Contacts of the helix formed by residues 328 - 350 (chain D) in PDB entry 4G5S
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 328 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLN* 4.1 1.8 - - - -
325D CYS* 2.7 29.8 + - + +
327D THR* 1.3 70.3 + - - +
329D THR* 1.3 65.8 + - - +
330D LYS* 3.3 21.4 + - - +
331D ASN* 3.3 19.9 + - + +
332D VAL* 3.2 23.2 + - - +
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Residues in contact with THR 329 (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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52D GLN* 3.1 33.4 + - - +
55D ILE* 4.2 15.3 - - + +
56D ILE* 3.9 20.3 - - + +
172D GLN* 4.5 3.5 + - - -
175D LEU* 4.0 9.4 - - - +
327D THR 3.4 3.2 + - - -
328D ASP* 1.3 73.4 + - - +
330D LYS* 1.3 64.1 + - - +
332D VAL* 3.4 2.8 + - - +
333D GLN* 2.9 25.2 + - - +
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ASP* 3.2 12.7 - - - +
329D THR* 1.3 78.3 - - - +
331D ASN* 1.3 63.1 + - - +
333D GLN* 3.1 17.6 + - - +
334D PHE* 3.0 23.3 + - - +
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Residues in contact with ASN 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C CIT 2.9 36.8 + - - +
271D LYS* 2.9 24.6 - - - +
324D THR* 3.6 6.4 - - - -
325D CYS* 3.5 20.5 + - + +
328D ASP* 3.3 27.5 + - + +
330D LYS* 1.3 79.1 - - - +
332D VAL* 1.3 59.9 + - - +
334D PHE* 3.2 7.9 + - - +
335D VAL* 2.9 44.7 + - - +
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 4.4 14.4 - - + -
52D GLN* 3.7 28.9 - - + -
53D MET* 3.7 22.4 - - + -
56D ILE* 4.3 0.4 - - + -
267D PHE* 5.6 5.4 - - + -
324D THR* 5.7 3.6 - - - -
325D CYS 4.0 4.0 - - - +
326D ALA* 3.7 28.7 - - + +
328D ASP 3.2 14.8 + - - +
329D THR 3.7 6.3 - - - +
330D LYS 3.2 0.4 - - - -
331D ASN* 1.3 74.5 - - - +
333D GLN* 1.3 66.7 + - - +
335D VAL* 3.8 4.8 - - - +
336D PHE* 2.9 24.4 + - + +
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Residues in contact with GLN 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ILE* 3.6 36.6 - - + +
57D HIS* 5.6 3.5 - - - +
329D THR* 2.9 16.6 + - - +
330D LYS* 3.3 18.7 - - - +
332D VAL* 1.3 76.4 - - - +
334D PHE* 1.3 57.6 + - - +
336D PHE* 3.8 3.5 - - - +
337D ASP* 2.9 30.7 + - + +
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Residues in contact with PHE 334 (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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279C LYS* 3.8 55.0 - - + -
402C CIT 3.8 37.5 - - + -
330D LYS 3.0 12.4 + - - +
331D ASN* 3.6 8.3 - - - +
333D GLN* 1.3 78.0 - - - +
335D VAL* 1.3 64.0 + - - +
337D ASP* 3.1 12.6 + - + +
338D ALA* 3.0 28.2 + - + +
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Residues in contact with VAL 335 (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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402C CIT 4.0 26.5 - - + +
267D PHE* 3.6 30.1 - - + -
322D HIS* 3.6 28.7 - - + -
324D THR* 4.0 10.5 - - + -
331D ASN* 2.9 37.7 + - - +
332D VAL* 3.8 5.4 - - - +
334D PHE* 1.3 75.8 - - - +
336D PHE* 1.3 58.9 + - - +
338D ALA* 3.1 7.3 + - - +
339D VAL* 2.9 27.1 + - + +
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Residues in contact with PHE 336 (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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36D LEU* 4.0 17.3 - - + -
49D ILE* 6.4 0.7 - - + -
53D MET* 3.6 28.5 - - + -
57D HIS* 3.5 28.7 - + + -
189D PHE* 3.6 23.1 - + - -
191D PHE* 4.0 10.5 - + - -
196D PHE* 3.8 20.9 - + - -
198D MET* 4.8 3.1 - - - -
222D ILE* 4.8 11.4 - - + -
267D PHE* 5.4 6.1 - + + -
332D VAL* 2.9 18.8 + - + +
333D GLN* 3.9 4.0 - - - +
335D VAL* 1.3 75.1 - - - +
337D ASP* 1.3 58.6 + - - +
339D VAL* 3.4 14.0 - - + +
340D THR* 2.6 53.6 + - - -
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Residues in contact with ASP 337 (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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191D PHE* 4.2 21.3 - - + -
333D GLN* 2.9 16.0 + - + +
334D PHE* 3.1 18.2 - - + +
336D PHE* 1.3 75.6 - - - +
338D ALA* 1.3 64.9 + - - +
340D THR* 3.1 10.0 + - - -
341D ASP* 3.0 43.3 + - - +
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Residues in contact with ALA 338 (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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322D HIS* 3.9 18.2 - - + -
334D PHE* 3.0 18.2 + - + +
335D VAL* 3.6 7.6 - - - +
337D ASP* 1.3 79.8 + - - +
339D VAL* 1.3 63.2 + - - +
341D ASP* 3.2 12.6 + - - +
342D VAL* 3.0 28.9 + - + +
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Residues in contact with VAL 339 (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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36D LEU* 5.6 0.4 - - + -
222D ILE* 4.9 4.7 - - + -
265D ILE* 3.4 42.6 - - + +
267D PHE* 4.1 11.4 - - + -
320D TYR* 6.1 1.1 - - + -
322D HIS* 3.9 21.3 - - + +
335D VAL 2.9 20.0 + - - +
336D PHE* 3.4 23.8 - - + +
338D ALA* 1.3 76.5 - - - +
340D THR* 1.3 58.4 + - - +
342D VAL* 3.1 11.1 + - - +
343D ILE* 2.9 42.7 + - + +
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Residues in contact with THR 340 (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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191D PHE* 3.4 23.2 - - + -
192D LYS* 4.3 14.1 - - + -
194D LEU* 5.0 3.6 - - + -
196D PHE* 3.9 18.7 - - + -
336D PHE* 2.6 41.9 + - - -
337D ASP 3.1 8.3 + - - -
339D VAL* 1.3 74.9 - - - +
341D ASP* 1.3 66.3 + - - +
343D ILE* 3.1 13.9 + - - +
344D ILE* 2.9 30.9 + - + +
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Residues in contact with ASP 341 (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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337D ASP* 3.0 31.0 + - - +
338D ALA* 3.4 11.0 - - - +
340D THR* 1.3 79.2 - - - +
342D VAL* 1.3 62.5 + - + +
344D ILE* 3.1 18.8 + - - +
345D LYS* 3.0 22.7 + - - +
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Residues in contact with VAL 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D SER* 5.2 2.9 - - - +
265D ILE* 5.9 3.8 - - + -
320D TYR* 3.7 56.3 - - + +
322D HIS* 5.7 3.4 - - + +
338D ALA* 3.0 20.7 + - + +
339D VAL* 3.3 10.8 - - - +
341D ASP* 1.3 75.4 - - + +
343D ILE* 1.3 64.9 + - + +
345D LYS* 3.2 8.7 + - - +
346D ASN* 3.0 28.1 + - - +
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Residues in contact with ILE 343 (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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34D VAL* 4.5 13.2 - - + -
36D LEU* 4.4 18.4 - - + -
194D LEU* 5.0 5.2 - - + -
196D PHE* 3.9 26.5 - - + -
219D THR* 4.5 15.9 - - + -
220D ALA* 4.7 11.7 - - + -
263D SER* 5.5 4.0 - - - -
265D ILE* 4.9 3.1 - - + -
339D VAL* 2.9 36.9 + - + +
340D THR* 3.3 11.7 - - + +
342D VAL* 1.3 76.1 - - + +
344D ILE* 1.3 55.5 + - + +
346D ASN* 3.2 8.3 + - + +
347D ASN* 2.5 49.6 + - - +
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Residues in contact with ILE 344 (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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192D LYS* 4.8 15.0 - - + +
194D LEU* 4.1 20.4 - - + -
340D THR* 2.9 27.3 + - + +
341D ASP* 3.3 21.1 - - - +
343D ILE* 1.3 75.7 - - - +
345D LYS* 1.3 64.2 + - - +
347D ASN* 2.9 20.5 + - + +
348D LEU* 2.9 30.1 + - + +
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Residues in contact with LYS 345 (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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341D ASP 3.0 12.2 + - - +
342D VAL* 3.5 10.8 - - - +
344D ILE* 1.3 77.0 - - - +
346D ASN* 1.3 62.6 + - - +
348D LEU* 3.0 11.4 + - - +
349D LYS* 3.0 26.7 + - - +
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Residues in contact with ASN 346 (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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263D SER* 2.4 31.6 + - - +
320D TYR* 3.6 24.1 + - - -
342D VAL* 3.0 16.6 + - - +
343D ILE* 3.7 9.2 - - - +
344D ILE 3.2 0.2 - - - -
345D LYS* 1.3 81.5 + - - +
347D ASN* 1.3 62.0 + - - +
348D LEU 3.2 0.2 - - - -
349D LYS* 3.5 11.1 + - - +
350D GLU* 3.2 31.9 + - - +
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Residues in contact with ASN 347 (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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32D LYS* 3.5 31.8 + - + +
33D GLU 5.5 1.4 - - - +
34D VAL* 5.1 4.9 - - - +
194D LEU* 5.0 8.3 - - - +
219D THR* 4.6 13.3 - - - +
343D ILE* 2.5 48.1 + - - +
344D ILE* 2.9 13.8 + - + +
346D ASN* 1.3 78.0 - - - +
348D LEU* 1.3 64.3 + - + +
350D GLU* 3.5 19.4 + - - +
351D CYS* 3.1 25.8 + - - -
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Residues in contact with LEU 348 (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 ILE* 2.9 30.7 + - + +
345D LYS* 3.0 10.5 + - - +
347D ASN* 1.3 83.6 - - + +
349D LYS* 1.3 61.9 + - - +
350D GLU 3.1 1.6 - - - -
351D CYS* 3.4 12.8 + - - +
353D LEU* 3.3 53.6 + - + +
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Residues in contact with LYS 349 (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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345D LYS 3.0 12.9 + - - +
346D ASN* 3.5 15.0 + - - +
347D ASN 3.3 0.2 - - - -
348D LEU* 1.3 78.5 - - - +
350D GLU* 1.3 62.2 + - + +
351D CYS 3.3 0.6 + - - -
352D GLY* 4.0 7.3 + - - -
353D LEU 4.8 8.5 + - - +
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Residues in contact with GLU 350 (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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32D LYS* 5.2 4.1 + - - +
219D THR* 5.6 7.8 - - - +
261D GLU* 3.9 21.1 - - - +
346D ASN* 3.2 21.1 + - - +
347D ASN* 3.7 20.8 - - - +
348D LEU 3.1 0.8 - - - -
349D LYS* 1.3 80.9 - - + +
351D CYS* 1.3 60.4 + - - +
352D GLY 3.5 1.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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