Contacts of the helix formed by residues 468 - 480 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A ASN* 4.8 0.5 + - - -
467A VAL* 1.3 77.0 - - - +
469A ARG* 1.3 63.4 + - - +
470A ASN* 3.4 4.9 + - - +
471A GLU* 2.7 40.2 + - - +
472A LEU* 3.1 23.6 + - - +
517A MET* 4.3 2.5 - - - -
419B ILE* 6.2 1.3 - - - -
492B ASP* 3.8 18.9 + - - -
493B VAL 3.7 7.4 - - - -
494B THR* 3.9 10.9 - - - +
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A SER* 1.3 75.7 - - - +
470A ASN* 1.3 67.5 + - - +
472A LEU* 3.3 2.4 + - - +
473A LEU* 3.1 46.0 + - + +
511A MET* 3.8 18.0 - - + +
517A MET* 2.5 55.2 + - + +
518A SER* 4.7 0.8 - - - +
519A GLU* 5.1 7.5 - - - +
560A ILE* 5.2 12.5 - - - +
492B ASP* 3.1 22.2 + - - +
493B VAL* 3.4 4.7 + - + +
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Residues in contact with ASN 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASN* 3.7 16.2 - - - +
468A SER* 3.3 3.2 + - - +
469A ARG* 1.3 82.1 + - - +
471A GLU* 1.3 68.3 + - - +
473A LEU* 3.2 14.2 + - - +
474A ASP* 2.8 32.5 + - - +
492B ASP* 3.4 17.9 + - - +
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Residues in contact with GLU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASN* 3.6 37.2 - - + +
464A LYS* 3.3 33.9 - - + +
466A LEU 4.0 2.6 - - - +
467A VAL* 3.3 18.9 - - + -
468A SER* 2.7 48.4 + - - +
470A ASN* 1.3 77.6 - - - +
472A LEU* 1.3 56.2 + - - +
474A ASP* 3.2 2.6 + - - +
475A LYS* 3.0 29.4 + - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A VAL* 4.0 24.5 - - + -
468A SER 3.1 19.7 + - - +
469A ARG 3.8 4.0 - - - +
471A GLU* 1.3 75.6 - - - +
473A LEU* 1.3 59.4 + - - +
475A LYS* 3.4 17.9 + - + +
476A LEU* 2.9 33.1 + - - +
507A ILE* 3.6 25.4 - - + +
511A MET* 4.0 26.0 - - + -
515A LEU* 3.7 30.3 - - + -
517A MET* 4.0 9.4 - - + -
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ARG* 3.1 51.5 + - + +
470A ASN* 3.7 14.4 - - - +
472A LEU* 1.3 76.3 - - - +
474A ASP* 1.3 55.8 + - - +
476A LEU* 3.2 4.6 + - + +
477A THR* 2.8 38.0 + - - -
511A MET* 4.0 12.8 - - + -
560A ILE* 3.8 23.6 - - + +
564A CYS* 3.4 25.6 - - - -
567A ARG* 4.0 10.3 - - - +
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Residues in contact with ASP 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A VAL* 2.9 32.3 - - + +
435A PRO* 3.2 9.9 - - - +
436A ASN* 3.1 40.4 + - + +
437A GLY* 5.3 1.7 - - - -
470A ASN* 2.8 22.1 + - - +
471A GLU 3.7 4.0 - - - +
473A LEU* 1.3 75.7 - - - +
475A LYS* 1.3 57.9 + - - +
477A THR* 3.4 2.1 + - - -
478A ALA* 3.0 27.2 + - - +
567A ARG* 2.5 35.0 + - - +
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ASN 5.8 0.2 + - - -
437A GLY* 5.7 2.9 - - - -
438A GLU* 6.3 6.5 - - + -
471A GLU 3.0 16.2 + - - +
472A LEU* 3.6 18.0 - - + +
474A ASP* 1.3 73.6 - - - +
476A LEU* 1.3 65.1 + - - +
477A THR 3.1 1.6 - - - -
478A ALA* 3.4 7.2 + - + +
479A LEU* 2.9 30.3 + - + +
503A ARG* 5.9 8.0 - - - +
507A ILE* 4.1 26.3 - - + +
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A LEU 2.9 14.0 + - - +
473A LEU* 3.4 8.5 - - + +
475A LYS* 1.3 77.1 - - - +
477A THR* 1.3 63.4 + - - +
479A LEU* 3.2 14.2 + - - +
480A LEU* 3.2 19.9 + - + +
504A ALA* 3.2 28.7 - - + +
507A ILE* 3.1 50.5 - - + -
508A ALA* 4.0 11.4 - - + +
511A MET* 4.8 1.6 - - - -
560A ILE* 3.7 30.1 - - + -
561A VAL* 4.3 7.9 - - + -
564A CYS* 4.1 12.6 - - + -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL* 3.7 18.9 - - + +
434A VAL* 4.4 4.5 - - + -
473A LEU 2.8 19.7 + - - -
474A ASP* 3.7 6.1 - - - -
475A LYS 3.1 0.2 - - - -
476A LEU* 1.3 75.5 - - - +
478A ALA* 1.3 67.1 + - - +
480A LEU* 2.9 16.2 + - - +
481A GLY 3.3 7.4 + - - -
564A CYS* 3.3 37.4 - - - +
567A ARG* 3.3 26.1 + - + -
568A ALA* 3.9 15.7 - - + +
571A ILE* 4.8 0.4 - - + -
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A HIS* 2.9 23.3 + - + +
430A VAL* 3.8 14.1 - - + +
431A SER* 3.6 33.7 - - - +
434A VAL* 5.9 0.2 - - + -
437A GLY* 5.9 1.3 - - - -
474A ASP 3.0 17.5 + - - +
475A LYS* 3.6 8.1 - - + +
477A THR* 1.3 77.4 - - - +
479A LEU* 1.3 62.6 + - - +
480A LEU 3.0 1.0 + - - -
481A GLY* 3.0 8.5 + - - -
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A HIS* 3.1 22.2 - - + -
475A LYS* 2.9 20.4 + - + +
476A LEU* 3.4 10.8 - - + +
477A THR 3.2 0.4 - - - -
478A ALA* 1.3 77.5 - - - +
480A LEU* 1.3 57.9 + - - +
483A ARG 5.4 0.3 + - - -
500A ASP* 3.3 35.0 - - - +
503A ARG* 3.6 38.4 - - + -
504A ALA* 3.8 13.5 - - + +
507A ILE* 3.6 31.6 - - + -
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A LEU* 3.4 13.7 - - + +
477A THR 2.9 10.0 + - - +
479A LEU* 1.3 79.8 - - - +
481A GLY* 1.3 57.3 + - - +
482A GLY 3.3 3.4 - - - -
483A ARG* 3.4 12.3 + - + +
484A ALA* 2.9 28.4 + - - +
500A ASP* 4.8 4.3 - - + +
501A ILE* 4.9 16.2 - - + -
504A ALA* 4.0 21.8 - - + -
561A VAL* 3.6 24.9 - - + +
564A CYS* 3.9 7.0 - - + -
565A TYR* 3.4 49.9 - - + +
568A ALA* 4.5 2.0 - - + -
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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