Contacts of the helix formed by residues 277 - 291 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A SER* 3.6 15.0 - - - +
110A ASP* 3.6 7.2 - - - -
111A MSE 5.6 0.2 - - - -
272A PRO* 2.9 22.6 + - - +
275A ILE* 3.5 1.9 - - - +
276A GLY* 1.3 81.2 - - - +
278A ILE* 1.3 64.5 + - - -
280A PRO* 3.5 3.8 - - - -
281A MSE 3.3 26.7 + - - +
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 2.7 12.1 + - - +
111A MSE 4.0 27.6 - - + -
114A TRP* 3.9 28.0 - - + -
125A VAL* 4.4 7.9 - - + -
129A LEU* 3.8 29.8 - - + -
272A PRO* 5.5 0.4 - - + -
277A GLY* 1.3 69.8 - - - -
279A GLN* 1.3 68.0 + - - +
281A MSE 3.1 19.6 + - - +
282A MSE 3.4 7.3 + - - +
309A ALA* 4.5 3.8 - - + +
313A ILE* 3.8 31.4 - - + -
356A LEU* 3.9 25.1 - - + -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.0 5.9 - - - +
80A ALA* 3.7 25.0 - - - +
110A ASP* 3.1 6.1 + - - +
114A TRP* 3.5 32.8 + - + +
129A LEU* 5.5 4.0 - - + +
278A ILE* 1.3 81.1 - - - +
280A PRO* 1.3 70.3 - - + +
282A MSE 3.0 28.7 + - + +
283A LYS* 3.4 18.0 + - + +
129B LEU 3.1 30.1 + - - -
130B GLY* 3.9 1.0 - - - -
282B MSE 5.3 4.8 - - - +
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Residues in contact with PRO 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 3.8 6.5 - - - +
275A ILE* 3.3 40.1 - - + +
276A GLY* 3.6 18.8 - - - +
277A GLY* 3.5 13.7 - - - -
278A ILE 3.8 0.2 - - - +
279A GLN* 1.3 96.1 - - + +
281A MSE 1.3 55.8 + - - +
283A LYS* 3.1 17.8 + - + +
284A ALA 2.9 23.7 + - - -
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Residues in contact with MSE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.2 35.9 - - + +
271A GLY* 3.6 15.9 - - - -
272A PRO* 4.0 8.1 - - + -
275A ILE* 3.5 19.3 - - + +
277A GLY 3.3 16.1 + - - +
278A ILE 3.1 9.9 + - - +
280A PRO* 1.3 77.6 - - - +
282A MSE 1.3 59.4 + - - +
284A ALA* 3.2 4.5 + - - +
285A ALA* 2.8 31.5 + - - +
295A ILE* 3.8 24.2 - - + -
297A ILE* 4.4 9.0 - - + -
313A ILE* 3.6 34.5 - - + -
317A ILE* 4.3 4.4 - - + +
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Residues in contact with MSE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.2 24.9 - - + +
278A ILE 3.8 10.5 - - - +
279A GLN* 3.0 19.5 + - + +
281A MSE 1.3 77.2 - - - +
283A LYS* 1.3 59.9 + - + +
285A ALA* 3.4 5.5 + - - +
286A ALA* 3.0 26.5 + - - +
313A ILE* 3.2 44.0 - - + +
316A ALA* 3.9 26.7 - - + +
317A ILE* 3.5 21.8 - - + -
283B LYS* 5.6 1.6 - - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.7 16.7 - - + +
279A GLN* 3.6 22.9 - - + +
280A PRO* 3.1 15.2 + - + +
282A MSE 1.3 76.1 - - + +
284A ALA* 1.3 65.3 + - - +
286A ALA* 3.1 5.3 + - - +
287A VAL* 3.1 25.8 + - - +
282B MSE 5.7 0.4 - - - +
286B ALA* 3.8 27.8 - - + +
289B GLU* 2.8 36.8 + - - -
318B PRO* 4.5 11.2 - - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.8 10.2 - - + +
256A VAL* 3.8 23.3 - - + +
270A ILE* 4.6 13.7 - - + -
275A ILE* 4.1 20.4 - - + -
280A PRO 2.9 12.7 + - - +
281A MSE 3.2 10.7 + - - +
283A LYS* 1.3 75.0 - - - +
285A ALA* 1.3 60.9 + - - +
287A VAL* 3.3 3.2 + - - +
288A ALA* 3.1 23.4 + - - +
295A ILE* 4.2 2.6 - - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A MSE 2.8 17.0 + - - +
282A MSE 3.6 6.5 - - - +
284A ALA* 1.3 78.4 - - - +
286A ALA* 1.3 56.8 + - - +
288A ALA 3.4 0.3 + - - -
289A GLU* 2.8 27.5 + - - +
295A ILE* 3.8 19.2 - - + +
317A ILE* 3.9 29.2 - - + -
318A PRO* 5.6 2.0 - - + -
319A ASN* 3.2 18.5 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A MSE 3.0 13.7 + - - +
283A LYS* 3.1 12.1 + - - +
285A ALA* 1.3 73.8 - - - +
287A VAL* 1.3 65.7 + - - +
289A GLU* 3.4 12.3 + - - +
290A ALA* 3.0 23.7 + - - +
253B LEU* 3.9 4.8 - - + +
283B LYS* 3.9 46.4 - - + +
286B ALA* 4.8 1.1 - - + -
287B VAL* 4.2 3.6 - - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.8 18.8 - - + -
256A VAL* 4.0 10.8 - - + -
257A TYR* 3.9 38.1 - - + -
260A CYS* 4.1 7.4 - - + -
283A LYS 3.1 14.5 + - - +
284A ALA 3.7 6.3 - - - +
285A ALA 3.3 0.2 - - - -
286A ALA* 1.3 76.8 - - - +
288A ALA* 1.3 64.0 + - - +
290A ALA* 3.1 6.1 + - - +
291A ALA* 3.1 19.8 + - - +
257B TYR* 4.8 5.0 - - + -
286B ALA 4.3 1.3 - - - +
287B VAL* 4.1 22.2 - - + +
290B ALA* 4.1 15.3 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 4.5 0.2 - - - +
260A CYS* 3.9 16.8 - - - -
268A ILE* 4.7 6.5 - - + -
284A ALA 3.1 17.3 + - - +
285A ALA 3.7 4.3 - - - +
287A VAL* 1.3 76.9 - - - +
289A GLU* 1.3 61.1 + - - +
291A ALA* 2.9 9.2 + - - +
293A LEU* 2.8 44.2 + - + +
294A LYS 4.8 0.4 - - - +
295A ILE* 3.8 21.5 - - + -
319A ASN* 3.9 0.9 - - - +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ALA 2.8 16.9 + - - +
286A ALA* 3.6 5.6 - - - +
287A VAL 3.2 0.2 - - - -
288A ALA* 1.3 76.1 - - - +
290A ALA* 1.3 57.4 + - - +
292A GLY* 2.9 19.3 + - - -
293A LEU 3.8 3.1 - - - +
318A PRO* 4.0 20.0 - - - +
319A ASN* 3.4 20.0 - - + +
253B LEU* 4.2 9.4 - - + -
254B TYR* 3.5 26.2 + - - +
283B LYS* 2.7 38.1 + - - -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ALA 3.0 14.6 + - - +
287A VAL 3.1 8.5 + - - +
289A GLU* 1.3 76.5 - - - +
291A ALA* 1.3 58.6 + - - +
292A GLY 3.3 0.4 - - - -
253B LEU* 3.8 22.2 - - + +
254B TYR* 3.4 26.1 - - - -
257B TYR* 3.6 38.6 - - + +
287B VAL* 4.3 7.2 - - + -
229F SER* 4.6 4.2 + - - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A CYS* 3.5 37.5 - - + -
263A ARG* 2.8 38.0 + - - +
287A VAL 3.1 4.4 + - - +
288A ALA 2.9 8.9 + - - +
290A ALA* 1.3 76.5 - - - +
292A GLY* 1.3 58.5 + - - +
293A LEU* 3.3 4.2 + - + +
257B TYR* 3.7 20.2 - - + +
229F SER* 3.8 7.9 + - - -
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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