Contacts of the helix formed by residues 382 - 398 (chain D) in PDB entry 3COG
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 ASP 382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE 5.2 1.7 - - - +
17A HIS* 3.0 27.5 + - - -
18A PHE* 4.1 2.3 + - - +
19A ALA* 3.0 35.2 + - - +
20A THR* 3.0 14.1 + - - +
381D GLU* 1.3 73.3 - - - +
383D GLU* 1.3 67.2 + - - +
384D GLU* 4.6 7.6 - - + +
385D ASP* 3.1 23.2 + - - +
386D LEU* 3.3 9.9 + - - +
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Residues in contact with GLU 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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271D LYS* 4.6 5.5 - - - +
272D ASN* 3.5 22.8 + - - +
275D ALA* 3.5 32.1 - - + +
381D GLU 3.4 3.8 + - - -
382D ASP* 1.3 70.7 - - - +
384D GLU* 1.3 64.1 + - - +
386D LEU* 3.1 7.1 + - - +
387D LEU* 3.0 39.8 + - + +
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Residues in contact with GLU 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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16A GLN* 2.6 29.6 + - - +
17A HIS* 3.3 17.8 + - - -
382D ASP* 3.2 7.4 + - + +
383D GLU* 1.3 81.2 - - - +
385D ASP* 1.3 78.3 + - - +
387D LEU* 4.0 6.0 - - - +
388D GLU* 3.0 30.5 + - + +
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Residues in contact with ASP 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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17A HIS* 2.9 32.0 + - - -
20A THR* 2.6 29.5 + - + +
334D LEU* 3.5 23.1 - - + +
382D ASP* 3.1 11.7 + - - +
384D GLU* 1.3 95.9 - - - +
386D LEU* 1.3 66.1 + - - +
388D GLU* 3.5 5.0 + - - +
389D ASP* 3.0 24.4 + - - +
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Residues in contact with LEU 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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272D ASN* 3.7 24.9 - - + +
276D VAL* 4.5 10.3 - - + -
334D LEU* 3.8 18.6 - - + -
335D PHE* 3.7 20.4 - - + -
346D SER* 3.2 26.7 - - - +
378D VAL* 3.6 26.5 - - + -
381D GLU* 3.8 19.7 - - + +
382D ASP 3.7 7.0 - - - +
383D GLU* 3.1 8.4 + - - +
385D ASP* 1.3 77.6 - - - +
387D LEU* 1.3 63.2 + - - +
389D ASP* 3.2 4.4 + - - +
390D LEU* 3.1 28.1 + - - +
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Residues in contact with LEU 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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275D ALA* 3.9 8.1 - - + +
276D VAL* 3.8 40.8 - - + +
279D PHE* 3.8 36.7 - - + -
383D GLU* 3.0 42.6 + - + +
384D GLU* 4.1 5.6 - - - +
386D LEU* 1.3 75.9 - - + +
388D GLU* 1.3 57.9 + - - +
390D LEU* 3.4 5.9 + - + +
391D ASP* 3.0 29.7 + - - +
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Residues in contact with GLU 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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384D GLU* 3.0 20.2 + - + +
385D ASP* 4.0 4.9 - - - +
387D LEU* 1.3 77.3 - - - +
389D ASP* 1.3 62.7 + - - +
391D ASP* 4.2 15.8 - - - +
392D GLN* 3.0 40.3 + - + +
395D LYS* 5.9 0.3 - - - -
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Residues in contact with ASP 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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332D LEU* 3.3 16.0 - - - +
333D LYS* 2.9 23.6 + - - +
334D LEU* 2.9 33.3 + - + -
335D PHE* 3.0 18.1 + - + -
385D ASP 3.0 17.5 + - - +
386D LEU* 3.2 5.6 + - - +
388D GLU* 1.3 76.6 - - - +
390D LEU* 1.3 62.4 + - - +
392D GLN* 2.9 24.6 + - - +
393D ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 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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276D VAL* 3.7 39.5 - - + -
279D PHE* 3.9 17.3 - - + -
280D LEU* 4.5 13.7 - - + -
328D PHE* 3.7 28.7 - - + -
332D LEU* 4.3 3.1 - - + -
335D PHE* 3.7 25.1 - - + -
376D LEU* 3.9 15.7 - - + -
386D LEU 3.1 20.9 + - - +
387D LEU* 3.8 5.2 - - + +
389D ASP* 1.3 76.6 - - - +
391D ASP* 1.3 56.1 + - - +
393D ALA* 3.8 0.7 - - - +
394D LEU* 2.9 37.0 + - + +
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Residues in contact with ASP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D PHE* 3.5 27.6 - - + -
283D ASN* 4.2 7.4 + - - -
285D TRP* 5.1 0.7 - - - -
387D LEU 3.0 18.5 + - - +
388D GLU* 3.6 19.4 - - - +
389D ASP 3.2 0.2 - - - -
390D LEU* 1.3 77.7 - - - +
392D GLN* 1.3 62.2 + - - +
394D LEU* 3.5 3.9 + - - +
395D LYS* 2.9 63.2 + - - +
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Residues in contact with GLN 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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331D ASN* 2.7 36.8 + - - +
333D LYS* 3.9 20.1 + - + +
388D GLU* 3.0 30.4 + - + +
389D ASP* 2.9 35.9 + - - +
391D ASP* 1.3 76.7 - - - +
393D ALA* 1.3 67.1 + - - +
395D LYS* 3.3 11.0 + - - +
396D ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 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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328D PHE* 3.5 46.2 - - + +
331D ASN* 4.0 7.2 - - - -
332D LEU* 3.7 16.8 - - + +
389D ASP 3.0 18.0 + - - +
392D GLN* 1.3 83.1 - - - +
394D LEU* 1.3 65.4 + - - +
396D ALA* 3.4 3.8 + - - +
397D ALA 3.2 15.9 + - - -
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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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279D PHE* 4.2 4.5 - - + -
280D LEU* 3.9 25.4 - - + -
283D ASN* 3.8 27.8 - - - +
285D TRP* 4.1 22.2 - - + -
286D VAL* 4.1 12.1 - - + -
316D PHE* 4.5 4.7 - - + -
318D ILE* 3.9 25.6 - - + -
328D PHE* 3.7 22.2 - - + -
390D LEU 2.9 22.7 + - - +
391D ASP 3.9 3.1 - - - +
393D ALA* 1.3 77.3 - - - +
395D LYS* 1.3 55.9 + - - +
397D ALA* 3.2 5.0 + - - +
398D HIS* 2.8 27.7 + - - -
399D PRO* 4.1 3.3 - - + +
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Residues in contact with LYS 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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285D TRP* 3.6 32.9 - - + -
388D GLU* 5.9 0.7 - - - -
391D ASP* 2.9 53.7 + - - +
392D GLN* 3.6 9.0 - - - +
393D ALA 3.3 0.2 - - - -
394D LEU* 1.3 73.2 - - - +
396D ALA* 1.3 61.3 + - - +
398D HIS* 2.8 29.2 + - - +
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Residues in contact with ALA 396 (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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327D ILE* 3.7 10.3 - - - +
331D ASN* 3.4 37.9 - - + +
392D GLN* 2.9 18.3 + - - +
393D ALA 3.6 4.5 - - - +
395D LYS* 1.3 76.8 - - - +
397D ALA* 1.3 58.5 + - - +
398D HIS* 3.4 14.0 + - - -
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Residues in contact with ALA 397 (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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318D ILE* 4.4 4.3 - - + -
324D HIS* 3.3 40.0 - - - +
327D ILE* 3.7 14.1 - - + +
328D PHE* 4.0 10.3 - - + +
393D ALA 3.2 11.6 + - - +
394D LEU 3.2 8.7 + - - +
396D ALA* 1.3 76.8 - - - +
398D HIS* 1.3 75.3 + - - +
399D PRO* 3.1 12.0 - - + -
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Residues in contact with HIS 398 (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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285D TRP* 3.7 23.8 - - + +
324D HIS* 4.5 1.9 + - - -
394D LEU 2.8 12.0 + - - -
395D LYS 2.8 24.1 + - - +
396D ALA* 3.4 14.5 + - - -
397D ALA* 1.3 76.8 + - - +
399D PRO* 1.3 71.8 - - - +
400D PRO* 4.7 0.2 - - - +
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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