Contacts of the helix formed by residues 487 - 499 (chain A) in PDB entry 1EX0
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 GLN 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A GLN* 3.1 38.6 + - + +
485A GLU 3.9 4.2 - - - +
486A GLY* 1.3 95.8 + - - +
488A GLU* 1.3 63.3 + - - +
489A GLU* 3.4 9.0 - - + +
490A GLU* 3.2 7.4 + - - +
491A ARG* 3.1 25.8 + - - +
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Residues in contact with GLU 488 (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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487A GLN* 1.3 76.6 - - - +
489A GLU* 1.3 70.8 + - + +
491A ARG* 2.9 47.9 + - - +
492A LEU* 2.9 33.4 + - + +
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Residues in contact with GLU 489 (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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483A PHE* 3.4 50.8 - - + -
484A GLN* 6.1 1.6 - - - +
487A GLN* 3.4 6.3 - - + +
488A GLU* 1.3 84.6 + - + +
490A GLU* 1.3 60.7 + - - +
492A LEU* 3.3 9.7 + - + +
493A ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 490 (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* 4.9 10.8 - - - +
457A ALA 5.5 1.7 - - - +
482A LYS* 4.9 6.0 - - + -
483A PHE* 3.7 22.6 - - + +
484A GLN 3.5 12.3 + - - +
485A GLU* 3.5 27.0 + - - +
486A GLY* 3.1 20.6 + - - -
487A GLN* 3.2 9.6 + - - +
489A GLU* 1.3 77.4 - - - +
491A ARG* 1.3 62.6 + - - +
493A ALA* 3.3 7.6 + - + +
494A LEU* 3.1 23.1 + - + +
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Residues in contact with ARG 491 (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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487A GLN 3.1 13.2 + - - +
488A GLU* 2.9 45.3 + - - +
490A GLU* 1.3 76.2 + - - +
492A LEU* 1.3 77.8 - - - +
494A LEU* 3.3 9.1 + - + +
495A GLU* 3.0 56.9 + - - +
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Residues in contact with LEU 492 (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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419A HIS 5.9 0.7 - - - +
488A GLU* 2.9 27.3 + - + +
489A GLU* 3.7 9.6 - - + +
491A ARG* 1.3 90.6 - - - +
493A ALA* 1.3 59.2 + - - +
495A GLU* 3.4 20.5 + - - +
496A THR* 2.9 38.9 + - - +
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Residues in contact with ALA 493 (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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418A LYS 3.4 26.0 - - - +
419A HIS* 3.4 20.9 - - - -
420A GLY* 3.2 13.7 - - - +
432A PHE* 4.4 8.1 - - + -
483A PHE* 4.8 0.2 - - + -
489A GLU 2.9 17.8 + - - +
490A GLU* 3.6 7.9 - - + +
491A ARG 3.3 0.2 - - - -
492A LEU* 1.3 76.2 - - - +
494A LEU* 1.3 58.8 + - - +
497A ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 494 (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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348A LEU* 3.5 32.3 - - + -
432A PHE* 4.2 15.9 - - + -
490A GLU* 3.1 16.6 + - + +
491A ARG* 3.8 8.3 - - + +
493A ALA* 1.3 74.2 - - - +
495A GLU* 1.3 67.5 + - - +
497A ALA* 5.0 0.4 - - + -
498A LEU* 3.0 41.6 + - + +
504A LYS* 3.8 29.8 - - + +
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Residues in contact with GLU 495 (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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491A ARG* 3.0 40.3 + - - +
492A LEU* 3.7 22.0 - - - +
493A ALA 3.3 0.2 - - - -
494A LEU* 1.3 80.1 - - - +
496A THR* 1.3 63.1 + - - +
498A LEU* 3.7 9.2 + - - +
499A MET* 3.6 35.2 + - + +
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Residues in contact with THR 496 (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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419A HIS 4.2 5.4 + - - -
420A GLY 3.4 15.0 - - - +
421A HIS* 3.7 24.7 + - + +
492A LEU* 2.9 27.4 + - - +
493A ALA 3.8 2.5 - - - -
495A GLU* 1.3 76.6 + - - +
497A ALA* 1.3 66.3 + - - +
499A MET* 2.9 25.4 + - - +
500A TYR* 3.2 36.5 - - + -
1342A PGO 4.9 1.8 - - - +
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Residues in contact with ALA 497 (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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420A GLY* 3.2 14.3 + - - +
422A VAL* 3.7 9.3 - - + +
432A PHE* 3.7 32.3 - - + -
493A ALA 2.9 19.7 + - - +
494A LEU* 3.3 4.9 + - + +
496A THR* 1.3 74.1 - - - +
498A LEU* 1.3 57.8 + - - +
500A TYR* 2.8 21.5 + - - -
502A ALA* 3.3 24.8 + - + -
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Residues in contact with LEU 498 (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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348A LEU* 4.2 5.6 - - + -
494A LEU* 3.0 37.7 + - + +
495A GLU* 3.9 8.3 - - - +
496A THR 3.2 0.4 - - - -
497A ALA* 1.3 75.9 - - - +
499A MET* 1.3 59.2 + - - +
500A TYR 3.3 0.6 + - - -
501A GLY 4.5 1.2 + - - -
502A ALA* 3.4 34.7 - - + +
503A LYS* 3.8 1.1 - - - +
504A LYS* 3.7 40.2 - - + +
383B PRO 5.1 1.6 - - - +
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Residues in contact with MET 499 (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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495A GLU* 3.6 38.6 + - + +
496A THR* 2.9 22.3 + - - +
498A LEU* 1.3 78.0 - - - +
500A TYR* 1.3 89.3 + - + +
501A GLY 3.7 1.8 - - - -
383B PRO 3.3 19.4 - - - +
384B ASP 4.0 1.9 - - - -
385B LEU 4.4 3.1 + - - +
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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