3 + - - +
568F ALA* 4.2 0.2 - - - -
572F ILE* 4.0 1.4 - - - +
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Residues in contact with GLY 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F HIS* 3.2 48.7 - - - -
426F GLY* 4.4 0.7 - - - -
427F HIS* 3.8 12.5 + - - +
480F LEU 3.4 0.6 - - - -
481F GLY* 1.3 74.1 - - - +
483F ARG* 1.3 64.0 + - - +
485F ALA* 3.0 5.2 + - - +
486F GLU* 2.9 24.4 + - - +
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Residues in contact with ARG 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F HIS* 4.2 5.5 - - - -
479F LEU 5.6 0.4 - - - +
480F LEU* 3.3 19.1 + - + +
482F GLY* 1.3 70.5 - - - +
484F ALA* 1.3 67.2 + - - +
486F GLU* 3.0 10.7 + - - +
487F GLU* 3.0 21.1 + - - +
493F VAL* 3.1 47.0 - - - +
494F THR 3.6 14.3 + - - -
497F ALA* 3.6 25.3 - - + +
498F ALA 5.3 0.4 - - - +
500F ASP* 5.2 1.6 + - + -
501F ILE* 3.6 31.8 - - + +
565F TYR* 3.3 29.5 + - + +
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Residues in contact with ALA 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480F LEU 2.8 14.4 + - - +
481F GLY 3.1 11.2 - - - +
483F ARG* 1.3 77.1 - - - +
485F ALA* 1.3 62.1 + - - +
487F GLU* 3.1 1.9 + - - +
488F VAL* 3.0 27.8 + - - +
565F TYR* 3.8 7.2 - - + -
568F ALA* 3.6 29.2 - - + -
569F LYS* 3.9 13.2 - - + -
572F ILE* 3.7 15.3 - - + -
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Residues in contact with ALA 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F TYR* 3.4 31.0 - - + +
426F GLY* 4.0 8.7 - - - -
481F GLY 2.9 11.9 + - - +
482F GLY 3.0 5.8 + - - +
484F ALA* 1.3 74.6 - - - +
486F GLU* 1.3 66.7 + - - +
489F VAL* 3.0 29.8 + - - +
490F PHE* 4.7 0.2 - - - -
572F ILE* 4.1 17.7 - - + -
579F LEU* 4.1 12.1 - - + -
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Residues in contact with GLU 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F ILE* 3.9 20.0 - - + +
422F TYR* 5.3 0.6 - - - +
423F HIS* 3.3 30.6 + - + +
482F GLY 2.9 17.4 + - - +
483F ARG* 3.4 11.2 - - - +
485F ALA* 1.3 77.0 - - - +
487F GLU* 1.3 57.1 + - - +
490F PHE* 3.1 34.3 + - + +
492F ASP 3.1 16.5 - - - +
493F VAL* 3.7 10.4 - - + -
494F THR* 2.9 55.2 + - - +
496F GLY* 4.2 6.4 - - - -
497F ALA* 4.2 3.8 + - - +
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Residues in contact with GLU 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483F ARG 3.0 6.0 + - - +
484F ALA 3.7 5.2 - - - +
486F GLU* 1.3 76.3 - - - +
488F VAL* 1.3 64.2 + - - +
491F GLY* 2.8 40.3 + - - +
492F ASP 4.1 7.2 - - - -
493F VAL* 4.8 8.2 - - + +
565F TYR* 2.6 42.2 + - - +
569F LYS* 3.7 26.0 + - + -
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Residues in contact with VAL 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484F ALA 3.0 15.7 + - - +
485F ALA 4.3 0.2 - - - +
487F GLU* 1.3 79.3 - - + +
489F VAL* 1.3 63.0 + - + +
491F GLY* 4.3 1.6 + - - -
569F LYS* 3.9 30.7 - - + +
572F ILE* 4.2 19.3 - - + -
573F ARG* 3.8 38.1 - - + +
576F ARG* 3.7 21.8 + - - +
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Residues in contact with VAL 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F ARG* 5.8 1.1 - - - +
422F TYR* 3.9 31.4 - - + +
485F ALA 3.0 19.0 + - - +
488F VAL* 1.3 83.0 - - + +
490F PHE* 1.3 88.7 + - + +
576F ARG* 3.5 42.0 + - - +
579F LEU* 4.2 10.5 - - + -
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Residues in contact with PHE 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F ARG* 4.3 16.4 - - + -
419F ILE* 3.9 43.7 - - + -
422F TYR* 3.5 39.7 - + + -
486F GLU* 3.1 28.7 + - + +
489F VAL* 1.3 91.5 - - + +
491F GLY* 1.3 58.0 + - - +
492F ASP* 3.0 15.7 + - - +
494F THR* 6.4 0.4 - - + -
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Residues in contact with GLY 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486F GLU 3.6 0.6 + - - -
487F GLU* 2.8 33.3 + - - +
488F VAL 4.3 1.9 + - - -
489F VAL 3.6 1.0 - - - -
490F PHE* 1.3 75.5 - - - +
492F ASP* 1.3 60.7 + - - +
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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