Contacts of the helix formed by residues 303 - 317 (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 THR 303 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU* 3.4 33.2 - - + -
32E PHE* 6.4 0.7 - - + -
34E VAL* 4.1 9.2 - - + -
50E GLU* 2.7 28.1 + - - +
302E THR* 1.3 83.1 + - - +
304E GLY* 1.3 66.0 + - - +
305E ILE* 3.1 9.2 + - - +
306E THR* 3.2 12.0 + - - -
307E THR* 3.3 12.6 + - - -
328E TRP* 4.2 5.2 + - - +
331E VAL* 4.8 3.6 - - + -
334E ASP* 3.3 13.0 - - - +
335E ILE* 3.5 21.7 - - + +
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Residues in contact with GLY 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E THR* 1.3 74.3 - - - +
305E ILE* 1.3 64.8 + - - +
306E THR 3.3 0.2 - - - -
307E THR* 3.2 6.6 + - - -
308E CYS* 2.9 28.1 + - - -
328E TRP* 4.0 1.1 - - - +
334E ASP* 2.9 27.4 + - - -
336E VAL* 3.5 10.5 - - - +
341E LEU* 3.4 16.2 - - - -
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 3.5 32.8 - - + -
48E ILE* 3.9 20.4 - - + +
49E GLY* 3.9 24.2 - - - +
50E GLU* 3.6 10.3 - - + +
111E MSE 4.1 6.1 - - - -
303E THR* 3.0 9.6 + - - +
304E GLY* 1.3 76.9 - - - +
306E THR* 1.3 63.8 + - - +
308E CYS* 3.1 6.6 + - - +
309E ALA* 3.1 19.1 + - - +
335E ILE* 3.8 14.1 - - + -
336E VAL* 3.6 7.1 - - + +
356E LEU* 4.6 0.8 - - + +
358E PHE* 3.9 32.0 - - + -
360E LEU* 4.1 8.7 - - + -
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Residues in contact with THR 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E GLU* 2.8 25.8 + - - +
111E MSE 4.1 15.9 - - + +
272E PRO* 4.7 2.9 - - + -
299E SER* 4.4 1.8 - - - +
300E SER* 4.2 7.2 - - - +
302E THR* 3.2 28.7 + - - +
303E THR 3.2 3.6 + - - -
305E ILE* 1.3 78.4 - - - +
307E THR* 1.3 57.6 + - - +
309E ALA* 3.0 7.4 + - - +
310E GLU* 2.8 60.5 + - + +
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Residues in contact with THR 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E TYR* 4.7 5.0 + - + +
299E SER* 5.7 0.9 + - - -
303E THR 3.3 6.4 + - - -
304E GLY* 3.2 12.5 + - - -
306E THR* 1.3 78.4 - - - +
308E CYS* 1.3 57.5 + - - +
310E GLU* 3.4 9.7 + - - +
311E HIS* 2.8 30.7 + - + +
326E ILE* 4.0 29.4 - - + +
327E MSE 4.8 1.7 + - - -
328E TRP* 3.4 33.7 + - + +
341E LEU* 4.1 17.0 - - + -
348E LEU* 4.9 7.4 - - + -
351E PHE* 5.6 0.2 - - + -
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Residues in contact with CYS 308 (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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304E GLY 2.9 18.3 + - - -
305E ILE 3.1 8.0 + - - +
307E THR* 1.3 73.8 - - - +
309E ALA* 1.3 65.4 + - - +
311E HIS* 3.5 5.3 - - - +
312E HIS* 3.1 32.1 + - + -
336E VAL* 4.9 0.7 - - - -
339E PRO* 4.7 3.1 - - - -
341E LEU* 4.0 22.9 - - - -
351E PHE* 4.4 9.4 - - - -
356E LEU* 3.4 22.4 - - + +
358E PHE* 3.7 33.9 - - + -
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Residues in contact with ALA 309 (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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111E MSE 3.7 42.6 - - + -
278E ILE* 4.6 7.0 - - + +
305E ILE 3.1 10.2 + - - +
306E THR 3.0 8.2 + - - +
308E CYS* 1.3 79.5 - - - +
310E GLU* 1.3 58.1 + - + +
312E HIS* 3.3 2.4 + - - +
313E ILE* 2.9 35.7 + - + +
356E LEU* 4.0 17.0 - - + +
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Residues in contact with GLU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E TYR* 5.0 5.4 - - + +
272E PRO* 3.5 29.5 - - + +
273E ARG* 6.1 0.3 - - - +
297E ILE* 3.0 32.3 - - + +
298E HIS 3.2 19.1 - - - +
299E SER* 2.8 30.3 + - - -
300E SER* 4.4 0.7 + - - -
306E THR* 2.8 40.9 + - - +
307E THR* 3.9 7.0 - - - +
309E ALA* 1.3 72.3 - - - +
311E HIS* 1.3 57.6 + - - +
313E ILE* 4.1 7.4 - - - -
314E GLY* 2.8 24.3 + - - -
325E GLN 4.6 5.4 - - - +
326E ILE* 5.4 0.9 - - - -
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Residues in contact with HIS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E VAL* 3.6 13.6 - - + +
139E TYR* 3.1 28.4 + - - +
307E THR* 2.8 18.6 + - + +
308E CYS* 3.5 9.4 - - - +
309E ALA 3.2 0.2 - - - -
310E GLU* 1.3 77.3 - - - +
312E HIS* 1.3 65.5 + - - +
314E GLY* 3.1 3.6 + - - -
315E LEU* 3.0 44.9 + - + +
348E LEU* 3.3 34.9 + - + +
349E ASP 3.7 3.0 + - - -
350E ALA* 3.5 3.8 - - - -
351E PHE* 3.2 54.7 + + + +
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Residues in contact with HIS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO* 4.0 5.4 - - + -
125E VAL* 3.9 21.5 - - + -
126E HIS* 2.9 46.5 + + - +
129E LEU* 4.7 2.5 - - - +
278E ILE* 5.9 0.2 - - + -
308E CYS* 3.1 24.2 + - - +
309E ALA 3.8 3.4 - - - +
311E HIS* 1.3 79.3 - - - +
313E ILE* 1.3 67.7 + - + +
315E LEU* 3.4 5.1 + - - +
316E ALA* 3.3 19.1 + - - +
351E PHE* 3.4 29.8 - + + +
353E LYS 4.8 1.1 - - - -
355E GLY 3.5 9.8 + - - -
356E LEU* 3.1 43.1 + - + -
357E GLY 4.1 0.4 + - - -
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Residues in contact with ILE 313 (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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129E LEU* 5.2 0.2 - - - -
272E PRO* 4.1 21.5 - - + -
278E ILE* 3.8 38.1 - - + -
281E MSE 3.9 35.0 - - + -
282E MSE 3.4 23.6 - - + +
297E ILE* 4.2 5.6 - - + -
309E ALA* 2.9 25.4 + - + +
310E GLU* 3.5 8.1 - - - +
312E HIS* 1.3 78.6 - - - +
314E GLY* 1.3 64.8 + - - +
316E ALA 3.3 7.3 + - - -
317E ILE* 3.3 28.0 + - + +
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Residues in contact with GLY 314 (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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134E ARG* 2.9 18.0 + - - -
137E VAL* 4.4 5.4 - - - -
297E ILE* 3.6 19.3 - - - -
310E GLU 2.8 11.3 + - - -
311E HIS 3.1 4.2 + - - -
313E ILE* 1.3 77.7 - - - +
315E LEU* 1.3 62.1 + - - +
317E ILE* 3.2 8.3 + - - +
320E LEU* 3.4 22.5 - - - +
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Residues in contact with LEU 315 (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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126E HIS* 3.4 36.8 - - + +
132E ALA* 3.9 7.0 - - + -
133E HIS* 2.7 29.5 + - - +
134E ARG* 3.6 34.7 + - + +
136E ALA 4.5 3.8 - - - -
137E VAL* 3.5 20.1 - - + +
311E HIS* 3.0 39.8 + - + +
312E HIS* 3.8 7.4 - - - +
313E ILE 3.4 0.2 - - - -
314E GLY* 1.3 75.6 - - - +
316E ALA* 1.3 59.1 + - - +
317E ILE 3.4 0.9 + - - -
350E ALA* 3.6 24.9 - - + -
351E PHE 4.3 0.2 - - - +
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Residues in contact with ALA 316 (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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126E HIS* 4.3 6.1 - - + +
129E LEU* 3.8 40.5 - - + +
131E GLY 3.6 15.7 - - - +
133E HIS* 3.4 14.1 + - - -
282E MSE 4.0 11.1 - - - +
312E HIS 3.3 13.4 + - - +
313E ILE 3.8 4.3 - - - +
314E GLY 3.2 1.0 - - - -
315E LEU* 1.3 76.8 - - - +
317E ILE* 1.3 59.0 + - - +
318E PRO* 3.6 5.0 - - - +
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E HIS* 3.9 1.3 - - - -
134E ARG* 2.7 31.0 + - - -
281E MSE 4.3 14.6 - - + +
282E MSE 3.5 17.7 - - + -
285E ALA* 3.8 25.1 - - + -
295E ILE* 4.5 4.7 - - + -
313E ILE* 3.3 35.9 - - + +
314E GLY 3.2 6.2 + - - +
316E ALA* 1.3 77.2 - - - +
318E PRO* 1.3 65.0 - - + +
319E ASN* 3.5 35.2 - - - +
320E LEU* 3.7 18.3 - - + +
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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