Contacts of the helix formed by residues 277 - 291 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107H SER* 3.8 10.0 - - - +
110H ASP* 3.4 13.2 - - - -
111H MSE 5.9 0.2 - - - -
272H PRO* 3.0 22.9 + - - +
275H ILE* 3.7 0.5 - - - +
276H GLY* 1.3 79.0 - - - +
278H ILE* 1.3 63.4 + - - -
280H PRO* 3.5 2.7 - - - -
281H MSE 3.1 29.6 + - - +
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Residues in contact with ILE 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H ASP* 2.6 12.5 + - - +
111H MSE 3.7 34.5 - - + -
114H TRP* 3.8 25.1 - - + -
125H VAL* 4.3 6.7 - - + -
129H LEU* 3.6 31.9 - - + -
272H PRO* 5.7 0.9 - - + -
277H GLY* 1.3 70.5 - - - -
279H GLN* 1.3 66.0 + - - +
281H MSE 3.0 19.8 + - - +
282H MSE 3.4 8.6 + - + +
309H ALA* 4.6 5.8 - - + +
312H HIS* 6.1 0.2 - - + -
313H ILE* 3.9 29.8 - - + -
356H LEU* 4.0 19.5 - - + -
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Residues in contact with GLN 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 2.9 32.3 + - - +
130D GLY* 3.9 2.1 - - - -
79H VAL* 4.2 3.3 - - - +
80H ALA* 3.5 26.5 - - - +
110H ASP* 3.2 4.7 + - - +
114H TRP* 3.7 30.1 - - + +
129H LEU* 5.4 4.9 - - + +
278H ILE* 1.3 77.9 - - - +
280H PRO* 1.3 73.1 - - + +
282H MSE 3.1 21.9 + - + +
283H LYS* 3.3 20.1 + - + +
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Residues in contact with PRO 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ILE* 6.5 0.2 - - + -
110H ASP* 3.7 7.2 - - - +
275H ILE* 3.4 39.5 - - + +
276H GLY* 3.4 18.4 - - - +
277H GLY 3.5 10.1 - - - -
278H ILE 3.5 3.8 - - - +
279H GLN* 1.3 95.4 - - + +
281H MSE 1.3 55.9 + - - +
283H LYS* 3.1 18.8 + - + +
284H ALA 3.0 22.5 + - - -
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Residues in contact with MSE 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ILE* 3.3 34.1 - - + +
271H GLY* 3.6 16.2 - - - +
272H PRO 4.0 8.1 - - - -
275H ILE* 3.4 18.8 - - + -
277H GLY 3.1 19.5 + - - +
278H ILE 3.0 9.5 + - - +
280H PRO* 1.3 77.2 - - - +
282H MSE 1.3 61.9 + - - +
284H ALA* 3.2 4.7 + - - +
285H ALA* 2.8 30.3 + - - +
295H ILE* 3.9 15.3 - - + -
297H ILE* 3.4 26.2 - - + -
313H ILE* 3.9 23.8 - - + -
317H ILE* 4.1 5.6 - - + +
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Residues in contact with MSE 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LYS* 5.6 1.6 - - - +
129H LEU* 4.3 26.0 - - + +
278H ILE 3.8 14.8 - - - +
279H GLN* 3.1 15.1 + - + +
281H MSE 1.3 77.1 - - - +
283H LYS* 1.3 59.8 + - + +
285H ALA* 3.4 6.2 + - - +
286H ALA* 3.0 26.9 + - - +
313H ILE* 3.3 50.5 - - + +
316H ALA* 3.7 27.4 - - + +
317H ILE* 3.6 15.5 - - + -
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Residues in contact with LYS 283 (chain H).
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 5.3 2.2 - - - +
286D ALA* 3.9 27.7 - - + +
289D GLU* 2.7 33.5 + - - +
318D PRO* 4.4 11.9 - - - +
253H LEU* 4.0 20.6 - - + -
279H GLN* 3.4 22.2 - - + +
280H PRO* 3.1 15.3 + - - +
282H MSE 1.3 76.8 - - + +
284H ALA* 1.3 65.0 + - - +
286H ALA* 3.2 3.8 + - - +
287H VAL* 3.2 26.5 + - - +
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Residues in contact with ALA 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H LEU* 4.1 10.5 - - + +
256H VAL* 3.9 27.8 - - + +
270H ILE* 4.7 14.6 - - + -
275H ILE* 4.2 13.7 - - + -
280H PRO 3.0 12.5 + - - +
281H MSE 3.2 11.4 + - - +
283H LYS* 1.3 77.1 - - - +
285H ALA* 1.3 63.7 + - - +
287H VAL* 3.3 3.8 + - - +
288H ALA* 3.0 23.7 + - - +
295H ILE* 4.3 3.5 - - + +
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Residues in contact with ALA 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H MSE 2.8 16.2 + - - +
282H MSE 3.5 7.0 - - - +
283H LYS 3.2 0.2 - - - -
284H ALA* 1.3 78.0 - - - +
286H ALA* 1.3 57.4 + - - +
288H ALA 3.4 0.3 + - - -
289H GLU* 2.8 26.3 + - - +
295H ILE* 3.8 14.1 - - + +
317H ILE* 3.8 40.6 - - + -
318H PRO* 5.5 2.0 - - + -
319H ASN* 3.1 12.4 + - - +
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Residues in contact with ALA 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 4.0 4.0 - - + +
283D LYS* 4.0 46.7 - - + +
286D ALA* 4.6 1.8 - - + -
287D VAL* 4.4 2.5 - - + -
282H MSE 3.0 13.9 + - - +
283H LYS* 3.2 12.3 + - - +
285H ALA* 1.3 74.7 - - - +
287H VAL* 1.3 66.3 + - - +
289H GLU* 3.2 12.6 + - - +
290H ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D TYR* 4.8 4.9 - - + -
286D ALA 4.3 1.1 - - - +
287D VAL* 4.1 23.6 - - + +
290D ALA* 4.0 13.0 - - + -
253H LEU* 3.7 20.0 - - + -
256H VAL* 4.1 7.2 - - + -
257H TYR* 3.9 38.4 - - + -
260H CYS* 4.1 11.0 - - + -
283H LYS 3.2 14.3 + - - +
284H ALA 3.7 5.8 - - - +
286H ALA* 1.3 76.2 - - - +
288H ALA* 1.3 63.2 + - - +
290H ALA* 3.2 5.4 + - - +
291H ALA* 3.1 20.6 + - - +
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Residues in contact with ALA 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H VAL* 4.6 1.1 - - + +
260H CYS* 3.9 16.2 - - - -
268H ILE* 4.7 6.3 - - + -
284H ALA 3.0 15.7 + - - +
285H ALA 3.7 4.5 - - - +
287H VAL* 1.3 77.1 - - - +
289H GLU* 1.3 60.3 + - - +
291H ALA* 3.0 8.5 + - - +
293H LEU* 2.8 44.4 + - + +
294H LYS 4.7 0.7 - - - +
295H ILE* 3.9 21.5 - - + -
319H ASN* 3.9 0.9 - - - +
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Residues in contact with GLU 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 4.1 10.0 - - + +
254D TYR* 3.4 26.5 + - - +
283D LYS* 2.7 38.4 + - - -
285H ALA 2.8 17.9 + - - +
286H ALA* 3.5 5.8 - - - +
288H ALA* 1.3 75.9 - - - +
290H ALA* 1.3 57.3 + - - +
292H GLY* 2.9 19.1 + - - -
293H LEU 3.8 3.4 - - - +
318H PRO* 3.9 20.6 - - - +
319H ASN* 3.4 19.4 - - + +
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 3.9 22.6 - - + +
254D TYR* 3.4 26.5 - - - -
257D TYR* 3.6 36.9 - - + +
287D VAL* 4.1 9.2 - - + -
229E SER* 4.6 3.5 + - - -
286H ALA 2.9 13.4 + - - +
287H VAL 3.5 9.0 - - - +
289H GLU* 1.3 77.5 - - - +
291H ALA* 1.3 58.7 + - - +
292H GLY 3.2 0.2 - - - -
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Residues in contact with ALA 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D TYR* 3.6 21.3 - - + +
229E SER* 3.9 7.3 + - - -
260H CYS* 3.6 34.1 - - + -
263H ARG* 2.8 38.0 + - - +
287H VAL 3.1 6.6 + - - +
288H ALA 3.0 8.5 + - - +
290H ALA* 1.3 76.5 - - - +
292H GLY* 1.3 59.8 + - - +
293H LEU* 3.3 4.1 + - + +
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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