Contacts of the helix formed by residues 468 - 480 (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 SER 468 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492E ASP* 3.8 20.2 + - - -
493E VAL 4.0 5.4 - - - -
494E THR* 4.2 12.3 - - - +
436F ASN* 5.3 0.3 + - - -
467F VAL* 1.3 76.5 - - - +
469F ARG* 1.3 65.1 + - - +
470F ASN* 3.6 3.3 + - - +
471F GLU* 2.7 43.6 + - - +
472F LEU* 3.0 22.3 + - - +
517F MET* 4.3 2.2 - - - -
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Residues in contact with ARG 469 (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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492E ASP* 3.6 12.7 + - - +
493E VAL* 3.4 15.1 + - - +
468F SER* 1.3 73.1 - - - +
470F ASN* 1.3 66.7 + - - +
472F LEU* 3.2 5.4 + - - +
473F LEU* 3.0 42.0 + - + +
511F MET* 3.7 20.8 - - + +
517F MET* 3.0 57.4 + - - +
519F GLU* 4.4 16.4 + - - +
560F ILE* 4.7 13.7 - - - +
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Residues in contact with ASN 470 (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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492E ASP* 3.3 23.4 + - - +
436F ASN* 4.2 13.9 - - - +
468F SER* 3.2 3.6 + - - +
469F ARG* 1.3 79.4 + - - +
471F GLU* 1.3 66.4 + - - +
473F LEU* 3.3 17.0 + - - +
474F ASP* 3.0 31.3 + - - +
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Residues in contact with GLU 471 (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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436F ASN* 4.0 33.6 - - + +
466F LEU 4.0 4.1 - - - +
467F VAL* 3.0 23.6 - - + +
468F SER* 2.7 46.8 + - - +
470F ASN* 1.3 75.6 - - - +
472F LEU* 1.3 58.3 + - - +
474F ASP* 3.1 4.7 + - - +
475F LYS* 2.8 29.5 + - - +
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Residues in contact with LEU 472 (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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467F VAL* 4.1 27.8 - - + -
468F SER 3.0 12.0 + - - +
469F ARG 3.2 7.8 + - - +
471F GLU* 1.3 76.9 - - - +
473F LEU* 1.3 58.3 + - - +
475F LYS* 3.2 18.6 + - + +
476F LEU* 2.9 31.2 + - - +
507F ILE* 3.9 20.7 - - + +
511F MET* 4.0 24.0 - - + -
515F LEU* 3.9 27.4 - - + -
517F MET* 4.0 18.2 - - - -
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Residues in contact with LEU 473 (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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469F ARG* 3.0 42.5 + - + +
470F ASN* 3.6 21.8 - - - +
471F GLU 3.2 0.2 - - - -
472F LEU* 1.3 75.0 - - - +
474F ASP* 1.3 62.1 + - - +
476F LEU* 3.1 4.1 + - + +
477F THR* 2.8 33.7 + - - -
511F MET* 4.7 9.9 - - + -
560F ILE* 4.0 20.2 - - + -
563F ASN* 6.5 0.2 - - + -
564F CYS* 3.6 24.6 - - - -
567F ARG* 4.5 4.9 - - - +
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Residues in contact with ASP 474 (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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434F VAL* 3.6 30.3 - - + +
435F PRO* 3.7 5.3 - - - +
436F ASN* 3.0 45.9 + - - +
437F GLY* 5.9 0.2 - - - -
470F ASN* 3.0 12.9 + - - +
471F GLU 3.5 6.5 - - - +
473F LEU* 1.3 77.6 - - - +
475F LYS* 1.3 63.6 + - - +
477F THR* 3.2 2.8 + - - -
478F ALA* 3.0 23.0 + - - +
567F ARG* 2.9 30.6 + - - +
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Residues in contact with LYS 475 (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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436F ASN 5.1 3.0 + - - +
438F GLU* 4.6 24.5 - - + +
454F GLY* 5.6 10.3 - - - -
471F GLU 2.8 13.6 + - - +
472F LEU* 3.2 22.2 + - + +
474F ASP* 1.3 77.7 - - - +
476F LEU* 1.3 62.0 + - - +
478F ALA* 3.5 6.8 + - - +
479F LEU* 3.2 28.6 + - + +
503F ARG* 4.7 17.6 - - - +
507F ILE* 4.3 28.0 - - + +
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Residues in contact with LEU 476 (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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472F LEU 2.9 15.4 + - - +
473F LEU* 3.4 6.1 - - + +
475F LYS* 1.3 75.1 - - - +
477F THR* 1.3 67.1 + - - +
479F LEU* 3.3 7.4 + - - +
480F LEU* 3.3 30.9 + - + +
504F ALA* 3.1 51.6 - - + +
507F ILE* 4.2 21.3 - - + -
508F ALA* 4.2 6.7 - - + +
511F MET* 4.6 4.5 - - - -
560F ILE* 3.9 27.8 - - + -
561F VAL* 4.3 6.7 - - + -
564F CYS* 4.1 9.9 - - + -
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Residues in contact with THR 477 (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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430F VAL* 3.3 23.6 - - + +
434F VAL* 4.7 2.0 - - + -
473F LEU 2.8 18.6 + - - -
474F ASP* 3.2 5.1 + - - -
476F LEU* 1.3 74.5 - - - +
478F ALA* 1.3 65.3 + - - +
480F LEU* 3.2 10.8 + - - -
481F GLY 3.2 8.7 + - - -
564F CYS* 3.7 32.2 + - - +
567F ARG* 3.2 28.1 + - + +
568F ALA* 3.9 16.7 - - + +
571F ILE* 4.4 7.9 - - + -
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Residues in contact with ALA 478 (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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427F HIS* 3.0 18.7 + - - -
430F VAL* 3.7 12.5 - - + +
431F SER* 3.5 31.2 - - - +
434F VAL* 5.3 1.8 - - + -
438F GLU* 6.2 5.2 - - + +
474F ASP 3.0 16.7 + - - +
475F LYS* 3.6 8.1 - - - +
477F THR* 1.3 76.2 - - - +
479F LEU* 1.3 64.4 + - - +
481F GLY* 2.9 13.5 + - - -
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Residues in contact with LEU 479 (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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427F HIS* 3.1 23.5 - - + -
454F GLY* 4.4 25.4 - - - -
475F LYS* 3.2 20.4 + - + +
476F LEU* 3.4 10.5 - - - +
478F ALA* 1.3 79.8 - - + +
480F LEU* 1.3 57.6 + - - +
481F GLY 3.2 0.2 - - - -
482F GLY 4.5 0.2 + - - -
483F ARG 5.2 0.5 + - - -
500F ASP* 3.3 48.2 - - - +
503F ARG* 3.7 24.5 - - + -
504F ALA* 3.9 9.2 - - + +
507F ILE* 3.5 32.1 - - + -
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Residues in contact with LEU 480 (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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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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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