Contacts of the helix formed by residues 384 - 397 (chain D) in PDB entry 5I94
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 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380D GLU 3.3 17.3 + - - -
381D ARG 3.1 8.3 + - - -
383D SER* 1.3 76.2 - - - +
385D ASP* 1.3 60.5 + - - -
386D ARG 3.4 2.9 - - - -
387D ASN* 3.3 10.7 + - - +
388D PHE* 3.0 31.1 + - - -
414D PHE* 4.3 8.3 - - - -
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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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392A TYR* 3.6 33.6 - - + +
395A LYS* 2.9 44.6 + - - +
396A GLU* 4.0 26.5 + - + +
383D SER* 3.0 20.3 + - - +
384D GLY* 1.3 74.8 - - - +
386D ARG* 1.3 66.1 + - - +
388D PHE* 3.2 2.9 + - - +
389D ALA* 3.0 19.4 + - - +
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Residues in contact with ARG 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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393A TYR* 4.9 18.1 + - + -
396A GLU* 3.9 37.3 + - + +
397A LYS* 6.3 2.9 - - - +
318D ASN 5.0 8.9 + - - -
319D LYS* 4.9 5.7 + - - +
321D PHE* 4.0 20.3 - - + -
334D ASN* 3.8 24.4 - - - +
384D GLY* 3.4 0.6 - - - -
385D ASP* 1.3 77.9 - - - +
387D ASN* 1.3 64.5 + - - +
389D ALA* 3.2 8.9 - - + +
390D ILE* 3.0 49.7 + - + +
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Residues in contact with ASN 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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334D ASN* 3.2 24.9 + - - +
338D ILE* 3.8 16.1 - - + +
380D GLU* 4.9 7.1 + - - -
384D GLY* 3.3 13.3 + - - +
385D ASP 3.2 0.4 - - - -
386D ARG* 1.3 79.9 + - - +
388D PHE* 1.3 49.8 + - - +
390D ILE* 3.0 11.8 + - - +
391D GLY* 2.7 33.1 + - - -
410D LEU* 4.1 10.3 - - + +
413D TYR* 3.3 20.0 + - - -
414D PHE* 3.2 35.1 - - + -
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Residues in contact with PHE 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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392A TYR* 3.8 33.4 - + + -
381D ARG* 4.3 13.2 - - + -
384D GLY 3.0 23.9 + - - -
385D ASP* 3.2 8.6 + - - +
387D ASN* 1.3 74.2 - - - +
389D ALA* 1.3 66.1 + - - +
391D GLY* 3.1 0.3 + - - -
392D TYR* 3.0 45.8 + + - -
406D MET* 5.1 1.1 - - + -
407D VAL* 4.5 23.1 - - + -
410D LEU* 3.4 27.6 - - + -
411D ASP* 5.1 4.9 - - - -
414D PHE* 3.8 27.4 - + - -
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Residues in contact with ALA 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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389A ALA* 3.9 14.8 - - - +
392A TYR* 3.5 8.6 - - - +
393A TYR* 3.7 39.7 - - + +
321D PHE* 4.4 6.2 - - + -
385D ASP 3.0 13.0 + - - +
386D ARG* 3.2 13.5 - - - +
388D PHE* 1.3 76.3 - - - +
390D ILE* 1.3 61.7 + - - +
392D TYR 3.5 0.3 + - - -
393D TYR* 3.2 24.3 + - - +
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Residues in contact with ILE 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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321D PHE* 3.9 31.2 - - + -
334D ASN* 3.8 18.6 - - + -
335D ALA* 3.7 25.1 - - + +
338D ILE* 4.0 6.7 - - + -
386D ARG* 3.0 45.2 + - - +
387D ASN* 3.0 16.3 + - - +
389D ALA* 1.3 75.4 - - - +
391D GLY* 1.3 63.8 + - - +
393D TYR* 3.5 1.0 + - - +
394D LEU* 3.0 44.8 + - + +
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Residues in contact with GLY 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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338D ILE* 5.3 0.7 - - - -
387D ASN 2.7 17.8 + - - -
388D PHE 3.1 3.7 + - - -
390D ILE* 1.3 74.8 - - - +
392D TYR* 1.3 57.0 + - - +
394D LEU* 3.5 10.0 - - - +
395D LYS 3.0 22.3 + - - -
400D PHE* 4.9 2.0 - - - -
406D MET* 3.5 34.2 - - - +
410D LEU* 4.6 7.6 - - - -
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Residues in contact with TYR 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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385A ASP* 3.6 44.6 - - + +
388A PHE* 3.9 26.6 - + + -
389A ALA* 3.7 12.1 - - - +
392A TYR* 3.6 33.0 + + - -
388D PHE* 3.0 32.5 + + - +
391D GLY* 1.3 72.9 - - - +
393D TYR* 1.3 56.1 + - - +
395D LYS* 3.0 12.6 + - + +
396D GLU* 2.7 36.2 + - - +
406D MET* 3.4 26.2 - - + +
407D VAL* 4.3 10.2 - - - +
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Residues in contact with TYR 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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319A LYS* 4.4 2.9 + - - +
321A PHE* 3.9 22.4 - + - -
386A ARG* 4.3 15.7 + - + -
389A ALA* 3.6 12.1 - - + +
601A 69V 3.1 60.8 + - - -
321D PHE* 3.8 20.9 - + + -
322D LEU* 3.8 27.4 - - + -
389D ALA 3.2 17.5 + - - +
390D ILE 3.8 3.8 - - - +
392D TYR* 1.3 75.6 - - - +
394D LEU* 1.3 59.0 + - + +
396D GLU* 3.1 8.2 + - + +
397D LYS* 2.9 55.0 + - + +
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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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321D PHE* 5.7 1.1 - - + -
322D LEU* 4.0 18.2 - - + -
328D PRO* 4.1 6.7 - - + -
335D ALA* 3.9 12.3 - - + +
338D ILE* 3.8 14.8 - - + -
339D VAL* 3.8 11.4 - - + -
390D ILE* 3.0 42.8 + - + +
391D GLY 3.5 0.2 - - - +
393D TYR* 1.3 76.2 - - + +
395D LYS* 1.3 57.5 + - - +
398D LYS 2.9 7.6 + - - -
399D CYS* 2.9 58.3 + - + -
400D PHE* 3.5 32.1 - - + -
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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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382A GLU 5.7 2.6 + - - -
385A ASP* 2.8 38.2 + - + +
391D GLY 3.0 14.2 + - - +
392D TYR* 3.0 17.4 + - + +
394D LEU* 1.3 74.1 - - - +
396D GLU* 1.3 65.0 + - - +
398D LYS* 3.0 20.8 + - - +
400D PHE* 3.8 10.9 - - + -
404D THR 5.7 4.3 - - - +
406D MET* 4.1 27.8 - - + +
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Residues in contact with GLU 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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385A ASP* 4.4 9.2 - - + +
386A ARG* 3.7 53.0 - - + +
392D TYR 2.7 19.6 + - - +
393D TYR* 3.1 8.9 + - + +
395D LYS* 1.3 75.0 - - - +
397D LYS* 1.3 82.0 + - - +
398D LYS* 3.3 23.0 + - - +
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Residues in contact with LYS 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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319A LYS* 3.3 26.6 - - - +
386A ARG* 5.5 5.4 - - - +
601A 69V 5.1 2.8 + - - +
322D LEU* 3.8 16.6 - - + -
326D ASP* 4.1 34.1 + - - +
393D TYR* 2.9 52.7 + - + +
396D GLU* 1.3 87.1 - - - +
398D LYS* 1.3 69.3 + - - +
399D CYS* 3.5 7.4 + - - -
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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