Contacts of the helix formed by residues 310 - 329 (chain D) in PDB entry 5U07
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 TYR 310 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D VAL* 5.1 1.3 - - + -
195D HIS* 3.6 49.1 - + + +
196D GLY 5.3 0.5 + - - -
230D THR* 4.2 18.2 - - + +
304D LEU* 3.6 31.7 + - + -
305D TYR 3.0 25.9 - - - -
306D GLY* 2.9 25.6 + - - -
309D GLY* 1.3 78.8 - - - -
311D THR* 1.3 56.7 + - - +
312D LEU* 3.4 2.4 - - - +
313D ARG* 3.2 6.7 + - - -
314D ALA* 2.6 38.0 + - + +
31H GLY* 3.9 20.0 - - - -
32H GLY* 3.9 7.0 - - - -
301H GLU* 2.7 20.3 + - - +
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Residues in contact with THR 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 5.4 5.6 - - + +
11D THR* 5.0 1.8 - - + -
230D THR* 4.9 8.5 - - + +
282D ASP* 3.4 31.4 - - - +
310D TYR* 1.3 75.4 - - - +
312D LEU* 1.3 72.6 + - - +
314D ALA* 3.8 3.8 - - - +
315D CYS* 2.9 31.5 + - - -
341D GLU* 6.0 2.7 - - - -
298H PRO* 5.2 4.5 - - + +
301H GLU* 3.4 30.1 + - + +
302H THR* 4.0 12.4 - - + +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ASP* 4.7 17.3 - - - +
309D GLY 4.7 1.3 - - - +
311D THR* 1.3 90.6 + - - +
313D ARG* 1.3 87.5 + - + +
315D CYS* 3.1 10.2 + - - +
316D GLN* 2.9 40.3 + - - +
341D GLU* 5.4 6.1 - - + -
344D THR* 5.5 11.0 - - + +
302H THR* 4.4 16.8 - - + -
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Residues in contact with ARG 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 4.1 23.2 - - + +
305D TYR* 2.5 48.1 + - - +
306D GLY 4.3 6.1 + - - -
308D ASP* 5.3 11.3 - - - +
309D GLY 3.6 20.8 + - - +
310D TYR* 3.2 5.8 + - - +
312D LEU* 1.3 89.1 - - + +
314D ALA* 1.3 58.2 + - - +
316D GLN* 3.4 8.6 + - - +
317D GLU* 2.9 29.3 + - - +
236N ARG* 5.2 5.9 - - - +
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Residues in contact with ALA 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 3.7 28.0 - - + +
194D VAL* 4.2 15.5 - - + -
230D THR* 5.3 0.7 - - - +
300D PHE* 3.9 15.7 - - + -
304D LEU* 3.9 7.8 - - + +
310D TYR* 2.6 24.5 + - + +
311D THR 3.8 2.0 - - - +
313D ARG* 1.3 70.2 - - - +
315D CYS* 1.3 66.7 + - - +
317D GLU* 3.3 1.7 + - - +
318D LEU* 2.9 25.6 + - - +
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Residues in contact with CYS 315 (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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9D ILE* 4.3 4.2 - - - +
282D ASP* 5.6 4.7 - - - -
283D LEU* 3.4 36.6 - - + +
311D THR* 2.9 27.9 + - - -
312D LEU* 3.2 10.1 - - - +
314D ALA* 1.3 78.1 - - - +
316D GLN* 1.3 64.0 + - + +
318D LEU* 3.2 3.9 + - - +
319D ASN* 2.9 20.3 + - - +
341D GLU* 3.1 28.3 - - - +
344D THR* 5.6 3.1 - - - +
346D LEU* 4.2 17.3 - - + +
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Residues in contact with GLN 316 (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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312D LEU* 2.9 28.1 + - - +
313D ARG* 4.0 6.5 - - - +
315D CYS* 1.3 76.8 - - + +
317D GLU* 1.3 62.1 + - - +
319D ASN* 3.1 11.4 + - + +
320D ASN* 2.9 30.6 + - - +
344D THR* 3.5 31.2 - - + +
346D LEU* 4.3 11.9 - - + -
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Residues in contact with GLU 317 (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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299D ALA* 3.5 29.2 - - + +
300D PHE* 4.3 15.3 - - + -
302D THR* 5.0 0.2 + - - -
304D LEU* 4.7 10.5 - - + +
313D ARG 2.9 18.6 + - - +
314D ALA* 3.6 4.9 - - - +
315D CYS 3.3 0.4 - - - -
316D GLN* 1.3 75.9 - - - +
318D LEU* 1.3 63.5 + - - +
320D ASN* 2.9 29.0 + - - +
321D TYR* 3.0 13.0 + - - +
236N ARG* 2.8 38.1 + - - -
239N GLN* 4.7 9.0 + - - +
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Residues in contact with LEU 318 (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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7D HIS* 4.8 4.9 - - + -
9D ILE* 4.3 10.5 - - + -
232D TYR* 3.6 31.0 - - + -
283D LEU* 4.9 11.7 - - + -
285D HIS* 4.8 4.3 - - + +
296D PHE* 3.8 25.0 - - + -
299D ALA* 4.7 5.6 - - - -
300D PHE* 4.2 13.2 - - + -
314D ALA 2.9 17.0 + - - +
315D CYS* 3.6 4.9 - - - +
317D GLU* 1.3 76.4 - - - +
319D ASN* 1.3 56.7 + - - +
321D TYR* 3.4 5.7 + - - +
322D ALA* 2.9 28.8 + - - +
349D LEU* 3.6 35.7 - - + -
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Residues in contact with ASN 319 (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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315D CYS 2.9 14.1 + - - +
316D GLN* 3.2 11.6 + - - +
317D GLU 3.1 0.2 - - - -
318D LEU* 1.3 77.6 - - - +
320D ASN* 1.3 67.7 + - - +
322D ALA* 3.4 3.4 + - - -
323D GLU* 2.9 26.6 + - - +
345D ASP 4.1 4.2 + - - -
346D LEU* 3.7 39.3 - - + +
347D ALA* 4.2 3.6 - - - +
348D ALA* 3.1 34.2 + - - +
349D LEU* 4.2 5.9 + - + -
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Residues in contact with ASN 320 (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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316D GLN* 2.9 22.3 + - - +
317D GLU* 2.9 22.6 + - - +
319D ASN* 1.3 81.6 + - - +
321D TYR* 1.3 64.1 + - - +
323D GLU* 3.2 19.1 + - - +
324D ARG* 3.0 38.4 + - - +
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Residues in contact with TYR 321 (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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296D PHE* 3.6 38.4 - + + -
298D PRO* 3.8 21.3 - - + +
299D ALA* 3.6 35.0 - - + -
317D GLU* 3.0 7.1 + - + +
318D LEU 3.9 5.6 - - - +
320D ASN* 1.3 76.0 - - - +
322D ALA* 1.3 63.5 + - - +
324D ARG* 3.3 16.3 - - + +
325D LEU* 2.9 47.4 + - + +
146N ASP* 4.1 2.9 + - - -
147N PRO* 3.5 22.8 - - + +
148N LEU* 4.4 1.6 - - - +
239N GLN* 5.0 10.1 - - + -
243N PHE* 3.6 28.6 - + - -
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Residues in contact with ALA 322 (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 HIS* 5.4 0.7 - - + -
296D PHE* 4.0 23.1 - - + -
318D LEU 2.9 18.7 + - - +
319D ASN 3.8 3.6 - - - +
321D TYR* 1.3 78.4 - - - +
323D GLU* 1.3 64.5 + - - +
325D LEU* 4.1 1.2 - - - +
326D ARG* 2.9 27.5 + - - +
335D ARG* 6.5 0.4 - - - -
348D ALA* 4.0 13.2 - - + +
349D LEU* 3.8 25.1 - - + -
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Residues in contact with GLU 323 (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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319D ASN* 2.9 16.4 + - - +
320D ASN* 3.3 23.4 - - - +
322D ALA* 1.3 76.3 - - - +
324D ARG* 1.3 59.3 + - + +
326D ARG* 3.3 5.1 + - - +
327D GLU* 2.9 27.3 + - + +
348D ALA* 3.4 16.2 - - + +
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Residues in contact with ARG 324 (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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320D ASN* 3.0 25.9 + - - +
321D TYR* 3.3 19.5 - - - +
323D GLU* 1.3 76.5 - - + +
325D LEU* 1.3 65.6 + - - +
327D GLU* 2.8 24.1 + - - +
328D VAL* 2.9 18.4 + - + +
239N GLN* 4.4 14.9 - - - +
240N ASN* 3.8 23.5 + - - +
243N PHE* 3.2 46.8 - - + +
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Residues in contact with LEU 325 (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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294D ILE* 4.2 14.6 - - + -
296D PHE* 3.7 20.4 - - + -
321D TYR* 2.9 46.8 + - + +
322D ALA* 4.2 2.5 - - - +
324D ARG* 1.3 77.7 - - - +
326D ARG* 1.3 62.6 + - - +
328D VAL* 3.9 4.3 - - - +
329D TRP* 3.0 57.7 + - + +
147N PRO* 3.8 17.9 - - + -
148N LEU* 4.0 8.3 - - + -
243N PHE* 3.7 20.6 - - + -
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Residues in contact with ARG 326 (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 ALA 2.9 19.7 + - - +
323D GLU* 3.7 5.6 - - - +
325D LEU* 1.3 77.6 - - - +
327D GLU* 1.3 62.0 + - - +
329D TRP 3.8 7.2 - - - +
330D PRO* 3.2 27.0 - - + +
331D ASP* 3.1 38.3 + - - +
333D ALA 4.7 2.8 + - - +
335D ARG* 2.9 49.9 - - - +
348D ALA* 4.8 8.3 - - - +
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Residues in contact with GLU 327 (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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323D GLU* 2.9 14.4 + - + +
324D ARG* 2.8 15.2 + - - +
326D ARG* 1.3 80.5 - - - +
328D VAL* 1.3 74.9 + - - +
330D PRO* 3.6 9.4 - - - +
247N LYS* 3.4 31.9 - - - +
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Residues in contact with VAL 328 (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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324D ARG* 2.9 10.9 + - + +
325D LEU* 3.9 5.4 - - - +
327D GLU* 1.3 90.3 + - - +
329D TRP* 1.3 86.9 + - + +
330D PRO* 3.5 6.3 - - - +
243N PHE* 3.9 25.1 - - + +
246N VAL* 3.9 24.0 - - + -
247N LYS* 3.7 28.7 - - + +
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Residues in contact with TRP 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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289D ARG* 5.2 5.7 + - - +
291D ASP* 5.2 10.3 - - - +
292D ARG* 3.7 30.5 - - - +
294D ILE* 6.4 0.4 - - + -
325D LEU* 3.0 44.5 + - + +
326D ARG* 3.2 13.9 - - - +
328D VAL* 1.3 96.2 + - + +
330D PRO* 1.3 68.2 - - - +
331D ASP* 3.3 7.3 + - + +
147N PRO 4.5 0.2 - - - -
148N LEU* 3.4 30.1 - - + -
150N VAL* 4.6 15.3 - - + -
153N ARG* 5.7 7.3 - - - +
243N PHE* 5.2 0.2 - + - -
246N VAL* 4.1 15.3 - - + -
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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