Contacts of the helix formed by residues 381 - 390 (chain D) in PDB entry 3B60
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 GLY 381 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D ALA 4.1 6.0 + - - -
359D LEU* 3.6 20.6 - - - +
379D GLY 3.9 1.4 + - - -
380D SER* 1.3 72.1 + - - +
382D LYS* 1.3 68.0 + - - +
384D THR* 3.1 10.9 - - - -
385D ILE* 2.8 27.4 + - - +
551D VAL* 5.5 2.0 - - - -
554D GLY* 4.1 10.7 - - - -
5004D ANP 3.1 10.3 - - - -
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Residues in contact with LYS 382 (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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374D LEU* 3.8 20.7 - - + +
375D VAL* 3.9 0.7 - - - -
376D GLY 3.2 42.2 - - - +
377D ARG 3.4 12.2 + - - -
380D SER* 2.5 18.0 + - - +
381D GLY* 1.3 77.8 - - - +
383D SER* 1.3 64.3 + - - +
384D THR 2.8 0.2 + - - -
385D ILE* 3.0 19.0 - - - +
386D ALA* 3.0 8.5 + - - +
535D ILE* 3.7 27.7 - - + +
536D ALA 5.2 0.7 - - - +
537D HIS* 4.0 11.9 - - + +
551D VAL* 3.8 20.1 - - + +
5004D ANP 2.4 58.4 + - - +
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Residues in contact with SER 383 (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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382D LYS* 1.3 76.6 - - - +
384D THR* 1.3 55.2 + - - +
386D ALA* 3.0 5.1 - - - +
387D SER* 2.9 30.5 + - - -
424D GLN* 3.2 18.5 + - - +
505D ASP* 2.7 31.6 + - - +
535D ILE* 4.4 0.8 - - - +
5004D ANP 2.3 40.6 + - - -
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Residues in contact with THR 384 (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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349D PHE* 4.4 4.7 - - + -
351D TYR* 2.8 39.3 + - + +
358D ALA* 5.1 1.8 - - + +
359D LEU* 3.3 23.3 - - + -
381D GLY* 3.1 15.5 - - - -
382D LYS 2.8 1.4 + - - -
383D SER* 1.3 69.7 - - - +
385D ILE* 1.3 63.9 + - - +
386D ALA 3.0 0.9 - - - -
387D SER* 3.0 8.0 + - - -
388D LEU* 2.8 35.8 + - + +
393D TYR* 6.0 0.2 - - - -
5004D ANP 2.7 33.8 + - - -
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Residues in contact with ILE 385 (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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344D PHE* 3.1 40.8 - - + -
359D LEU* 3.9 17.7 - - + -
362D ILE* 5.4 5.6 - - + -
364D LEU* 4.7 9.0 - - + -
366D ILE* 6.1 1.8 - - + -
374D LEU* 4.3 28.7 - - + -
381D GLY 2.8 21.8 + - - +
382D LYS* 3.0 15.0 - - - +
384D THR* 1.3 74.4 - - - +
386D ALA* 1.3 64.5 + - - +
388D LEU* 2.7 19.6 + - - +
389D ILE* 2.9 31.6 + - + +
533D LEU* 6.0 2.5 - - + -
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Residues in contact with ALA 386 (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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374D LEU* 6.4 1.1 - - + -
382D LYS 3.0 13.1 + - - +
383D SER* 3.0 22.9 - - - +
385D ILE* 1.3 80.2 - - - +
387D SER* 1.3 57.1 + - - +
389D ILE* 3.4 19.7 + - - +
390D THR* 4.4 1.7 + - - -
421D LEU* 5.5 3.9 - - + +
424D GLN* 5.6 0.2 - - - +
503D ILE* 3.6 34.1 - - + +
505D ASP* 4.0 13.5 - - + +
533D LEU* 5.1 4.0 - - + -
535D ILE* 4.6 6.5 - - + -
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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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351D TYR* 4.9 2.4 + - - -
383D SER 2.9 13.1 + - - -
384D THR* 3.0 14.9 + - - -
386D ALA* 1.3 73.5 - - - +
388D LEU* 1.3 63.0 + - - +
389D ILE 3.2 0.9 - - - -
390D THR* 3.1 7.3 + - - -
392D PHE* 3.0 51.7 + - - +
393D TYR* 4.7 12.0 - - - -
421D LEU* 5.5 5.4 - - - -
424D GLN* 6.0 3.1 - - - -
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Residues in contact with LEU 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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344D PHE* 6.1 2.7 - - + -
347D VAL* 5.4 3.8 - - + -
349D PHE* 3.4 47.8 - - + -
359D LEU* 3.9 18.2 - - + -
384D THR* 2.8 17.5 + - + +
385D ILE* 2.7 12.0 + - + +
387D SER* 1.3 77.7 + - - +
389D ILE* 1.3 64.2 + - - +
391D ARG* 3.2 11.5 + - - +
392D PHE 5.1 2.5 - - - +
393D TYR* 4.8 9.4 - - + +
394D ASP* 5.5 0.4 - - - +
395D ILE* 4.3 21.1 - - + +
400D ILE* 3.3 28.6 - - + +
407D LEU* 4.0 4.7 - - + +
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Residues in contact with ILE 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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342D LEU* 4.0 31.2 - - + -
344D PHE* 5.6 4.3 - - + -
366D ILE* 6.1 0.2 - - + -
385D ILE* 2.9 51.3 + - + +
386D ALA* 3.4 15.7 - - - +
387D SER 3.2 0.2 - - - -
388D LEU* 1.3 76.6 - - - +
390D THR* 1.3 58.2 + - + +
391D ARG 2.8 11.4 + - - -
400D ILE* 5.1 12.6 - - + -
407D LEU* 2.9 24.6 - - + +
415D LEU* 4.9 2.8 - - - +
419D VAL* 5.4 1.6 - - + -
501D ILE* 4.9 10.8 - - + -
503D ILE* 4.0 21.5 - - + -
533D LEU* 5.1 8.1 - - + -
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Residues in contact with THR 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ILE* 4.5 11.9 - - + -
386D ALA 5.0 0.7 - - - +
387D SER* 3.1 4.0 + - - -
388D LEU 3.3 0.2 - - - -
389D ILE* 1.3 79.8 - - + +
391D ARG* 1.3 60.8 + - - +
392D PHE* 2.8 49.9 + - + -
415D LEU* 5.3 5.8 - - - -
416D ARG* 3.3 23.7 + - - +
419D VAL* 3.3 42.0 - - + -
421D LEU* 5.2 6.0 - - + +
503D ILE* 4.4 7.0 - - + -
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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