Contacts of the helix formed by residues 386 - 395 (chain D) in PDB entry 1A4Y
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 CYS 386 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382D SER 3.7 3.4 - - - -
383D ASP* 3.2 12.5 + - - +
385D SER* 1.3 77.6 - - - +
387D SER* 1.3 56.6 + - - +
389D LEU* 3.8 9.2 - - - -
390D ALA* 2.9 29.1 + - - +
409D LEU* 3.3 38.1 - - - -
413D GLY* 3.5 39.7 - - - +
416D GLN* 3.9 7.4 - - + +
417D LEU* 3.8 12.3 - - + +
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Residues in contact with SER 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP 4.4 1.2 + - - -
384D SER 3.7 13.4 + - - -
386D CYS* 1.3 74.1 - - - +
388D SER* 1.3 68.0 + - - +
390D ALA* 3.5 4.1 + - - +
391D ALA* 3.1 24.4 + - - +
416D GLN* 3.1 25.2 + - - -
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Residues in contact with SER 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D ARG* 4.0 27.0 + - - +
361D CYS* 4.0 17.0 - - - +
384D SER 5.3 0.9 - - - -
385D SER* 3.2 13.7 - - - -
387D SER* 1.3 84.4 + - - +
389D LEU* 1.3 62.4 + - - -
391D ALA* 3.2 7.1 + - - +
392D THR* 3.0 25.8 + - - -
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Residues in contact with LEU 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D VAL* 4.4 12.6 - - + -
361D CYS* 3.9 22.2 - - - -
374D LEU* 5.8 2.9 - - + -
376D LEU* 4.5 18.8 - - + -
381D VAL* 4.4 6.3 - - + -
385D SER* 3.0 26.7 + - - +
386D CYS* 3.8 12.6 - - - +
388D SER* 1.3 76.3 - - - +
390D ALA* 1.3 62.7 + - - +
392D THR* 3.2 3.9 + - - +
393D LEU* 3.0 30.9 + - + +
402D LEU* 4.6 20.0 - - + -
404D LEU* 4.0 25.1 - - + -
409D LEU* 5.4 0.4 - - + -
417D LEU* 3.9 9.9 - - + -
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Residues in contact with ALA 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D CYS 2.9 20.1 + - - +
387D SER* 3.8 7.2 - - - +
388D SER 3.3 0.2 - - - -
389D LEU* 1.3 76.0 - - - +
391D ALA* 1.3 61.9 + - - +
393D LEU* 3.4 10.1 + - - +
394D LEU* 3.6 5.0 + - - +
416D GLN* 3.5 25.4 - - + +
417D LEU* 4.0 6.4 - - + +
420D SER* 2.6 36.1 + - - +
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Residues in contact with ALA 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D SER 3.1 18.1 + - - +
388D SER* 3.2 6.5 + - - +
390D ALA* 1.3 77.0 - - - +
392D THR* 1.3 59.0 + - - +
394D LEU* 3.2 9.4 + - - +
395D ALA* 2.8 29.2 + - + +
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Residues in contact with THR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D CYS* 3.3 30.9 + - - +
364D LEU* 3.6 43.5 - - + -
365D GLY* 4.0 8.4 + - - +
388D SER 3.0 16.2 + - - -
389D LEU* 3.2 5.1 + - - -
391D ALA* 1.3 73.0 - - - +
393D LEU* 1.3 57.6 + - + +
394D LEU 3.0 5.6 - - - -
395D ALA* 4.1 7.0 - - - -
396D ASN* 2.8 33.8 + - + +
399D LEU* 6.4 0.2 - - + -
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Residues in contact with LEU 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D LEU* 3.0 20.5 + - + +
390D ALA* 3.6 11.7 - - - +
391D ALA 3.2 0.4 - - - -
392D THR* 1.3 77.8 - - + +
394D LEU* 1.3 59.7 + - - +
396D ASN 3.6 10.9 - - - +
399D LEU* 4.2 27.8 - - + -
402D LEU* 4.3 21.3 - - + -
417D LEU* 4.4 22.0 - - + +
420D SER* 4.3 10.1 - - - -
421D VAL* 4.2 21.5 - - + -
425D GLY 4.8 0.7 - - - +
426D CYS* 3.8 25.0 - - - +
427D LEU 5.3 0.2 + - - -
428D LEU* 4.3 19.5 - - + -
431D LEU* 5.6 1.6 - - + -
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D ALA 3.6 3.6 + - - +
391D ALA* 3.2 8.8 + - - +
392D THR 3.0 0.2 - - - -
393D LEU* 1.3 80.5 - - - +
395D ALA* 1.3 61.0 + - - +
396D ASN 3.5 1.6 - - - -
397D HIS* 3.5 19.8 + - - -
420D SER* 3.3 48.5 - - - +
423D GLN* 4.0 23.8 - - + +
425D GLY* 4.6 6.9 - - - +
426D CYS* 4.1 15.7 - - + +
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D GLY* 4.2 25.7 - - - +
366D GLN 5.4 0.9 - - - +
367D PRO* 6.2 0.3 - - - +
391D ALA 2.8 17.4 + - - +
392D THR* 4.1 7.0 - - - -
394D LEU* 1.3 80.2 - - - +
396D ASN* 1.3 59.5 + - - +
397D HIS* 3.5 15.6 + - - -
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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