Contacts of the helix formed by residues 303 - 317 (chain D) in PDB entry 2PGW
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 THR 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.4 33.7 - - + -
32D PHE* 6.0 1.6 - - + -
34D VAL* 4.1 10.3 - - + -
50D GLU* 2.6 29.7 + - - +
302D THR* 1.3 86.0 + - - +
304D GLY* 1.3 65.2 + - - +
305D ILE* 3.0 8.6 + - - +
306D THR* 3.1 12.6 + - - -
307D THR* 3.3 11.5 + - - -
328D TRP* 4.2 5.9 + - - +
331D VAL* 4.9 3.6 - - + -
334D ASP* 3.2 13.2 - - - +
335D ILE* 3.5 17.2 - - + +
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Residues in contact with GLY 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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303D THR* 1.3 68.7 - - - +
305D ILE* 1.3 65.1 + - - +
307D THR* 3.2 9.5 + - - -
308D CYS* 3.0 28.9 + - - -
328D TRP* 3.9 1.9 - - - +
334D ASP* 2.8 32.7 + - - -
336D VAL* 3.4 8.7 - - - +
341D LEU* 3.6 14.8 - - - +
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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
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36D LEU* 3.9 20.0 - - + -
48D ILE* 4.2 9.9 - - + -
49D GLY* 3.9 7.0 - - - -
50D GLU* 3.6 23.8 - - + +
111D MSE 3.1 33.4 - - + +
303D THR* 3.0 5.4 - - - +
304D GLY* 1.3 76.9 - - - +
306D THR* 1.3 61.7 + - - +
308D CYS* 3.2 6.1 + - - +
309D ALA 3.2 16.5 + - - -
335D ILE* 3.5 23.6 - - + -
336D VAL* 3.5 4.5 - - + +
358D PHE* 3.9 20.8 - - + -
360D LEU* 3.9 25.4 - - + -
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Residues in contact with THR 306 (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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50D GLU* 2.6 27.9 + - - +
111D MSE 4.3 12.6 - - - -
272D PRO* 4.8 8.1 - - + -
299D SER* 4.6 2.2 - - - +
300D SER* 4.0 7.4 - - - +
302D THR* 3.2 28.9 + - - +
303D THR 3.1 3.6 + - - -
305D ILE* 1.3 75.3 - - - +
307D THR* 1.3 66.3 + - - +
309D ALA* 3.2 2.2 + - - +
310D GLU* 2.8 53.0 + - + +
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Residues in contact with THR 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D TYR* 4.7 5.5 + - + +
303D THR 3.3 5.8 + - - -
304D GLY* 3.2 12.1 + - - -
305D ILE 3.2 0.4 - - - -
306D THR* 1.3 80.1 - - - +
308D CYS* 1.3 57.0 - - - +
310D GLU* 3.4 11.2 + - - +
311D HIS* 2.8 27.9 + - + +
326D ILE* 3.9 32.1 - - + +
327D MSE 4.7 1.7 + - - -
328D TRP* 3.4 32.8 + - + +
341D LEU* 4.2 15.7 - - + -
348D LEU* 4.9 6.7 - - + -
351D PHE* 5.8 0.2 - - + -
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Residues in contact with CYS 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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304D GLY 3.0 17.4 + - - -
305D ILE 3.5 7.6 - - - +
307D THR* 1.3 74.3 - - - +
309D ALA* 1.3 65.2 + - - +
311D HIS* 3.1 7.2 + - - +
312D HIS* 3.0 30.1 + - - -
336D VAL* 4.8 0.7 - - - -
339D PRO* 4.4 5.4 - - - -
341D LEU* 3.9 23.8 - - - -
351D PHE* 4.3 8.5 - - + -
356D LEU* 3.5 20.6 - - + +
358D PHE* 3.8 32.8 - - + -
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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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111D MSE 3.4 44.2 - - + -
272D PRO* 5.4 2.9 - - + -
278D ILE* 4.3 8.6 - - + +
305D ILE 3.2 3.2 + - - -
306D THR 3.2 5.8 + - - +
308D CYS* 1.3 78.4 - - - +
310D GLU* 1.3 60.0 + - + +
312D HIS* 3.2 4.2 + - - +
313D ILE* 2.9 35.8 + - + +
356D LEU* 3.6 17.6 - - + +
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Residues in contact with GLU 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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137D VAL* 5.5 0.5 - - - +
139D TYR* 5.0 6.1 + - + -
272D PRO* 3.7 24.8 - - + +
297D ILE* 3.1 32.3 - - + +
298D HIS 3.3 19.6 - - - +
299D SER* 3.0 27.7 + - - -
300D SER* 4.7 0.7 + - - -
306D THR* 2.8 40.5 + - + +
307D THR* 3.7 8.7 - - - +
309D ALA* 1.3 75.6 - - - +
311D HIS* 1.3 57.9 + - - +
313D ILE* 4.1 7.9 - - - -
314D GLY* 2.9 22.3 + - - -
325D GLN 4.3 7.4 - - - +
326D ILE* 5.3 1.0 - - - -
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 3.7 14.2 - - + +
139D TYR* 3.1 28.9 - - - +
307D THR* 2.8 18.2 + - + +
308D CYS 3.4 7.0 - - - +
309D ALA 3.1 0.2 - - - -
310D GLU* 1.3 77.8 - - - +
312D HIS* 1.3 66.1 + - - +
314D GLY* 3.3 2.4 + - - -
315D LEU* 3.1 43.2 + - + +
348D LEU* 3.4 29.6 + - + +
349D ASP 3.6 3.6 + - - -
350D ALA* 3.5 1.8 - - - -
351D PHE* 3.1 62.8 - + + +
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Residues in contact with HIS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 3.8 11.0 - - + -
125D VAL* 3.9 22.4 - - + -
126D HIS* 3.1 41.8 + + - +
129D LEU* 4.6 1.9 - - - +
308D CYS* 3.0 26.0 + - - -
309D ALA 3.7 4.9 - - - +
311D HIS* 1.3 78.0 - - - +
313D ILE* 1.3 67.8 + - - +
315D LEU* 3.4 6.2 + - - +
316D ALA* 3.1 23.4 + - - +
351D PHE* 4.0 21.3 - - + +
353D LYS 4.8 1.1 - - - -
355D GLY 3.8 11.0 - - - -
356D LEU* 3.0 44.1 + - + -
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Residues in contact with ILE 313 (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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129D LEU* 5.1 0.4 - - - -
272D PRO* 4.0 19.1 - - + -
278D ILE* 3.9 38.4 - - + -
281D MSE 3.8 33.9 - - + -
282D MSE 3.4 22.8 - - + +
297D ILE* 4.0 4.7 - - + -
309D ALA 2.9 22.4 + - - +
310D GLU* 3.6 13.2 - - - +
312D HIS* 1.3 75.7 - - - +
314D GLY* 1.3 65.0 + - - +
316D ALA* 3.1 13.3 + - - +
317D ILE* 3.1 27.8 + - + +
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Residues in contact with GLY 314 (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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134D ARG* 2.8 22.4 + - - -
137D VAL* 4.5 6.5 - - - -
297D ILE* 3.7 17.5 - - - -
310D GLU 2.9 11.9 + - - -
311D HIS 3.7 3.4 - - - -
312D HIS 3.2 0.2 - - - -
313D ILE* 1.3 77.3 - - - +
315D LEU* 1.3 58.9 + - - +
317D ILE* 3.3 7.3 + - - +
320D LEU* 3.4 22.8 - - - +
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Residues in contact with LEU 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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126D HIS* 3.3 32.8 - - + +
132D ALA* 3.2 12.0 - - + -
133D HIS* 2.8 29.5 + - - -
134D ARG* 3.7 29.1 + - + +
136D ALA 4.6 3.1 - - - -
137D VAL* 3.6 19.9 - - + +
311D HIS* 3.1 39.4 + - + +
312D HIS* 3.8 7.4 - - - +
313D ILE 3.3 0.2 - - - -
314D GLY* 1.3 76.1 - - - +
316D ALA* 1.3 59.9 + - - +
317D ILE 3.5 0.5 + - - -
350D ALA* 3.5 29.6 - - + -
351D PHE 4.4 0.7 - - - +
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Residues in contact with ALA 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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126D HIS* 4.3 4.5 - - + +
129D LEU* 3.8 29.9 - - + +
131D GLY 3.7 12.8 - - - +
133D HIS* 3.4 18.0 + - - -
282D MSE 3.7 22.6 - - - +
312D HIS 3.1 14.5 + - - +
313D ILE 3.1 6.5 + - - +
315D LEU* 1.3 78.7 - - - +
317D ILE* 1.3 57.5 + - - +
318D PRO* 3.5 4.2 - - - +
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D HIS* 4.0 1.6 - - - -
134D ARG* 2.8 28.8 + - - -
281D MSE 4.2 14.4 - - + +
282D MSE 3.5 17.5 - - + -
285D ALA* 3.9 23.1 - - + -
295D ILE* 4.4 4.3 - - + -
313D ILE* 3.1 36.2 + - + +
314D GLY 3.3 5.3 + - - +
316D ALA* 1.3 76.1 - - - +
318D PRO* 1.3 63.0 - - - +
319D ASN* 3.3 39.7 - - - +
320D LEU* 3.7 19.6 - - + +
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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