Contacts of the helix formed by residues 468 - 480 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C ASN* 5.1 0.5 + - - -
467C VAL* 1.3 75.4 - - - +
469C ARG* 1.3 66.2 + - - +
470C ASN* 3.4 7.8 + - - +
471C GLU* 3.0 36.9 + - - +
472C LEU* 3.1 21.4 + - - +
517C MET* 4.4 2.9 - - - -
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Residues in contact with ARG 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C SER* 1.3 74.2 - - - +
470C ASN* 1.3 60.4 + - - +
472C LEU* 3.2 5.7 + - - +
473C LEU* 3.0 46.1 + - + +
511C MET* 3.9 20.4 - - + +
517C MET* 2.7 65.5 + - + +
518C SER* 4.8 0.4 - - - +
519C GLU* 3.3 26.6 + - - -
560C ILE* 5.0 10.1 - - - +
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Residues in contact with ASN 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ASN* 4.0 14.8 - - - +
468C SER* 3.2 6.8 + - - +
469C ARG* 1.3 78.1 + - - +
471C GLU* 1.3 59.2 + - - +
473C LEU* 3.2 16.2 + - - +
474C ASP* 2.8 36.1 + - - +
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Residues in contact with GLU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C ASN* 3.8 33.8 - - + +
464C LYS* 2.4 38.2 + - - -
467C VAL* 2.9 25.4 - - + +
468C SER* 3.0 32.2 + - - +
470C ASN* 1.3 74.9 - - - +
472C LEU* 1.3 60.2 + - - +
474C ASP* 3.3 2.8 + - - +
475C LYS* 2.8 30.1 + - - +
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C VAL* 3.7 30.1 - - + -
468C SER 3.1 10.5 + - - +
469C ARG 3.2 7.2 + - - +
471C GLU* 1.3 77.2 - - - +
473C LEU* 1.3 53.6 + - - +
475C LYS* 3.2 27.4 + - + +
476C LEU* 2.6 38.6 + - - +
507C ILE* 4.2 13.0 - - + +
511C MET* 3.9 34.1 - - + -
515C LEU* 3.9 22.2 - - + -
517C MET* 4.2 9.9 - - - -
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C ARG* 3.0 39.8 + - + +
470C ASN* 3.6 20.0 - - - +
472C LEU* 1.3 75.5 - - - +
474C ASP* 1.3 62.2 + - - +
476C LEU* 3.4 4.2 + - + +
477C THR* 2.9 28.8 + - - -
511C MET* 4.1 14.6 - - + -
560C ILE* 3.7 22.4 - - + -
564C CYS* 3.7 22.4 - - - -
567C ARG* 4.1 11.7 - - - +
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Residues in contact with ASP 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C VAL* 3.3 24.3 - - + +
435C PRO* 3.2 12.5 - - - +
436C ASN* 3.0 40.9 + - + +
437C GLY* 5.7 0.9 - - - -
470C ASN* 2.8 19.2 + - - +
471C GLU 3.6 3.6 - - - +
473C LEU* 1.3 74.8 - - - +
475C LYS* 1.3 64.5 + - - +
477C THR* 3.1 3.6 + - - -
478C ALA* 3.0 23.3 + - - +
567C ARG* 2.6 38.3 + - - +
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Residues in contact with LYS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C ASN 5.8 0.6 + - - -
437C GLY* 6.2 2.2 - - - -
438C GLU* 5.3 20.1 + - + +
457C LEU* 4.3 19.0 - - + +
458C HIS 6.3 0.2 - - - -
459C LEU 4.7 10.7 + - - -
460C PRO* 5.3 2.2 - - - +
461C GLU* 5.1 13.7 - - - +
471C GLU 2.8 20.5 + - - +
472C LEU* 3.6 24.6 - - + +
474C ASP* 1.3 72.0 - - - +
476C LEU* 1.3 62.4 + - - +
478C ALA* 3.3 8.2 + - - +
479C LEU* 3.1 25.1 + - + +
503C ARG* 5.8 5.5 - - - +
507C ILE* 4.1 26.5 - - + +
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Residues in contact with LEU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LEU 2.6 18.5 + - - +
473C LEU* 3.6 7.2 - - + +
475C LYS* 1.3 74.0 - - - +
477C THR* 1.3 61.1 + - - +
479C LEU* 3.3 10.4 + - - +
480C LEU* 3.3 33.9 + - + +
504C ALA* 3.3 45.8 - - + +
507C ILE* 3.9 28.3 - - + -
508C ALA* 4.2 4.3 - - + +
511C MET* 4.1 10.8 - - - -
560C ILE* 4.0 26.2 - - + -
561C VAL* 4.4 10.1 - - + -
564C CYS* 4.0 9.0 - - + -
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Residues in contact with THR 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C VAL* 3.3 25.1 - - + +
434C VAL* 4.1 11.0 - - + -
473C LEU 2.9 17.7 + - - -
474C ASP* 3.4 8.1 - - - -
476C LEU* 1.3 75.1 - - - +
478C ALA* 1.3 65.4 + - - +
480C LEU* 3.4 1.9 + - - -
481C GLY 3.3 12.0 + - - -
564C CYS* 3.6 36.1 + - - +
567C ARG* 3.6 17.4 + - + -
568C ALA* 3.8 16.6 - - + +
571C ILE* 4.5 0.9 - - + -
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C HIS* 3.1 15.4 + - - -
430C VAL* 3.6 11.6 - - + +
431C SER* 3.6 32.3 - - - +
434C VAL* 5.5 1.8 - - + -
437C GLY* 5.9 2.5 - - - -
438C GLU 6.2 0.2 - - - +
457C LEU* 3.7 13.4 - - + +
474C ASP 3.0 13.8 + - - +
475C LYS* 3.3 10.1 + - - +
477C THR* 1.3 75.5 - - - +
479C LEU* 1.3 66.4 + - - +
481C GLY* 2.8 13.0 + - - -
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Residues in contact with LEU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C HIS* 3.0 22.6 - - + -
454C GLY 5.0 0.4 - - - +
457C LEU* 3.6 29.6 - - + +
458C HIS* 3.5 33.2 - - + +
475C LYS* 3.1 18.0 + - + +
476C LEU* 3.4 11.7 - - - +
477C THR 3.3 0.2 - - - -
478C ALA* 1.3 75.1 - - - +
480C LEU* 1.3 57.7 + - - +
482C GLY* 5.0 0.2 - - - -
483C ARG 5.1 0.2 + - - -
500C ASP* 3.5 25.8 - - - +
503C ARG* 3.4 35.9 - - + -
504C ALA* 4.0 13.0 - - + +
507C ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B PRO* 4.8 11.2 - - + +
476C LEU* 3.3 21.1 + - + +
477C THR 3.4 5.8 + - - +
478C ALA 3.1 0.6 - - - -
479C LEU* 1.3 76.0 - - - +
481C GLY* 1.3 58.6 + - - +
482C GLY 3.3 2.0 - - - -
483C ARG* 3.4 11.9 + - + +
484C ALA* 2.9 27.8 + - - +
500C ASP* 4.9 2.5 - - + +
501C ILE* 4.8 15.7 - - + +
504C ALA* 4.2 17.9 - - + -
561C VAL* 3.7 24.0 - - + +
564C CYS* 4.1 7.9 - - + -
565C TYR* 3.6 49.0 - - + +
568C ALA* 4.4 1.8 - - + -
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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