Contacts of the helix formed by residues 277 - 291 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F SER* 3.7 10.9 - - - +
110F ASP* 3.4 12.3 - - - -
111F MSE 5.9 0.2 - - - -
272F PRO* 2.9 23.7 + - - +
275F ILE* 3.8 0.7 - - - +
276F GLY* 1.3 80.2 - - - +
278F ILE* 1.3 61.6 + - - -
279F GLN 3.6 0.7 - - - -
280F PRO* 3.7 2.7 - - - -
281F MSE 3.2 29.8 + - - +
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Residues in contact with ILE 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ASP* 2.6 12.3 + - - +
111F MSE 4.0 27.4 - - + -
114F TRP* 4.1 21.1 - - + -
125F VAL* 4.3 9.2 - - + -
129F LEU* 3.7 29.4 - - + -
272F PRO* 5.4 1.1 - - + -
277F GLY* 1.3 71.6 - - - -
279F GLN* 1.3 67.1 + - - +
281F MSE 3.2 13.3 + - - +
282F MSE 3.3 13.3 + - - +
309F ALA* 4.4 8.3 - - + +
312F HIS* 6.0 0.2 - - + -
313F ILE* 3.8 30.1 - - + -
356F LEU* 3.9 27.1 - - + -
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Residues in contact with GLN 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU 3.1 28.7 + - - -
130C GLY* 3.6 7.8 - - - -
79F VAL* 4.2 2.1 - - - +
80F ALA* 3.3 29.8 + - - +
110F ASP* 3.1 5.2 + - - +
114F TRP* 3.7 32.1 - - + +
129F LEU* 5.5 3.3 - - + +
278F ILE* 1.3 80.7 - - - +
280F PRO* 1.3 69.7 - - + +
282F MSE 3.0 27.8 + - + +
283F LYS* 3.3 18.4 + - + +
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Residues in contact with PRO 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ILE* 6.5 0.7 - - + -
110F ASP* 3.9 6.3 - - - +
275F ILE* 3.3 40.6 - - + +
276F GLY* 3.6 17.3 - - - +
277F GLY 3.7 9.0 - - - -
278F ILE 3.6 3.1 - - - +
279F GLN* 1.3 96.8 - - + +
281F MSE 1.3 54.0 - - - +
283F LYS* 3.1 17.4 + - + +
284F ALA 2.9 23.6 + - - -
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Residues in contact with MSE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F ILE* 3.2 35.7 - - + +
271F GLY* 3.7 20.9 - - - +
272F PRO* 4.0 8.3 - - + -
275F ILE* 3.6 12.8 - - + -
277F GLY 3.2 20.1 + - - +
278F ILE 3.2 10.0 + - - +
279F GLN 3.2 0.4 - - - -
280F PRO* 1.3 75.8 - - - +
282F MSE 1.3 63.0 + - - +
284F ALA* 3.3 4.5 + - + +
285F ALA* 2.8 30.5 + - - +
295F ILE* 4.0 22.0 - - + -
297F ILE* 4.2 9.6 - - + -
313F ILE* 3.8 34.3 - - + -
317F ILE* 4.3 5.4 - - + +
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Residues in contact with MSE 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LYS* 5.7 1.0 - - - +
129F LEU* 4.3 24.9 - - + +
278F ILE 3.6 13.9 - - - +
279F GLN* 3.0 16.2 + - + +
281F MSE 1.3 78.4 - - - +
283F LYS* 1.3 57.4 + - + +
285F ALA* 3.4 5.8 + - - +
286F ALA* 3.0 27.5 + - - +
313F ILE* 3.3 52.3 - - + +
316F ALA* 3.9 26.2 - - + +
317F ILE* 3.5 14.8 - - + -
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Residues in contact with LYS 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C MSE 5.7 1.1 - - - +
286C ALA* 3.9 26.2 - - + +
289C GLU* 2.7 37.6 + - - -
318C PRO* 4.4 12.4 - - - +
253F LEU* 3.9 18.5 - - + +
279F GLN* 3.7 22.7 - - + +
280F PRO* 3.1 17.2 + - + +
282F MSE 1.3 76.3 - - + +
284F ALA* 1.3 64.4 + - - +
286F ALA* 3.1 6.2 + - - +
287F VAL* 3.1 25.3 + - - +
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Residues in contact with ALA 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F LEU* 4.0 9.1 - - - +
256F VAL* 3.9 21.8 - - + +
270F ILE* 4.7 13.2 - - + -
275F ILE* 3.3 29.2 - - + -
280F PRO 2.9 5.9 + - - -
281F MSE 3.3 9.6 + - - +
283F LYS* 1.3 76.6 - - - +
285F ALA* 1.3 63.1 + - - +
287F VAL* 3.3 4.2 + - - +
288F ALA* 3.0 24.2 + - - +
295F ILE* 4.7 3.1 - - + -
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Residues in contact with ALA 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F MSE 2.8 17.1 + - - +
282F MSE 3.6 5.6 - - - +
283F LYS 3.2 0.2 - - - -
284F ALA* 1.3 77.6 - - - +
286F ALA* 1.3 57.8 + - - +
288F ALA 3.4 0.2 + - - -
289F GLU* 2.8 27.6 + - - +
295F ILE* 3.8 14.6 - - + +
317F ILE* 3.8 39.3 - - + -
318F PRO* 5.6 2.5 - - + -
319F ASN* 3.1 13.3 + - - +
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Residues in contact with ALA 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.0 3.9 - - + +
283C LYS* 3.8 45.5 - - + +
286C ALA* 4.7 2.2 - - + -
287C VAL* 4.3 2.9 - - + +
282F MSE 3.0 14.2 + - - +
283F LYS* 3.1 13.0 + - - +
285F ALA* 1.3 73.2 - - - +
287F VAL* 1.3 65.8 + - - +
289F GLU* 3.3 11.7 + - - +
290F ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 4.8 4.7 - - + -
286C ALA 4.2 1.6 - - - +
287C VAL* 4.1 23.6 - - + +
290C ALA* 4.1 13.9 - - + -
253F LEU* 3.9 19.5 - - + -
256F VAL* 3.9 11.2 - - + -
257F TYR* 3.9 37.9 - - + +
260F CYS* 4.0 7.2 - - + -
283F LYS 3.1 14.0 + - - +
284F ALA 3.6 6.3 - - - +
286F ALA* 1.3 76.5 - - - +
288F ALA* 1.3 62.8 + - - +
290F ALA* 3.2 5.9 + - - +
291F ALA* 3.2 20.3 + - - +
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Residues in contact with ALA 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F VAL* 4.9 0.4 - - + -
260F CYS* 3.9 15.0 - - - -
268F ILE* 4.8 5.4 - - + -
284F ALA 3.0 16.5 + - - +
285F ALA 3.6 3.8 - - - +
287F VAL* 1.3 75.3 - - - +
289F GLU* 1.3 62.6 + - - +
291F ALA* 3.0 9.5 + - - +
293F LEU* 2.8 43.6 + - + +
294F LYS 4.7 0.7 - - - +
295F ILE* 3.7 23.6 - - + -
319F ASN* 3.9 1.6 - - - +
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Residues in contact with GLU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 4.1 11.7 - - + +
254C TYR* 3.5 25.4 + - - +
283C LYS* 2.8 36.7 + - - -
285F ALA 2.8 17.1 + - - +
286F ALA* 3.5 7.4 - - - +
287F VAL 3.2 0.2 - - - -
288F ALA* 1.3 76.1 - - - +
290F ALA* 1.3 57.7 + - - +
292F GLY* 2.9 19.4 + - - -
293F LEU 3.8 3.4 - - - +
318F PRO* 4.0 19.9 - - - +
319F ASN* 3.4 19.7 - - + +
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 3.7 25.1 - - + +
254C TYR* 3.3 27.0 - - - -
257C TYR* 3.6 35.8 - - + +
287C VAL* 4.2 8.7 - - + -
286F ALA 2.9 17.6 + - - +
287F VAL 3.2 5.6 + - - +
289F GLU* 1.3 75.2 - - - +
291F ALA* 1.3 58.1 + - - +
292F GLY 3.2 0.4 - - - -
229H SER* 4.5 3.6 + - - -
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Residues in contact with ALA 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C TYR* 3.7 20.2 - - + +
260F CYS* 3.6 36.8 - - + -
263F ARG* 2.7 34.8 + - - +
287F VAL 3.2 5.3 + - - +
288F ALA 3.0 9.0 + - - +
290F ALA* 1.3 76.2 - - - +
292F GLY* 1.3 61.7 + - - +
293F LEU* 3.4 3.7 + - + +
229H SER* 3.7 9.1 + - - -
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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