Contacts of the helix formed by residues 277 - 291 (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 GLY 277 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D SER* 3.6 13.9 - - - +
110D ASP* 3.5 8.7 - - - -
111D MSE 5.7 0.2 - - - -
272D PRO* 2.8 27.5 + - - +
275D ILE* 3.6 1.2 - - - +
276D GLY* 1.3 76.1 - - - +
278D ILE* 1.3 62.7 + - - -
280D PRO* 3.5 3.4 - - - -
281D MSE 3.2 29.3 + - - +
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Residues in contact with ILE 278 (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 ASP* 2.7 12.3 + - - +
111D MSE 4.1 24.5 - - + -
114D TRP* 4.1 20.4 - - + -
125D VAL* 4.3 7.2 - - + -
129D LEU* 3.7 31.0 - - + -
272D PRO* 5.4 0.2 - - + -
277D GLY* 1.3 71.5 - - - -
279D GLN* 1.3 66.8 + - - +
281D MSE 3.0 18.5 + - - +
282D MSE 3.3 8.7 + - + +
309D ALA* 4.3 11.4 - - + +
313D ILE* 3.9 28.9 - - + -
356D LEU* 3.9 28.7 - - + -
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Residues in contact with GLN 279 (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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79D VAL* 4.3 2.4 - - - +
80D ALA* 3.3 29.4 - - - +
110D ASP* 3.1 5.4 + - - +
114D TRP* 3.8 34.4 - - + +
129D LEU* 5.4 3.9 - - + +
278D ILE* 1.3 77.5 - - - +
280D PRO* 1.3 72.2 - - + +
282D MSE 2.9 28.1 + - + +
283D LYS* 3.3 18.2 + - + +
129H LEU 3.0 30.5 + - - -
130H GLY* 3.9 0.9 - - - -
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Residues in contact with PRO 280 (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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83D ILE* 6.5 0.7 - - + -
110D ASP* 3.7 8.1 - - - +
275D ILE* 3.3 42.1 - - + +
276D GLY* 3.4 17.7 - - - +
277D GLY 3.5 8.1 - - - -
278D ILE 3.5 2.9 - - - -
279D GLN* 1.3 97.5 - - + +
281D MSE 1.3 56.4 + - - +
283D LYS* 3.2 15.9 + - + +
284D ALA 2.9 23.6 + - - -
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Residues in contact with MSE 281 (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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270D ILE* 3.2 31.6 - - + +
271D GLY* 3.6 25.8 - - - +
272D PRO* 4.0 3.8 - - + -
275D ILE* 3.6 11.4 - - + -
277D GLY 3.2 19.5 + - - +
278D ILE 3.0 11.5 + - - +
280D PRO* 1.3 74.9 - - - +
282D MSE 1.3 63.7 + - - +
284D ALA* 3.7 4.2 - - - +
285D ALA* 2.9 31.2 + - - +
295D ILE* 3.9 21.3 - - + -
297D ILE* 4.1 10.3 - - + -
313D ILE* 3.8 39.0 - - + -
317D ILE* 4.2 5.1 - - + +
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Residues in contact with MSE 282 (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* 4.2 25.1 - - + +
278D ILE 3.7 13.5 - - - +
279D GLN* 2.9 16.8 + - + +
281D MSE 1.3 78.6 - - - +
283D LYS* 1.3 59.1 + - + +
285D ALA* 3.5 5.1 + - - +
286D ALA* 3.0 26.7 + - - +
313D ILE* 3.4 42.8 - - + +
316D ALA* 3.7 28.5 - - - +
317D ILE* 3.5 20.6 - - + -
283H LYS* 5.3 2.8 - - - +
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Residues in contact with LYS 283 (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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253D LEU* 3.9 17.4 - - + +
279D GLN* 3.7 22.7 - - + +
280D PRO* 3.2 15.5 + - + +
281D MSE 3.2 0.6 - - - -
282D MSE 1.3 76.9 - - + +
284D ALA* 1.3 65.7 + - - +
286D ALA* 3.1 5.5 + - - +
287D VAL* 3.1 25.5 + - - +
282H MSE 5.6 1.8 - - - +
286H ALA* 4.0 26.3 - - + +
289H GLU* 2.7 35.9 + - - -
318H PRO* 4.4 11.6 - - - +
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Residues in contact with ALA 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 3.9 10.4 - - - +
256D VAL* 3.9 22.0 - - + +
270D ILE* 4.7 14.4 - - + -
275D ILE* 4.1 18.8 - - + -
280D PRO 2.9 16.3 + - - +
281D MSE 3.7 9.4 - - + +
283D LYS* 1.3 76.6 - - - +
285D ALA* 1.3 63.2 + - - +
287D VAL* 3.2 5.7 + - - +
288D ALA* 3.1 22.1 + - - +
295D ILE* 4.7 2.2 - - + -
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Residues in contact with ALA 285 (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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281D MSE 2.9 17.9 + - - +
282D MSE 3.8 5.2 - - - +
284D ALA* 1.3 75.6 - - - +
286D ALA* 1.3 57.7 + - - +
288D ALA 3.4 0.3 + - - -
289D GLU* 2.8 26.4 + - - +
295D ILE* 3.7 20.3 - - + +
317D ILE* 3.9 36.3 - - + -
318D PRO* 5.7 1.8 - - + -
319D ASN* 3.2 13.1 + - - +
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Residues in contact with ALA 286 (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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282D MSE 3.0 15.4 + - - +
283D LYS* 3.1 12.3 + - - +
285D ALA* 1.3 74.5 - - - +
287D VAL* 1.3 64.6 + - - +
289D GLU* 3.2 11.9 + - - +
290D ALA* 2.9 24.4 + - - +
253H LEU* 4.1 3.7 - - + +
283H LYS* 3.9 45.5 - - + +
286H ALA* 4.6 1.8 - - + -
287H VAL* 4.5 2.2 - - + -
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Residues in contact with VAL 287 (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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253D LEU* 3.8 20.0 - - + -
256D VAL* 3.9 11.7 - - + -
257D TYR* 3.9 39.0 - - + +
260D CYS* 4.2 5.6 - - + -
283D LYS 3.1 13.6 + - - +
284D ALA 3.2 7.4 + - - +
286D ALA* 1.3 75.5 - - - +
288D ALA* 1.3 63.2 + - - +
290D ALA* 3.2 5.7 + - - +
291D ALA* 3.1 20.4 + - - +
257H TYR* 4.8 3.7 - - + -
286H ALA 4.3 1.6 - - - +
287H VAL* 4.1 32.5 - - + +
290H ALA* 4.1 6.3 - - + -
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Residues in contact with ALA 288 (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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256D VAL* 4.5 0.6 - - + +
260D CYS* 3.9 12.3 - - - -
268D ILE* 4.5 8.3 - - + -
284D ALA 3.1 13.4 + - - +
285D ALA 3.5 8.1 - - - +
287D VAL* 1.3 78.0 - - - +
289D GLU* 1.3 61.0 + - - +
291D ALA 3.1 8.0 + - - -
293D LEU* 2.8 44.5 + - + +
295D ILE* 3.7 24.0 - - + -
319D ASN* 3.8 1.3 - - - +
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Residues in contact with GLU 289 (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 ALA 2.8 17.9 + - - +
286D ALA* 3.5 6.8 - - - +
288D ALA* 1.3 76.8 - - - +
290D ALA* 1.3 62.5 + - - +
292D GLY* 3.0 13.9 + - - -
293D LEU 3.9 3.4 - - - -
318D PRO* 3.9 18.3 - - - +
319D ASN* 3.4 21.5 - - + +
253H LEU* 4.0 11.4 - - + +
254H TYR* 3.4 28.8 + - - +
283H LYS* 2.7 35.2 + - - +
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Residues in contact with ALA 290 (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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229C SER* 4.5 2.9 + - - -
286D ALA 2.9 12.6 + - - +
287D VAL 3.5 9.2 - - - +
289D GLU* 1.3 76.6 - - - +
291D ALA* 1.3 57.7 + - - +
292D GLY 3.3 0.4 - - - -
253H LEU* 3.7 23.3 - - + +
254H TYR* 3.3 26.7 - - - -
257H TYR* 3.6 36.6 - - + +
287H VAL* 4.0 11.4 - - + -
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Residues in contact with ALA 291 (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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229C SER* 3.8 6.9 + - - -
260D CYS* 3.7 26.0 - - + -
263D ARG* 2.6 38.2 + - - +
287D VAL 3.1 4.6 + - - +
288D ALA 3.1 8.8 + - - +
289D GLU 3.1 1.0 - - - -
290D ALA* 1.3 76.6 - - - +
292D GLY* 1.3 61.7 + - - +
293D LEU* 3.3 3.8 + - + +
257H TYR* 3.7 29.2 - - + +
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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