Contacts of the helix formed by residues 405 - 418 (chain A) in PDB entry 5JEL
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 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A MET* 6.1 0.2 - - - -
382A GLY* 3.4 36.0 + - - -
383A GLY* 4.4 1.4 + - - -
385A SER 4.8 0.2 - - - -
386A SER* 4.4 19.8 + - - -
387A LEU 3.8 6.6 + - - -
389A ASN* 5.8 0.6 - - - +
404A THR* 1.3 73.4 - - - +
406A ASP* 1.3 61.7 + - - +
408A TYR* 3.3 7.0 + - - +
409A LYS* 2.9 47.4 + - - +
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Residues in contact with ASP 406 (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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386A SER* 5.8 4.2 - - - -
404A THR* 3.3 6.6 + - - +
405A SER* 1.3 80.8 - - - +
407A GLN* 1.3 57.8 + - + +
409A LYS* 3.6 12.5 + - - +
410A ALA* 3.0 30.5 + - - +
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Residues in contact with GLN 407 (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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388A GLU* 4.7 5.3 + - - +
402A SER 4.1 3.5 - - - +
403A LEU* 3.6 23.7 - - + +
404A THR* 3.0 48.2 + - - +
406A ASP* 1.3 75.7 - - + +
408A TYR* 1.3 64.0 + - - +
410A ALA* 3.3 6.9 + - - +
411A TYR* 3.0 39.3 + - + +
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Residues in contact with TYR 408 (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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192A LEU* 4.4 10.1 - - + -
329A LEU* 3.6 5.4 - - - +
333A THR* 4.7 4.7 - - + -
375A LEU* 2.7 54.3 + - + +
378A MET* 3.5 39.9 - - + -
379A ALA* 3.9 21.8 - - + -
382A GLY* 6.4 0.4 - - - -
391A VAL* 4.9 3.4 - - + -
403A LEU* 4.1 21.0 - - + +
404A THR 2.9 17.4 + - - +
405A SER* 3.6 8.1 - - - +
407A GLN* 1.3 76.9 - - - +
409A LYS* 1.3 63.9 + - + +
411A TYR* 3.2 4.9 + - - +
412A LEU* 3.0 48.8 + - + +
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Residues in contact with LYS 409 (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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330A ILE* 5.2 4.1 - - + +
333A THR* 3.5 49.5 + - + +
334A GLU* 4.3 18.1 - - - +
405A SER* 2.9 33.4 + - - +
406A ASP* 4.0 12.1 + - - +
408A TYR* 1.3 79.0 - - + +
410A ALA* 1.3 61.8 + - - +
412A LEU* 3.4 10.7 + - - +
413A GLN* 3.2 22.5 + - - +
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Residues in contact with ALA 410 (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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406A ASP 3.0 19.1 + - - +
407A GLN* 3.5 7.6 - - - +
408A TYR 3.2 0.2 - - - -
409A LYS* 1.3 77.8 - - - +
411A TYR* 1.3 67.0 + - + +
413A GLN* 3.4 6.4 + - - +
414A ASP* 3.1 22.7 + - - +
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Residues in contact with TYR 411 (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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189A GLU 3.7 21.2 + - - -
190A ASN* 3.0 35.7 + - + +
191A PRO* 3.6 23.5 - - + +
192A LEU* 3.7 15.0 - - + +
403A LEU* 3.8 32.7 - - + +
407A GLN* 3.0 27.7 + - + +
408A TYR* 3.2 4.9 + - - +
410A ALA* 1.3 76.9 - - + +
412A LEU* 1.3 60.3 + - - +
414A ASP* 4.5 2.2 - - + -
415A LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 412 (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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192A LEU* 3.6 20.9 - - + -
326A ILE* 3.8 21.2 - - + +
329A LEU* 3.7 35.4 - - + -
330A ILE* 3.8 22.7 - - + -
333A THR* 4.4 11.0 - - + -
375A LEU* 4.8 2.7 - - + -
408A TYR* 3.0 47.8 + - + +
409A LYS* 3.7 10.1 - - - +
411A TYR* 1.3 76.4 - - - +
413A GLN* 1.3 59.2 + - - +
415A LEU* 3.3 5.3 + - + +
416A VAL* 3.0 28.9 + - - +
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Residues in contact with GLN 413 (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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330A ILE* 3.7 24.3 - - + +
409A LYS 3.2 10.4 + - - +
410A ALA* 3.7 10.1 - - - +
411A TYR 3.3 0.2 - - - -
412A LEU* 1.3 80.0 - - - +
414A ASP* 1.3 62.4 + - - +
416A VAL* 3.1 15.5 + - - +
417A GLU* 3.0 57.0 + - - +
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Residues in contact with ASP 414 (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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190A ASN* 2.8 31.2 + - - +
193A LYS* 3.2 29.4 + - - -
410A ALA 3.1 16.3 + - - +
411A TYR* 4.5 2.5 - - + -
413A GLN* 1.3 75.8 - - - +
415A LEU* 1.3 63.6 + - - +
417A GLU* 3.4 28.6 + - - +
418A GLY 3.7 1.7 + - - -
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Residues in contact with LEU 415 (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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190A ASN* 3.5 6.8 - - - +
192A LEU* 3.9 36.1 - - + +
193A LYS* 4.0 24.1 + - + +
195A LEU* 4.4 11.9 - - + -
196A LEU* 4.4 20.4 - - + -
322A LEU* 5.2 2.7 - - + -
326A ILE* 4.0 33.9 - - + -
375A LEU* 5.9 0.2 - - + -
411A TYR 2.9 18.6 + - - +
412A LEU* 3.5 4.7 - - + +
414A ASP* 1.3 77.0 - - - +
416A VAL* 1.3 61.5 + - - +
418A GLY* 3.2 9.7 + - - -
419A MET* 3.1 25.5 - - - +
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Residues in contact with VAL 416 (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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326A ILE* 3.7 22.9 - - + +
327A VAL* 3.7 32.1 - - + +
330A ILE* 4.3 4.0 - - + -
412A LEU 3.0 14.3 + - - +
413A GLN* 3.1 31.4 + - - +
415A LEU* 1.3 76.4 - - - +
417A GLU* 1.3 66.7 + - + +
418A GLY 3.3 0.7 + - - -
419A MET* 3.3 15.7 + - - +
421A PHE* 3.5 29.1 - - + -
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Residues in contact with GLU 417 (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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413A GLN* 3.0 47.4 + - - +
414A ASP* 3.6 22.4 - - - +
415A LEU 3.2 0.6 - - - -
416A VAL* 1.3 79.0 - - + +
418A GLY* 1.3 58.8 + - - +
419A MET 3.4 3.6 + - - +
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Residues in contact with GLY 418 (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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193A LYS* 4.7 9.2 - - - -
196A LEU* 5.8 0.9 - - - +
414A ASP 3.7 5.4 + - - -
415A LEU 3.2 7.3 + - - -
416A VAL 3.1 0.4 - - - -
417A GLU* 1.3 79.0 - - - +
419A MET* 1.3 62.6 + - - +
420A ASP* 4.6 3.3 - - - +
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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