Contacts of the helix formed by residues 277 - 291 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G SER* 3.7 13.4 - - - +
110G ASP* 3.5 8.7 - - - -
111G MSE 5.8 0.2 - - - -
272G PRO* 2.9 23.3 + - - +
275G ILE* 3.5 1.0 - - - +
276G GLY* 1.3 80.1 - - - +
278G ILE* 1.3 63.4 + - - -
280G PRO* 3.6 2.2 - - - -
281G MSE 3.1 29.6 + - - +
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Residues in contact with ILE 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G ASP* 2.7 11.7 + - - +
111G MSE 4.0 26.5 - - + -
114G TRP* 4.1 21.1 - - + -
125G VAL* 4.3 7.4 - - + -
129G LEU* 3.7 33.0 - - + -
272G PRO* 5.4 0.4 - - + -
277G GLY* 1.3 70.6 - - - -
279G GLN* 1.3 68.0 + - - +
281G MSE 3.0 18.9 + - - +
282G MSE 3.4 6.9 + - - +
309G ALA* 4.4 9.2 - - + +
312G HIS* 5.9 0.7 - - + -
313G ILE* 3.7 31.9 - - + +
356G LEU* 4.1 25.8 - - + -
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Residues in contact with GLN 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E LEU 2.9 32.5 + - - -
130E GLY* 3.7 3.0 - - - -
79G VAL* 4.4 1.7 - - - +
80G ALA* 3.3 28.8 + - - +
110G ASP* 3.1 5.7 + - - +
114G TRP* 3.8 32.1 - - + +
129G LEU* 5.4 3.7 - - + +
278G ILE* 1.3 79.5 - - - +
280G PRO* 1.3 72.3 - - + +
282G MSE 2.9 29.2 + - + +
283G LYS* 3.4 16.9 + - + +
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Residues in contact with PRO 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ILE* 6.5 0.2 - - + -
110G ASP* 3.8 7.9 - - - +
253G LEU* 5.0 0.2 - - - +
275G ILE* 3.4 39.8 - - + +
276G GLY* 3.6 17.7 - - - +
277G GLY 3.6 9.2 - - - -
278G ILE 3.5 3.1 - - - -
279G GLN* 1.3 95.5 - - + +
281G MSE 1.3 55.8 + - - +
283G LYS* 3.1 16.8 + - + +
284G ALA 3.0 23.2 + - - -
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Residues in contact with MSE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.1 34.8 - - + +
271G GLY* 3.6 14.8 - - - -
272G PRO* 3.9 8.5 - - + -
275G ILE* 3.4 19.1 - - + -
277G GLY 3.1 18.3 + - - +
278G ILE 3.0 12.8 + - - +
280G PRO* 1.3 77.4 - - - +
282G MSE 1.3 57.8 + - - +
284G ALA* 3.4 4.3 + - + +
285G ALA* 2.9 28.8 + - - +
295G ILE* 3.9 23.1 - - + -
297G ILE* 4.4 7.9 - - + -
313G ILE* 3.7 34.3 - - + -
317G ILE* 4.2 8.0 - - + +
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Residues in contact with MSE 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E GLN* 5.5 6.1 - - - +
283E LYS* 5.6 1.2 - - - +
129G LEU* 4.1 32.8 - - + +
278G ILE 3.7 9.9 - - - +
279G GLN* 2.9 20.6 + - + +
281G MSE 1.3 77.4 - - - +
283G LYS* 1.3 59.0 + - + +
285G ALA* 3.4 5.4 + - + +
286G ALA* 3.0 27.9 + - - +
313G ILE* 4.6 5.2 - - - +
316G ALA* 3.1 48.2 - - + +
317G ILE* 4.1 16.4 - - + -
318G PRO* 5.1 4.3 - - + -
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Residues in contact with LYS 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E MSE 5.6 0.9 - - - +
286E ALA* 3.9 26.6 - - + +
289E GLU* 2.6 36.3 + - - -
318E PRO* 4.4 12.2 - - - +
253G LEU* 3.6 19.4 - - + +
279G GLN* 3.8 22.0 - - + +
280G PRO* 3.1 16.5 + - + +
282G MSE 1.3 77.2 - - + +
284G ALA* 1.3 65.2 + - - +
286G ALA* 3.3 4.4 + - - +
287G VAL* 3.1 26.9 + - - +
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Residues in contact with ALA 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G LEU* 3.7 9.3 - - - +
256G VAL* 3.9 22.8 - - + +
270G ILE* 4.6 14.4 - - + -
275G ILE* 4.2 20.4 - - + -
280G PRO 3.0 15.9 + - - +
281G MSE 3.7 7.4 - - + +
282G MSE 3.3 0.2 - - - -
283G LYS* 1.3 76.6 - - - +
285G ALA* 1.3 62.5 + - - +
287G VAL* 3.3 3.9 + - - +
288G ALA* 3.1 23.4 + - - +
295G ILE* 4.2 3.1 - - + +
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Residues in contact with ALA 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G MSE 2.9 19.4 + - - +
282G MSE 3.6 8.1 - - + +
284G ALA* 1.3 76.8 - - - +
286G ALA* 1.3 55.7 + - - +
288G ALA 3.4 0.5 + - - -
289G GLU* 2.8 27.0 + - - +
295G ILE* 3.7 15.0 - - + +
317G ILE* 3.7 39.5 - - + -
318G PRO* 5.7 1.6 - - + -
319G ASN* 3.1 12.4 + - - +
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Residues in contact with ALA 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E LEU* 4.1 4.4 - - + +
283E LYS* 3.9 45.8 - - + +
286E ALA* 4.6 1.8 - - + -
287E VAL* 4.2 2.8 - - + +
282G MSE 3.0 17.5 + - - +
283G LYS* 3.5 8.7 - - - +
284G ALA 3.3 0.2 - - - -
285G ALA* 1.3 73.9 - - - +
287G VAL* 1.3 65.6 + - - +
289G GLU* 3.3 12.3 + - - +
290G ALA* 3.0 23.7 + - - +
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Residues in contact with VAL 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E TYR* 4.8 5.1 - - + -
286E ALA 4.4 1.6 - - - +
287E VAL* 4.1 23.8 - - + +
290E ALA* 4.1 15.3 - - + -
253G LEU* 3.9 17.5 - - + +
256G VAL* 4.1 10.8 - - + -
257G TYR* 3.9 37.5 - - + -
260G CYS* 4.1 7.4 - - + -
283G LYS 3.1 14.7 + - - +
284G ALA 3.7 7.0 - - - +
285G ALA 3.3 0.2 - - - -
286G ALA* 1.3 75.6 - - - +
288G ALA* 1.3 64.7 + - - +
290G ALA* 3.2 5.7 + - - +
291G ALA* 3.1 20.3 + - - +
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Residues in contact with ALA 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G VAL* 4.5 1.1 - - + +
260G CYS* 3.9 16.6 - - - -
268G ILE* 4.7 5.6 - - + -
284G ALA 3.1 11.1 + - - +
285G ALA 3.6 7.2 - - - +
287G VAL* 1.3 78.5 - - - +
289G GLU* 1.3 61.4 + - - +
291G ALA* 3.0 9.2 + - - +
293G LEU* 2.8 44.7 + - + +
294G LYS 4.8 0.4 - - - +
295G ILE* 3.7 22.7 - - + -
319G ASN* 3.9 0.4 - - - +
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Residues in contact with GLU 289 (chain G).
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* 4.2 10.7 - - + +
254E TYR* 3.5 25.7 + - - +
283E LYS* 2.8 36.8 + - - -
285G ALA 2.8 16.9 + - - +
286G ALA* 3.5 5.9 - - - +
287G VAL 3.2 0.2 - - - -
288G ALA* 1.3 76.8 - - - +
290G ALA* 1.3 57.9 + - - +
292G GLY* 2.8 20.1 + - - -
293G LEU 3.8 3.1 - - - +
318G PRO* 3.8 19.2 - - - +
319G ASN* 3.4 20.8 - - + +
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Residues in contact with ALA 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D SER* 4.4 3.8 + - - -
253E LEU* 3.8 23.1 - - + +
254E TYR* 3.4 27.0 - - - -
257E TYR* 3.6 37.9 - - + +
287E VAL* 4.3 7.2 - - + -
286G ALA 3.0 12.4 + - - +
287G VAL 3.5 9.0 - - - +
289G GLU* 1.3 78.7 - - - +
291G ALA* 1.3 57.5 + - - +
292G GLY 3.2 0.4 + - - -
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Residues in contact with ALA 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D SER* 3.7 8.5 + - - -
232D ALA* 4.0 0.2 - - - +
257E TYR* 3.8 19.7 - - + +
260G CYS* 3.5 38.1 - - + -
263G ARG* 3.0 31.6 + - - +
287G VAL 3.1 5.9 + - - +
288G ALA 3.0 9.4 + - - +
290G ALA* 1.3 75.4 - - - +
292G GLY* 1.3 62.8 + - - +
293G LEU* 3.6 3.5 + - + -
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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