Contacts of the helix formed by residues 277 - 291 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E SER* 3.6 11.1 - - - +
110E ASP* 3.4 13.5 - - - -
111E MSE 5.9 0.2 - - - -
272E PRO* 3.0 21.3 + - - +
275E ILE* 3.5 0.9 - - - +
276E GLY* 1.3 79.8 - - - +
278E ILE* 1.3 63.0 + - - -
280E PRO* 3.4 3.4 - - - -
281E MSE 3.2 30.5 + - - +
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Residues in contact with ILE 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ASP* 2.6 13.0 + - - +
111E MSE 3.6 34.5 - - + -
114E TRP* 3.8 22.4 - - + -
125E VAL* 4.3 8.3 - - + -
129E LEU* 3.7 32.1 - - + -
272E PRO* 5.6 0.7 - - + -
277E GLY* 1.3 70.9 - - - -
279E GLN* 1.3 66.7 + - - +
281E MSE 3.1 17.5 + - - +
282E MSE 3.4 9.6 + - + +
309E ALA* 4.6 6.7 - - + +
313E ILE* 3.8 28.9 - - + -
356E LEU* 3.9 20.4 - - + -
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Residues in contact with GLN 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E VAL* 4.2 4.5 - - - +
80E ALA* 3.6 31.1 - - - +
110E ASP* 3.1 5.3 + - - +
114E TRP* 3.6 34.3 - - + +
129E LEU* 5.4 3.6 - - + -
278E ILE* 1.3 77.9 - - - +
280E PRO* 1.3 74.9 - - + +
282E MSE 2.9 28.3 + - + +
283E LYS* 3.3 25.4 + - + +
129G LEU 4.0 16.3 + - - -
130G GLY* 3.8 3.3 - - - -
133G HIS* 5.7 1.4 - - - -
282G MSE 5.5 6.3 - - - +
316G ALA 5.8 0.6 + - - -
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Residues in contact with PRO 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 3.8 6.7 - - - +
253E LEU* 5.3 0.3 - - - +
275E ILE* 3.3 38.1 - - + +
276E GLY* 3.5 17.9 - - - +
277E GLY* 3.4 14.1 - - - -
278E ILE 3.7 0.4 - - - +
279E GLN* 1.3 95.0 - - + +
281E MSE 1.3 60.8 + - - +
283E LYS* 3.0 17.8 + - + +
284E ALA 2.9 18.9 + - - -
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Residues in contact with MSE 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ILE* 3.2 35.0 - - + +
271E GLY* 3.6 22.2 - - - -
272E PRO* 4.0 4.7 - - + -
275E ILE* 3.4 13.2 - - + -
277E GLY 3.2 18.6 + - - +
278E ILE 3.1 11.1 + - - +
279E GLN 3.1 0.6 - - - -
280E PRO* 1.3 80.4 - - - +
282E MSE 1.3 57.9 + - - +
284E ALA* 3.3 5.4 + - + +
285E ALA* 2.9 28.8 + - - +
295E ILE* 4.0 21.5 - - + +
297E ILE* 4.3 8.7 - - + -
313E ILE* 3.9 39.5 - - + -
317E ILE* 4.3 6.9 - - + +
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Residues in contact with MSE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E LEU* 4.3 25.6 - - + +
278E ILE 3.4 15.0 + - - +
279E GLN* 2.9 17.3 + - + +
281E MSE 1.3 77.3 - - - +
283E LYS* 1.3 60.0 + - + +
285E ALA* 3.4 4.9 + - - +
286E ALA* 3.0 26.9 + - - +
313E ILE* 3.4 44.9 - - + +
316E ALA* 4.0 26.0 - - + +
317E ILE* 3.5 21.1 - - + -
283G LYS* 5.6 0.7 - - - +
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Residues in contact with LYS 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E LEU* 3.9 18.3 - - + +
279E GLN* 3.7 29.9 - - + +
280E PRO* 3.0 14.9 + - + +
282E MSE 1.3 76.3 - - + +
284E ALA* 1.3 63.9 + - - +
286E ALA* 3.2 4.3 + - - +
287E VAL* 3.1 26.9 + - - +
282G MSE 5.6 1.6 - - - +
286G ALA* 3.9 27.4 - - + +
289G GLU* 2.8 37.1 + - - -
318G PRO* 4.3 13.3 - - - +
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Residues in contact with ALA 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E LEU* 4.0 10.9 - - + +
256E VAL* 3.9 21.0 - - + +
270E ILE* 4.7 14.4 - - + -
275E ILE* 4.2 20.4 - - + -
280E PRO 2.9 12.4 + - - +
281E MSE 3.6 11.2 - - - +
283E LYS* 1.3 74.5 - - - +
285E ALA* 1.3 63.2 + - - +
287E VAL* 3.2 4.7 + - - +
288E ALA* 3.0 21.8 + - - +
295E ILE* 4.6 3.6 - - + -
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Residues in contact with ALA 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E MSE 2.9 17.2 + - - +
282E MSE 3.6 5.8 - - - +
284E ALA* 1.3 77.2 - - - +
286E ALA* 1.3 56.0 + - - +
288E ALA 3.4 0.2 + - - -
289E GLU* 2.8 26.5 + - - +
295E ILE* 3.8 16.1 - - + +
317E ILE* 3.8 39.3 - - + -
318E PRO* 5.6 2.0 - - + -
319E ASN* 3.3 12.6 + - - +
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Residues in contact with ALA 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E MSE 3.0 15.4 + - - +
283E LYS* 3.2 11.6 + - - +
285E ALA* 1.3 77.4 - - - +
287E VAL* 1.3 62.6 + - - +
289E GLU* 3.3 12.9 + - - +
290E ALA* 3.0 23.2 + - - +
253G LEU* 4.0 4.3 - - - +
283G LYS* 3.9 45.3 - - + +
286G ALA* 4.6 2.5 - - + -
287G VAL* 4.4 2.4 - - + +
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Residues in contact with VAL 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E LEU* 3.7 19.5 - - + -
256E VAL* 4.3 4.7 - - + -
257E TYR* 4.0 41.1 - - + +
260E CYS* 4.2 8.7 - - + -
283E LYS 3.1 15.1 + - - +
284E ALA 3.7 6.1 - - - +
286E ALA* 1.3 77.3 - - - +
288E ALA* 1.3 61.3 + - - +
290E ALA* 3.3 4.7 + - - +
291E ALA* 3.2 20.1 + - - +
257G TYR* 4.7 5.0 - - + -
286G ALA* 4.2 3.6 - - + +
287G VAL* 4.1 31.0 - - + +
290G ALA* 4.3 4.0 - - + -
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Residues in contact with ALA 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E VAL* 4.5 0.6 - - + +
260E CYS* 3.9 15.5 - - - -
268E ILE* 4.7 5.6 - - + -
284E ALA 3.0 16.2 + - - +
285E ALA 3.7 4.0 - - - +
287E VAL* 1.3 75.5 - - - +
289E GLU* 1.3 61.8 + - - +
291E ALA* 3.1 8.5 + - - +
293E LEU* 2.8 44.9 + - + +
294E LYS 4.7 0.9 - - - +
295E ILE* 3.8 22.7 - - + -
319E ASN* 3.9 1.3 - - - +
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Residues in contact with GLU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E ALA 2.8 16.8 + - - +
286E ALA* 3.5 5.3 - - - +
287E VAL 3.2 0.2 - - - -
288E ALA* 1.3 77.4 - - - +
290E ALA* 1.3 57.9 + - - +
292E GLY* 2.9 17.8 + - - -
293E LEU 3.8 3.4 - - - +
318E PRO* 4.1 18.2 - - - +
319E ASN* 3.4 19.7 - - + +
253G LEU* 4.0 10.0 - - + +
254G TYR* 3.4 26.6 + - - +
283G LYS* 2.6 40.5 + - - -
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 4.5 4.0 + - - -
286E ALA 3.0 13.0 + - - +
287E VAL 3.3 9.8 + - - +
289E GLU* 1.3 76.2 - - - +
291E ALA* 1.3 57.6 + - - +
292E GLY 3.3 0.6 + - - -
253G LEU* 3.9 22.0 - - + +
254G TYR* 3.3 26.4 - - - -
257G TYR* 3.7 37.2 - - + +
287G VAL* 4.1 9.9 - - + -
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Residues in contact with ALA 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 3.8 5.9 + - - -
232A ALA* 3.9 0.2 - - - +
260E CYS* 3.5 37.9 - - + -
263E ARG* 2.5 45.2 + - - +
287E VAL 3.2 5.5 + - - +
288E ALA 3.1 8.8 + - - +
290E ALA* 1.3 76.0 - - - +
292E GLY* 1.3 58.7 + - - +
293E LEU* 3.3 4.8 + - + +
257G TYR* 3.7 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
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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