Contacts of the helix formed by residues 329 - 347 (chain D) in PDB entry 6B0Z
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 PRO 329 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.6 31.4 - - + -
327D THR 3.3 9.0 - - - +
328D ASN* 1.3 90.4 - - - +
330D ILE* 1.3 58.0 + - - +
331D ALA 3.3 2.5 - - - -
332D SER* 3.2 7.8 + - - +
333D ILE* 2.8 41.1 + - + +
373D THR* 4.3 0.2 - - + -
394D THR* 5.7 2.7 - - + +
397D PHE* 3.5 35.9 - - + -
398D MET* 4.3 18.8 - - - +
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Residues in contact with ILE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 4.0 16.8 - - + -
289D GLY 4.2 0.2 - - - +
290D MET* 3.6 28.5 - - + -
328D ASN* 2.9 19.5 + - - +
329D PRO* 1.3 77.2 - - - +
331D ALA* 1.3 58.4 + - - +
333D ILE* 3.1 10.0 + - + +
334D PHE* 2.8 48.6 + - + -
363D SER* 3.6 29.8 - - - +
367D ILE* 3.8 19.7 - - + -
397D PHE* 4.0 19.7 - - + -
401D LEU* 4.5 0.7 - - + -
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 4.7 2.7 - - - -
289D GLY 3.0 22.2 + - - +
291D MET 3.4 26.0 - - - +
292D THR* 3.5 14.3 - - - +
307D ALA* 3.7 6.1 - - + +
309D HIS* 3.7 23.8 - - + +
329D PRO 3.3 0.6 - - - -
330D ILE* 1.3 75.5 - - - +
332D SER* 1.3 63.5 + - - +
334D PHE* 3.3 1.5 + - - -
335D ALA* 3.0 21.3 + - - +
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Residues in contact with SER 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D THR* 4.0 10.1 + - - -
22D ILE* 4.5 10.6 - - - +
23D TRP* 4.3 16.0 - - - -
26D ILE* 3.6 17.9 - - - -
307D ALA* 4.0 8.6 - - - +
309D HIS* 3.9 19.4 + - - -
328D ASN 4.9 0.3 + - - -
329D PRO* 3.2 12.0 + - - +
331D ALA* 1.3 77.2 - - - +
333D ILE* 1.3 62.3 - - - +
335D ALA* 3.3 13.7 + - - +
336D TRP* 3.3 20.1 - - - -
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Residues in contact with ILE 333 (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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26D ILE* 3.7 27.8 - - + -
30D LEU* 3.6 16.2 - - + -
329D PRO* 2.8 27.3 + - + +
330D ILE* 3.4 10.3 - - + +
332D SER* 1.3 76.0 - - - +
334D PHE* 1.3 61.6 + - + +
336D TRP* 2.9 21.3 + - - +
337D THR* 3.0 25.8 + - + +
359D LEU* 4.2 14.8 - - + -
363D SER* 4.0 20.0 - - - +
398D MET* 4.7 0.9 - - + -
401D LEU* 3.6 31.0 - - + -
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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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112D ILE* 3.6 25.4 - - + -
292D THR* 3.5 20.2 - - + -
330D ILE* 2.8 40.6 + - + +
333D ILE* 1.3 77.5 - - + +
335D ALA* 1.3 60.8 + - - +
337D THR* 3.3 6.9 + - - -
338D ARG* 2.8 62.1 + - - +
360D GLU* 3.4 57.7 - - + -
363D SER* 4.1 14.8 - - - -
364D ILE* 4.3 6.5 - - + -
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Residues in contact with ALA 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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23D TRP* 4.8 11.2 - - + -
71D VAL* 3.5 6.8 - - + +
292D THR* 3.9 4.9 - - - +
305D ALA* 3.4 20.7 - - - +
306D GLU* 3.6 37.7 - - - +
307D ALA 4.0 1.1 - - - +
331D ALA 3.0 9.4 + - - +
332D SER* 3.4 13.0 - - - +
333D ILE 3.2 0.4 - - - -
334D PHE* 1.3 77.2 - - - +
336D TRP* 1.3 60.4 + - - +
338D ARG* 4.8 0.4 - - - -
339D GLY 3.1 16.1 + - - -
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Residues in contact with TRP 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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10D VAL* 5.1 1.8 - - + -
12D GLU* 3.5 22.7 - - + -
23D TRP* 3.2 39.8 - + - -
26D ILE* 4.0 19.2 - - + +
27D LYS* 3.5 34.5 - - + +
31D ILE* 4.4 34.3 - - + -
32D PHE* 5.6 0.9 - + - -
37D LEU* 4.2 22.9 - - + -
39D LEU* 4.6 7.2 - - + -
71D VAL* 4.0 23.3 - - + -
332D SER 3.3 23.1 - - - -
333D ILE* 2.9 8.7 + - + +
335D ALA* 1.3 74.2 - - - +
337D THR* 1.3 60.9 + - + +
339D GLY* 3.0 2.9 + - - -
340D LEU* 2.8 47.9 + - + +
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Residues in contact with THR 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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31D ILE* 5.9 0.2 - - + -
333D ILE* 3.0 19.8 + - + +
334D PHE* 3.3 13.5 + - - -
336D TRP* 1.3 74.0 - - + +
338D ARG* 1.3 58.6 + - - +
340D LEU* 4.6 4.3 - - + +
341D ALA* 3.2 27.2 + - - +
356D ALA* 3.5 17.7 - - - +
359D LEU* 3.7 38.8 - - + -
360D GLU* 2.6 43.5 + - + +
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Residues in contact with ARG 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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110D GLU* 3.5 40.1 + - - +
111D ALA 5.0 0.4 + - - -
112D ILE* 4.2 8.5 - - - +
203D LYS* 4.1 13.7 - - - +
292D THR* 3.3 29.4 + - + +
294D VAL* 4.3 25.2 - - + +
303D VAL* 5.4 2.3 - - - +
305D ALA* 4.7 3.1 - - + -
334D PHE* 2.8 46.8 + - - +
335D ALA* 4.1 2.7 - - - +
337D THR* 1.3 76.6 + - - +
339D GLY* 1.3 64.4 + - - +
341D ALA* 3.6 5.8 + - + +
342D HIS* 3.2 21.0 + - - +
360D GLU* 3.8 20.0 + - - -
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Residues in contact with GLY 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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69D VAL* 3.4 27.1 - - - +
70D GLY 5.5 0.4 - - - -
71D VAL* 4.3 8.3 - - - -
303D VAL* 5.2 3.8 - - - -
305D ALA* 4.5 6.4 - - - +
335D ALA 3.1 13.0 + - - -
336D TRP 3.0 6.0 + - - -
338D ARG* 1.3 77.3 - - - +
340D LEU* 1.3 58.4 + - - +
342D HIS* 3.2 5.9 + - - +
343D ARG* 3.0 23.2 + - - +
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Residues in contact with LEU 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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10D VAL* 4.2 29.8 - - + -
31D ILE* 4.5 19.1 - - + -
35D VAL* 5.2 3.6 - - + -
37D LEU* 4.3 13.7 - - + -
71D VAL* 6.0 1.1 - - + -
336D TRP* 2.8 38.7 + - + +
337D THR* 4.4 5.8 - - + +
339D GLY* 1.3 72.8 - - - -
341D ALA* 1.3 53.0 + - - +
343D ARG* 3.2 6.0 + - - +
344D ALA* 2.6 36.5 + - - +
352D LEU* 3.5 22.4 - - + +
355D PHE* 4.1 29.2 - - + -
356D ALA* 4.5 6.5 - - + -
359D LEU* 6.2 0.4 - - + -
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Residues in contact with ALA 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 THR 3.2 21.3 + - - +
338D ARG* 3.9 8.5 - - + +
339D GLY 3.2 0.2 - - - -
340D LEU* 1.3 76.9 - - - +
342D HIS* 1.3 62.4 + - - +
344D ALA* 3.4 8.6 + - - +
345D LYS* 3.1 21.7 + - - +
353D ALA* 5.4 3.6 - - - +
356D ALA* 4.2 11.8 - - + +
360D GLU* 5.6 1.8 - - - +
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Residues in contact with HIS 342 (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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69D VAL* 3.7 20.4 - - + -
202D SER* 5.6 6.6 + - - -
300D GLY 4.0 9.0 - - - -
301D LYS* 2.4 42.6 + - - -
303D VAL* 3.4 39.0 - - + +
338D ARG 3.2 10.8 + - - +
339D GLY 3.2 9.3 + - - +
341D ALA* 1.3 75.6 - - - +
343D ARG* 1.3 59.7 + - - +
345D LYS* 3.1 14.1 + - + +
346D LEU* 2.9 44.0 + - + +
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Residues in contact with ARG 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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7D GLY 3.4 23.1 - - - +
9D SER* 3.1 32.8 + - - +
10D VAL* 4.4 11.2 - - + -
67D HIS 2.4 32.3 + - - -
68D ASN* 4.1 6.7 - - - +
69D VAL* 3.8 18.3 - - + +
339D GLY 3.0 13.4 + - - +
340D LEU* 3.5 11.0 - - - +
342D HIS* 1.3 76.3 - - - +
344D ALA* 1.3 63.8 + - - +
346D LEU* 3.2 23.0 + - - +
347D ASP* 3.1 60.4 + - - +
349D ASN* 4.9 0.4 - - + +
352D LEU* 4.0 4.7 - - + -
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Residues in contact with ALA 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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340D LEU 2.6 20.5 + - - +
341D ALA 3.6 7.4 - - - +
343D ARG* 1.3 73.0 - - - +
345D LYS* 1.3 57.0 + - - +
348D ASN* 3.1 7.3 + - - -
349D ASN* 2.8 42.4 + - - +
352D LEU* 3.8 7.4 - - + -
353D ALA* 3.4 39.3 - - + +
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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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202D SER* 6.2 6.3 - - - -
300D GLY 4.5 10.3 + - - -
301D LYS* 5.9 0.2 - - - +
341D ALA 3.1 13.8 + - - +
342D HIS* 3.1 17.2 + - + +
344D ALA* 1.3 76.8 - - - +
346D LEU* 1.3 90.7 + - + +
348D ASN* 3.3 15.1 + - - +
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Residues in contact with LEU 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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68D ASN* 4.0 11.4 - - + +
69D VAL* 3.9 6.1 - - + -
301D LYS* 3.7 45.5 - - + +
342D HIS* 2.9 31.1 + - + +
343D ARG* 3.2 30.3 + - - +
345D LYS* 1.3 100.3 + - - +
347D ASP* 1.3 69.4 + - - +
348D ASN* 3.7 7.8 + - - -
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Residues in contact with ASP 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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7D GLY 4.7 3.5 - - - +
8D GLY* 4.9 4.9 - - - -
9D SER 5.5 0.2 + - - -
343D ARG* 3.1 51.3 + - - +
346D LEU* 1.3 80.5 - - - +
348D ASN* 1.3 76.1 + - - +
349D ASN* 3.0 12.8 + - + +
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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