Contacts of the helix formed by residues 303 - 317 (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 THR 303 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F LEU* 3.5 31.4 - - + -
32F PHE* 6.4 0.2 - - + -
34F VAL* 3.9 12.3 - - + -
50F GLU* 2.8 27.0 + - - +
302F THR* 1.3 85.1 + - - +
304F GLY* 1.3 67.0 + - - +
305F ILE* 3.0 17.0 + - - +
306F THR* 3.2 12.3 + - - -
307F THR* 3.3 12.7 + - - -
328F TRP* 4.1 6.1 + - - +
331F VAL* 4.9 3.1 - - + -
334F ASP* 3.4 13.0 - - - -
335F ILE* 3.6 11.3 - - + +
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Residues in contact with GLY 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F THR* 1.3 74.5 + - - +
305F ILE* 1.3 65.0 + - - +
307F THR* 3.4 6.9 - - - -
308F CYS* 3.0 28.9 + - - -
328F TRP* 3.9 1.3 - - - +
334F ASP* 2.8 28.4 + - - -
336F VAL* 3.4 12.6 - - - -
341F LEU* 3.5 11.7 - - - -
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Residues in contact with ILE 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 3.4 33.0 - - + -
48F ILE* 3.9 18.8 - - + +
49F GLY* 3.9 18.4 - - - +
50F GLU* 3.5 16.6 - - + +
111F MSE 4.2 4.5 - - - -
303F THR* 3.0 11.4 + - - +
304F GLY* 1.3 78.8 - - - +
306F THR* 1.3 63.1 + - - +
308F CYS* 3.3 3.8 + - - +
309F ALA* 3.1 19.1 + - - +
335F ILE* 3.8 12.6 - - + -
336F VAL* 3.5 2.3 - - + +
356F LEU* 4.8 0.4 - - + +
358F PHE* 3.9 27.6 - - + -
360F LEU* 3.9 23.8 - - + -
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Residues in contact with THR 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F GLU* 2.5 36.2 + - - +
111F MSE 4.0 16.0 - - + +
272F PRO* 4.8 2.0 - - + -
299F SER* 4.5 2.0 - - - +
300F SER* 4.2 7.0 - - - +
302F THR* 3.3 24.0 + - - +
303F THR 3.2 2.6 + - - -
305F ILE* 1.3 73.3 - - - +
307F THR* 1.3 56.9 + - - +
309F ALA* 3.1 7.3 + - - +
310F GLU* 2.7 63.4 + - + +
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Residues in contact with THR 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F TYR* 4.6 5.3 + - + +
299F SER* 5.7 0.5 + - - -
303F THR 3.3 6.0 + - - -
304F GLY* 3.2 11.4 + - - -
306F THR* 1.3 78.4 - - - +
308F CYS* 1.3 57.3 + - - +
310F GLU* 3.4 10.6 + - - +
311F HIS* 2.8 28.7 + - + +
326F ILE* 4.0 20.1 - - + +
327F MSE 4.8 1.6 + - - -
328F TRP* 3.3 45.9 + - + +
341F LEU* 4.3 15.9 - - + -
348F LEU* 4.8 7.6 - - + -
351F PHE* 5.6 0.2 - - + -
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Residues in contact with CYS 308 (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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304F GLY 3.0 17.7 + - - -
305F ILE 3.6 7.4 - - - +
306F THR 3.2 0.2 - - - -
307F THR* 1.3 73.3 - - - +
309F ALA* 1.3 66.8 + - - +
311F HIS* 3.1 7.4 + - - +
312F HIS* 3.1 31.0 + - - -
336F VAL* 4.8 1.6 - - - -
339F PRO* 4.6 2.7 - - - -
341F LEU* 3.8 23.1 - - - -
351F PHE* 4.0 11.7 - - + -
356F LEU* 3.7 17.7 - - + +
358F PHE* 3.7 33.9 - - + -
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Residues in contact with ALA 309 (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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111F MSE 3.6 42.2 - - + -
278F ILE* 4.4 7.5 - - + +
305F ILE 3.1 11.0 + - - +
306F THR 3.1 6.9 + - - +
308F CYS* 1.3 78.1 - - - +
310F GLU* 1.3 62.9 + - + +
311F HIS 3.2 0.2 + - - -
312F HIS* 3.3 2.3 + - - +
313F ILE* 3.1 30.5 + - + +
356F LEU* 3.8 15.9 - - + +
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Residues in contact with GLU 310 (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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137F VAL* 5.4 0.7 - - - +
139F TYR* 4.9 5.7 + - + +
272F PRO* 3.6 25.2 - - + +
273F ARG* 6.1 0.2 - - - +
297F ILE* 3.2 30.1 - - + +
298F HIS 3.2 19.4 - - - +
299F SER* 2.8 32.0 + - - -
300F SER* 4.8 0.7 + - - -
306F THR* 2.7 43.1 + - + +
307F THR* 3.8 7.5 - - - +
309F ALA* 1.3 71.9 - - - +
311F HIS* 1.3 57.1 + - - +
313F ILE* 4.1 7.9 - - - -
314F GLY* 3.0 22.2 + - - -
325F GLN 4.3 7.6 - - - +
326F ILE* 5.3 0.9 - - - -
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Residues in contact with HIS 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F VAL* 3.6 17.7 - - + +
139F TYR* 3.1 26.7 + - - +
307F THR* 2.8 19.3 + - + +
308F CYS* 3.3 10.3 - - - +
309F ALA 3.1 0.4 - - - -
310F GLU* 1.3 74.9 - - - +
312F HIS* 1.3 67.9 + - - +
314F GLY* 3.2 2.8 + - - -
315F LEU* 3.0 39.4 + - + +
348F LEU* 3.2 34.1 + - + +
349F ASP 3.8 2.0 + - - -
350F ALA* 3.5 8.9 - - - -
351F PHE* 3.0 53.7 + + + +
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Residues in contact with HIS 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PRO* 3.7 15.7 - - + -
125F VAL* 4.0 21.5 - - + -
126F HIS* 2.9 43.6 + - - +
129F LEU* 4.7 2.0 - - - +
308F CYS* 3.1 23.7 + - - +
309F ALA 4.0 3.4 - - - +
311F HIS* 1.3 80.4 - - - +
313F ILE* 1.3 66.9 + - + +
315F LEU* 3.4 6.3 + - - +
316F ALA* 3.1 24.8 + - - +
351F PHE* 3.6 27.2 - + + +
353F LYS 4.8 0.9 - - - -
355F GLY 3.8 3.8 - - - -
356F LEU* 2.9 40.9 + - + -
357F GLY* 4.6 0.2 - - - -
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Residues in contact with ILE 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F LEU* 5.2 0.2 - - - -
272F PRO* 4.1 17.5 - - + -
278F ILE* 3.8 45.3 - - + -
281F MSE 3.8 28.7 - - + -
282F MSE 3.3 23.5 - - + +
297F ILE* 4.3 4.7 - - + -
309F ALA 3.1 23.3 + - - +
310F GLU* 3.7 9.4 - - - +
311F HIS 3.2 0.2 - - - -
312F HIS* 1.3 77.1 - - - +
314F GLY* 1.3 64.5 + - - +
316F ALA* 3.3 0.6 + - - -
317F ILE* 3.2 36.4 + - + +
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Residues in contact with GLY 314 (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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134F ARG* 2.8 27.1 + - - -
137F VAL* 4.3 6.1 - - - -
297F ILE* 3.5 13.7 - - - -
310F GLU 3.0 11.7 + - - -
311F HIS 3.2 4.2 + - - -
313F ILE* 1.3 77.7 - - - +
315F LEU* 1.3 53.3 + - - +
317F ILE* 3.3 6.6 + - - +
320F LEU* 3.2 28.6 - - - +
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Residues in contact with LEU 315 (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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126F HIS* 3.4 35.7 - - + +
132F ALA* 3.3 11.2 - - + -
133F HIS* 2.7 29.7 + - - -
134F ARG* 3.5 35.4 + - + +
136F ALA 4.5 0.7 - - - -
137F VAL* 3.6 22.6 - - + +
311F HIS* 3.0 39.8 + - + +
312F HIS* 3.8 7.9 - - - +
314F GLY* 1.3 74.8 - - - +
316F ALA* 1.3 59.7 + - - +
317F ILE 3.4 0.7 + - - -
350F ALA* 3.8 21.5 - - + -
351F PHE 4.4 0.2 - - - +
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Residues in contact with ALA 316 (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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126F HIS* 4.3 6.0 - - + +
129F LEU* 3.8 36.9 - - + +
131F GLY 3.7 14.1 - - - +
133F HIS* 3.4 17.8 + - - -
282F MSE 3.9 14.7 - - - +
312F HIS 3.1 16.9 + - - +
313F ILE 3.8 3.8 - - - +
314F GLY 3.3 0.2 - - - -
315F LEU* 1.3 75.7 - - - +
317F ILE* 1.3 59.7 + - - +
318F PRO* 3.5 4.0 - - - +
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F HIS* 4.0 1.1 - - - -
134F ARG* 2.7 29.6 + - - -
281F MSE 4.3 14.6 - - + +
282F MSE 3.5 16.6 - - + -
285F ALA* 3.8 25.1 - - + -
295F ILE* 4.5 4.9 - - + -
313F ILE* 3.2 36.6 + - + +
314F GLY 3.3 4.6 + - - +
315F LEU 3.3 1.0 - - - -
316F ALA* 1.3 77.4 - - - +
318F PRO* 1.3 63.1 - - + +
319F ASN* 3.3 38.4 - - - +
320F LEU* 3.7 19.1 - - + +
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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
------------------------------------------------------------
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