Contacts of the helix formed by residues 296 - 311 (chain D) in PDB entry 5D0A
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 296 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D PHE* 3.6 18.0 - - - -
292D GLY 4.9 0.5 - - - +
293D SER 2.9 14.8 + - - +
294D TRP 3.4 1.2 + - - -
295D ARG* 1.3 84.9 + - - +
297D LYS* 1.3 63.4 + - - -
298D LYS 3.4 1.0 + - - -
299D PRO* 3.7 6.2 - - - +
300D ILE* 3.9 8.7 - - - +
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Residues in contact with LYS 297 (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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278D ILE* 3.7 28.3 - - + +
279D SER 4.3 6.1 - - - +
280D ASN* 2.5 33.7 + - - +
283D PHE* 3.5 36.9 - - + -
296D GLY* 1.3 71.9 - - - -
298D LYS* 1.3 62.3 + - - +
299D PRO 3.5 0.4 - - - -
300D ILE* 3.3 4.4 + - + +
301D GLN* 2.8 55.7 + - + +
329D ARG* 3.7 18.0 - - - +
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Residues in contact with LYS 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LYS* 3.2 45.8 + - + +
295D ARG 5.4 0.9 - - - +
296D GLY 3.4 0.4 - - - -
297D LYS* 1.3 79.1 - - - +
299D PRO* 1.4 73.3 - - + +
301D GLN* 3.3 3.3 + - - +
302D ARG* 2.9 22.5 + - + +
329D ARG* 3.8 46.2 - - + +
330D PRO* 6.3 0.4 - - - +
331D VAL* 4.4 22.1 - - + +
332D ILE* 4.1 8.0 - - + +
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Residues in contact with PRO 299 (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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219D THR 3.5 20.6 - - - +
220D GLN* 4.2 6.7 - - - +
221D THR 3.7 21.5 - - - +
222D LYS* 4.4 9.4 - - + -
238D TYR* 6.5 0.7 - - + -
295D ARG* 3.8 29.6 - - + +
296D GLY 3.7 10.5 - - - +
298D LYS* 1.4 95.0 - - + +
300D ILE* 1.3 60.8 + - + +
302D ARG* 3.3 8.2 + - + +
303D ASN* 2.9 36.7 + - - +
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Residues in contact with ILE 300 (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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96D PHE* 3.8 31.0 - - + -
219D THR 5.7 0.2 - - - +
237D LEU* 3.5 28.5 - - + +
238D TYR* 4.0 7.9 - - + -
275D LEU* 4.2 26.5 - - + -
283D PHE* 4.4 13.9 - - + -
287D PHE* 5.7 0.4 - - + -
292D GLY 3.7 20.9 - - - +
296D GLY 3.9 17.7 - - - +
297D LYS* 3.3 6.9 + - - +
298D LYS 3.2 0.4 - - - -
299D PRO* 1.3 79.3 - - + +
301D GLN* 1.3 60.2 + - + +
303D ASN* 3.3 2.9 + - - +
304D ALA* 2.9 26.7 + - - +
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Residues in contact with GLN 301 (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 LEU* 2.8 31.8 + - + +
276D LEU* 3.5 19.4 + - + +
277D ALA 4.7 0.2 - - - -
278D ILE* 3.7 20.8 + - + +
297D LYS* 2.8 38.7 + - + +
298D LYS 3.8 3.1 - - - +
300D ILE* 1.3 72.3 - - + +
302D ARG* 1.3 66.4 + - - +
304D ALA* 3.3 7.7 + - - +
305D ILE* 3.0 28.1 + - + +
329D ARG* 2.9 41.6 + - - +
332D ILE* 4.1 11.7 - - + -
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Residues in contact with ARG 302 (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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218D LEU 2.9 24.2 + - - -
219D THR* 3.6 10.5 + - - +
221D THR* 3.0 31.8 + - - -
222D LYS 5.6 0.2 - - - -
223D GLY 3.0 27.7 + - - -
225D LEU* 3.9 29.1 - - - +
233D ILE* 5.3 0.2 - - - +
298D LYS* 2.9 17.6 + - + +
299D PRO* 3.6 4.4 + - + +
301D GLN* 1.3 76.0 - - - +
303D ASN* 1.3 87.3 + - - +
305D ILE* 3.3 8.8 + - - +
306D LEU* 3.2 29.0 + - + +
331D VAL* 4.0 11.2 - - + -
332D ILE* 3.9 13.3 - - + +
335D THR* 3.8 25.8 - - + +
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Residues in contact with ASN 303 (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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219D THR* 2.9 32.1 + - - +
233D ILE* 3.8 16.4 - - + +
236D ARG 3.8 15.9 - - - +
237D LEU* 2.8 31.0 + - - +
299D PRO 2.9 19.0 + - - +
300D ILE 3.7 4.3 - - - +
301D GLN 3.2 0.2 - - - -
302D ARG* 1.3 99.6 + - - +
304D ALA* 1.3 60.3 + - - +
306D LEU* 3.4 9.6 + - - +
307D ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 304 (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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237D LEU* 3.6 15.0 - - + +
272D LEU* 4.1 18.9 - - + +
275D LEU* 4.1 23.1 - - + -
276D LEU* 4.6 5.4 - - + -
300D ILE 2.9 16.5 + - - +
301D GLN* 3.6 6.3 - - - +
302D ARG 3.3 0.2 - - - -
303D ASN* 1.3 75.8 - - - +
305D ILE* 1.3 64.4 + - - +
307D ALA* 3.4 1.6 + - - +
308D LEU* 3.1 30.3 + - - +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D LEU* 3.6 20.6 - - + -
301D GLN* 3.0 20.3 + - + +
302D ARG* 3.3 9.4 + - - +
304D ALA* 1.3 75.9 - - - +
306D LEU* 1.3 61.8 + - - +
308D LEU* 3.3 8.0 + - - +
309D ALA* 3.1 19.6 + - - +
320D LEU* 4.0 9.2 - - + -
323D LEU* 4.4 5.2 - - + -
332D ILE* 4.0 43.7 - - + +
335D THR* 3.6 22.0 - - + +
336D ALA* 3.8 10.8 - - + +
339D ALA* 3.5 25.4 - - + +
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LEU* 3.7 31.2 - - + -
230D ARG* 3.9 26.4 - - + +
233D ILE* 4.4 17.2 - - + +
234D GLY 4.7 1.3 - - - -
302D ARG* 3.2 26.1 + - + +
303D ASN* 3.6 20.2 - - - +
304D ALA 3.3 0.2 - - - -
305D ILE* 1.3 78.5 - - - +
307D ALA* 1.3 55.5 + - - +
309D ALA* 3.3 7.2 + - - +
310D HIS* 2.9 26.7 + - - +
335D THR* 3.8 18.8 - - + -
338D TRP* 3.7 27.3 - - + -
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Residues in contact with ALA 307 (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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234D GLY 3.6 21.7 + - - +
235D ASN* 3.8 17.7 - - + +
237D LEU* 5.0 0.7 - - + -
272D LEU* 3.8 25.6 - - + -
303D ASN 2.9 17.2 + - - +
304D ALA 3.8 2.7 - - - +
305D ILE 3.3 0.2 - - - -
306D LEU* 1.3 73.8 - - - +
308D LEU* 1.3 60.9 + - - +
310D HIS* 3.1 4.5 + - - +
311D PHE* 2.9 32.6 + - - -
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Residues in contact with LEU 308 (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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92D ARG* 4.6 5.4 - - + -
272D LEU* 3.7 32.1 - - + -
273D LYS* 4.3 6.3 - - + -
276D LEU* 3.5 37.9 - - + -
304D ALA 3.1 18.8 + - - +
305D ILE 3.3 7.4 + - - +
307D ALA* 1.3 76.8 - - - +
309D ALA* 1.3 56.3 + - - +
311D PHE* 3.3 3.5 + - - +
312D LYS* 3.0 22.2 + - - -
313D ASP* 3.1 42.7 + - + +
316D ALA* 3.8 16.8 - - + -
320D LEU* 4.7 9.0 - - + -
343D ILE* 4.1 3.2 - - + +
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Residues in contact with ALA 309 (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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305D ILE 3.1 12.6 + - - +
306D LEU 3.4 8.7 - - - +
307D ALA 3.2 0.2 - - - -
308D LEU* 1.3 75.3 - - - +
310D HIS* 1.3 62.9 + - - +
312D LYS* 3.1 20.8 + - - +
338D TRP* 3.9 26.9 - - + -
339D ALA* 3.9 17.3 - - + -
342D LYS* 4.0 19.4 - - + +
343D ILE* 3.9 13.2 - - - +
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Residues in contact with HIS 310 (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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230D ARG 5.6 4.7 - - - +
231D THR* 5.1 10.4 + - - -
233D ILE* 6.2 0.4 - - + -
234D GLY* 3.8 40.5 + - - +
235D ASN* 4.2 1.0 + - - +
306D LEU 2.9 13.9 + - - +
307D ALA 3.1 10.1 + - - +
309D ALA* 1.3 78.1 - - - +
311D PHE* 1.3 87.4 + + - +
312D LYS* 3.2 4.9 + - - +
342D LYS* 6.4 0.7 - - - +
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Residues in contact with PHE 311 (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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87D SER* 4.4 9.6 - - - -
92D ARG* 3.5 69.8 + - + +
93D ARG 3.6 21.3 - - - -
235D ASN* 3.6 31.2 - - + -
272D LEU* 3.9 9.2 - - + -
307D ALA 2.9 21.6 + - - +
308D LEU* 3.3 4.7 + - - +
310D HIS* 1.3 91.6 - + - +
312D LYS* 1.3 70.7 + - - +
313D ASP* 3.3 5.3 + - + +
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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
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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