Contacts of the helix formed by residues 303 - 317 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.5 31.0 - - + -
32A PHE* 6.5 0.4 - - + -
34A VAL* 3.9 14.1 - - + -
50A GLU* 2.8 27.4 + - - +
302A THR* 1.3 83.0 + - - +
304A GLY* 1.3 66.4 + - - +
305A ILE* 3.1 17.3 + - - +
306A THR* 3.2 11.8 + - - -
307A THR* 3.4 12.0 + - - -
328A TRP* 4.3 4.8 - - - +
331A VAL* 5.1 1.8 - - + -
334A ASP* 3.4 13.5 - - - -
335A ILE* 3.6 12.1 - - + +
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A THR* 1.3 74.1 + - - +
305A ILE* 1.3 62.8 - - - +
306A THR 3.3 0.2 - - - -
307A THR* 3.2 8.5 + - - -
308A CYS* 3.0 28.1 + - - -
328A TRP* 4.0 1.7 - - - +
334A ASP* 2.8 28.4 + - - -
336A VAL* 3.4 8.5 - - - +
341A LEU* 3.4 15.4 - - - +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.4 33.0 - - + -
48A ILE* 4.1 13.2 - - + -
49A GLY* 4.1 14.8 - - - +
50A GLU* 3.5 8.7 - - - +
111A MSE 3.1 38.5 - - + +
303A THR* 3.0 6.7 - - - +
304A GLY* 1.3 77.4 - - - +
306A THR* 1.3 62.2 - - - +
308A CYS* 3.2 5.4 + - - +
309A ALA 3.2 10.7 + - - -
335A ILE* 3.6 13.5 - - + -
336A VAL* 3.5 4.4 - - + +
358A PHE* 3.7 22.9 - - + -
360A LEU* 3.9 25.4 - - + -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 2.7 34.4 + - - +
111A MSE 4.2 12.1 - - - -
272A PRO* 4.9 6.1 - - + -
299A SER* 4.3 3.6 - - - +
300A SER* 4.3 4.9 - - - +
302A THR* 3.1 29.4 + - - +
303A THR 3.2 1.3 + - - -
305A ILE* 1.3 73.2 - - - +
307A THR* 1.3 67.4 + - - +
309A ALA* 3.2 1.7 + - + -
310A GLU* 2.8 54.6 + - + +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 4.8 4.4 + - + +
299A SER* 5.7 0.7 + - - -
303A THR 3.4 5.1 + - - -
304A GLY* 3.2 12.9 + - - -
306A THR* 1.3 80.6 - - - +
308A CYS* 1.3 56.4 + - - +
310A GLU* 3.9 9.6 - - - +
311A HIS* 3.0 27.6 + - + +
326A ILE* 3.8 30.8 - - + +
327A MSE 4.8 1.6 + - - -
328A TRP* 3.3 33.8 + - + +
341A LEU* 4.0 17.5 - - + -
348A LEU* 4.9 6.5 - - + -
351A PHE* 5.7 0.4 - - + -
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Residues in contact with CYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLY 3.0 17.6 + - - -
305A ILE 3.6 7.2 - - - +
306A THR 3.1 0.4 - - - -
307A THR* 1.3 76.0 - - - +
309A ALA* 1.3 65.3 + - - +
311A HIS* 3.3 6.3 + - - +
312A HIS* 3.1 31.1 + - - -
336A VAL* 4.8 1.1 - - - -
339A PRO* 4.6 3.1 - - - -
341A LEU* 3.8 24.2 - - - -
351A PHE* 4.3 9.4 - - + -
356A LEU* 3.5 21.8 - - + +
358A PHE* 3.7 32.3 - - + -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A MSE 3.3 43.5 - - + -
272A PRO* 5.3 2.5 - - + -
278A ILE* 4.5 8.6 - - + +
305A ILE 3.2 5.7 + - - -
306A THR* 3.7 4.7 - - - +
308A CYS* 1.3 74.9 - - - +
310A GLU* 1.3 60.8 + - + +
312A HIS* 3.1 4.3 + - - +
313A ILE* 2.9 36.3 + - + +
356A LEU* 3.7 17.6 - - + +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 5.5 0.2 - - - +
139A TYR* 5.1 4.3 - - + -
272A PRO* 3.6 28.8 - - + +
273A ARG* 5.5 1.4 + - - +
297A ILE* 3.1 32.9 - - + +
298A HIS 3.2 17.8 - - - +
299A SER* 2.9 32.8 + - - -
300A SER* 4.9 0.5 + - - -
306A THR* 2.8 36.2 + - + +
307A THR* 4.0 7.0 - - - +
309A ALA* 1.3 74.4 - - + +
311A HIS* 1.3 57.0 + - - +
313A ILE* 4.0 8.3 - - - -
314A GLY* 3.0 21.3 + - - -
325A GLN 4.3 7.4 - - - +
326A ILE* 5.4 0.9 - - - -
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Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.7 13.1 - - + +
139A TYR* 3.1 27.8 + - - +
307A THR* 3.0 19.5 + - + +
308A CYS* 3.4 9.4 - - - +
309A ALA 3.1 0.4 - - - -
310A GLU* 1.3 74.9 - - - +
312A HIS* 1.3 68.5 + - - +
314A GLY* 3.2 2.4 + - - -
315A LEU* 3.0 42.6 + - + +
348A LEU* 3.5 22.2 + - + +
349A ASP 3.4 14.5 + - - -
350A ALA* 3.6 2.2 - - - -
351A PHE* 3.1 55.7 - + + +
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 3.7 14.4 - - + -
125A VAL* 3.8 21.5 + - + -
126A HIS* 3.2 46.8 + + - +
129A LEU* 4.5 2.2 - - - +
308A CYS* 3.1 25.7 + - + -
309A ALA 3.1 5.8 + - - +
311A HIS* 1.3 78.8 - - - +
313A ILE* 1.3 66.3 + - + +
315A LEU* 3.4 1.8 + - - +
316A ALA* 3.1 24.8 + - - +
351A PHE* 3.6 26.1 - - + +
353A LYS 4.9 0.9 - - - -
355A GLY 3.8 4.3 - - - -
356A LEU* 3.2 41.6 + - + -
357A GLY 4.1 0.2 + - - -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.0 1.6 - - - -
272A PRO* 4.0 29.4 - - + -
278A ILE* 3.8 44.0 - - + -
281A MSE 3.6 19.5 - - + -
282A MSE 3.2 27.8 - - + +
297A ILE* 4.7 3.4 - - + -
309A ALA* 2.9 27.1 + - + +
310A GLU* 3.7 8.1 - - - +
312A HIS* 1.3 74.8 - - - +
314A GLY* 1.3 63.3 + - - +
316A ALA* 3.2 2.8 + - - -
317A ILE* 3.2 35.0 + - + +
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 2.8 21.2 + - - -
137A VAL* 4.4 5.4 - - - -
297A ILE* 3.5 21.3 - - - -
310A GLU 3.0 10.7 + - - -
311A HIS 3.2 3.6 + - - -
313A ILE* 1.3 77.3 - - - +
315A LEU* 1.3 58.9 + - - +
317A ILE* 3.2 8.1 + - - +
320A LEU* 3.3 21.7 - - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A HIS* 3.3 36.6 - - + +
132A ALA* 3.4 7.1 - - + -
133A HIS* 2.7 29.3 + - - -
134A ARG* 3.4 37.9 + - + +
136A ALA 4.5 3.6 - - - +
137A VAL* 3.8 17.9 - - + +
311A HIS* 3.0 41.0 + - + +
312A HIS* 3.7 7.0 - - - +
313A ILE 3.4 0.2 - - - -
314A GLY* 1.3 75.4 - - - +
316A ALA* 1.3 58.9 - - - +
317A ILE 3.4 0.7 + - - -
350A ALA* 3.5 23.1 - - + -
351A PHE 4.3 0.2 - - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A HIS* 4.4 4.5 - - + -
129A LEU* 3.7 42.2 - - + +
131A GLY 3.6 14.3 - - - +
133A HIS* 3.5 14.7 + - - -
282A MSE 3.9 10.7 - - - +
312A HIS 3.1 17.1 + - - +
313A ILE 3.2 4.2 + - - +
314A GLY 3.2 0.4 - - - -
315A LEU* 1.3 75.8 - - - +
317A ILE* 1.3 59.4 + - - +
318A PRO* 3.6 5.4 - - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS* 4.1 1.6 - - - -
134A ARG* 2.7 28.8 + - - -
281A MSE 4.3 15.0 - - + +
282A MSE 3.5 16.8 - - + -
285A ALA* 3.9 23.6 - - + -
295A ILE* 4.5 4.5 - - + -
297A ILE* 5.4 0.2 - - + -
313A ILE* 3.3 36.6 - - + +
314A GLY 3.2 6.5 + - - +
316A ALA* 1.3 77.9 - - - +
318A PRO* 1.3 65.9 - - + +
319A ASN* 3.5 36.3 - - - +
320A LEU* 3.7 17.3 - - + +
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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