Contacts of the helix formed by residues 468 - 480 (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 SER 468 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419D ILE* 6.0 0.7 - - - -
492D ASP* 3.7 16.3 + - - -
493D VAL 3.4 12.6 - - - -
494D THR* 3.9 12.5 - - - +
436E ASN* 5.1 0.2 + - - -
467E VAL* 1.3 76.6 - - - +
469E ARG* 1.3 60.8 + - - +
470E ASN* 4.3 1.6 - - - +
471E GLU* 3.0 38.4 + - - +
472E LEU* 2.8 29.5 + - - +
517E MET* 4.1 2.9 - - - -
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Residues in contact with ARG 469 (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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492D ASP* 3.2 18.6 + - - +
493D VAL* 3.2 11.7 + - + +
468E SER* 1.3 73.1 - - - +
470E ASN* 1.3 60.6 + - - +
472E LEU* 3.1 4.9 + - - +
473E LEU* 2.8 50.7 + - + +
511E MET* 3.4 30.2 - - + +
517E MET* 2.2 62.6 + - + +
518E SER* 4.4 2.8 - - - +
519E GLU* 5.2 12.0 + - - +
560E ILE* 4.7 15.0 - - - +
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Residues in contact with ASN 470 (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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492D ASP* 2.9 25.3 + - - +
436E ASN* 4.3 12.3 - - - +
468E SER* 3.3 2.0 - - - +
469E ARG* 1.3 80.4 + - - +
471E GLU* 1.3 64.4 + - - +
473E LEU* 3.1 18.2 + - - +
474E ASP* 2.8 31.5 + - - +
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Residues in contact with GLU 471 (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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436E ASN* 3.7 41.3 - - + +
464E LYS* 2.9 36.4 + - - +
467E VAL* 3.3 24.4 - - + +
468E SER* 3.0 35.0 + - - +
470E ASN* 1.3 76.0 - - - +
472E LEU* 1.3 59.3 + - - +
474E ASP* 3.2 3.6 + - - +
475E LYS* 2.9 26.6 + - - +
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Residues in contact with LEU 472 (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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467E VAL* 3.9 29.2 - - + -
468E SER 2.8 13.8 + - - +
469E ARG* 3.5 8.1 - - - +
471E GLU* 1.3 75.6 - - - +
473E LEU* 1.3 64.5 + - - +
475E LYS* 3.2 20.4 + - + +
476E LEU* 2.9 27.0 + - - +
507E ILE* 4.3 17.3 - - + +
510E ASN* 6.3 0.2 - - + -
511E MET* 3.8 33.0 - - + -
515E LEU* 3.8 22.2 - - + -
517E MET* 4.4 6.7 - - + -
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Residues in contact with LEU 473 (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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469E ARG* 2.8 39.4 + - + +
470E ASN* 3.1 22.4 + - - +
472E LEU* 1.3 75.6 - - - +
474E ASP* 1.3 66.2 + - - +
476E LEU* 3.2 6.2 + - + +
477E THR* 3.0 27.1 + - - -
511E MET* 3.9 21.8 - - + -
560E ILE* 4.0 24.9 - - + +
564E CYS* 3.8 12.9 - - - -
567E ARG* 4.2 5.2 - - - +
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Residues in contact with ASP 474 (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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434E VAL* 3.2 30.5 - - + +
435E PRO* 4.1 5.0 - - - +
436E ASN* 2.9 45.3 + - - +
437E GLY* 5.5 0.8 - - - -
470E ASN* 2.8 16.4 + - - +
471E GLU 3.4 7.9 - - - +
473E LEU* 1.3 73.1 - - - +
475E LYS* 1.3 66.3 + - - +
477E THR* 3.3 3.0 + - - -
478E ALA* 3.1 21.5 + - - +
567E ARG* 2.7 33.3 + - - +
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Residues in contact with LYS 475 (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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436E ASN 5.2 2.2 + - - +
437E GLY* 6.2 1.1 - - - -
438E GLU* 5.7 18.4 - - + +
471E GLU 2.9 13.4 + - - +
472E LEU* 3.4 23.5 - - + +
473E LEU 3.2 0.2 - - - -
474E ASP* 1.3 76.7 - - - +
476E LEU* 1.3 62.5 + - - +
478E ALA* 3.2 8.2 + - - +
479E LEU* 3.0 27.1 + - + +
503E ARG* 4.0 21.8 - - - +
507E ILE* 3.6 28.8 - - + +
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Residues in contact with LEU 476 (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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472E LEU 2.9 16.2 + - - +
473E LEU* 3.2 14.3 + - + +
475E LYS* 1.3 78.4 - - - +
477E THR* 1.3 62.6 + - - +
479E LEU* 3.1 10.4 + - - +
480E LEU* 3.1 34.2 + - + +
504E ALA* 3.6 39.3 - - + +
507E ILE* 3.8 25.4 - - + -
508E ALA* 4.7 2.0 - - + +
511E MET* 3.9 11.7 - - - -
560E ILE* 3.9 23.3 - - + -
561E VAL* 4.3 14.6 - - + -
564E CYS* 3.8 9.2 - - - -
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Residues in contact with THR 477 (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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430E VAL* 3.5 19.7 - - + +
434E VAL* 4.5 2.5 - - + -
473E LEU 3.0 15.8 + - - -
474E ASP* 3.7 4.9 - - - -
475E LYS 3.2 0.2 - - - -
476E LEU* 1.3 72.9 - - - +
478E ALA* 1.3 66.8 + - - +
480E LEU* 3.1 6.1 + - - +
481E GLY* 3.1 16.5 + - - -
564E CYS* 3.7 23.8 - - - +
567E ARG* 3.5 31.0 + - - -
568E ALA* 3.7 24.8 - - + +
571E ILE* 4.5 4.5 - - + -
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Residues in contact with ALA 478 (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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427E HIS* 2.9 17.8 + - + +
430E VAL* 3.4 17.5 - - + +
431E SER* 3.3 29.4 - - - +
434E VAL* 5.8 0.7 - - + -
437E GLY* 6.2 1.8 - - - -
474E ASP 3.1 10.5 + - - +
475E LYS* 3.5 11.0 - - + +
477E THR* 1.3 79.1 - - - +
479E LEU* 1.3 56.0 + - - +
481E GLY* 2.7 23.0 + - - -
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Residues in contact with LEU 479 (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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427E HIS* 3.0 26.1 - - + +
475E LYS* 3.0 20.2 + - + +
476E LEU* 3.1 10.7 + - - +
478E ALA* 1.3 76.6 - - - +
480E LEU* 1.3 58.4 + - - +
482E GLY 4.3 0.3 + - - -
500E ASP* 3.3 37.0 - - - +
503E ARG* 3.6 40.4 - - + -
504E ALA* 3.6 18.8 - - + +
507E ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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