Contacts of the helix formed by residues 303 - 317 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.4 32.5 - - + -
32B PHE* 5.2 0.7 - - + -
34B VAL* 3.9 13.9 - - + -
50B GLU* 2.7 27.4 + - - +
302B THR* 1.3 85.6 + - - +
304B GLY* 1.3 64.9 + - - +
305B ILE* 3.0 10.3 + - - +
306B THR* 3.1 12.0 + - - -
307B THR* 3.3 12.4 + - - -
328B TRP* 4.2 5.5 + - - -
331B VAL* 4.8 3.6 - - + -
334B ASP* 3.4 13.0 - - - -
335B ILE* 3.5 16.5 - - + +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 1.3 71.3 - - - +
305B ILE* 1.3 56.8 + - - +
306B THR 3.3 0.2 - - - -
307B THR* 3.2 8.1 + - - -
308B CYS* 2.9 33.4 + - - -
328B TRP* 3.9 2.2 - - - +
334B ASP* 2.8 32.8 + - - -
336B VAL* 3.4 11.0 - - - +
341B LEU* 3.5 13.4 - - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.4 32.8 - - + -
48B ILE* 4.1 13.5 - - + +
49B GLY* 4.1 15.9 - - - +
50B GLU* 3.6 22.2 - - + +
111B MSE 4.2 4.7 - - - -
303B THR* 3.0 5.2 - - - +
304B GLY* 1.3 76.7 - - - +
306B THR* 1.3 63.5 + - - +
308B CYS* 3.2 5.4 + - - +
309B ALA* 3.0 19.8 + - - +
335B ILE* 3.8 5.6 - - + -
336B VAL* 3.5 4.9 - - + +
356B LEU* 5.0 0.9 - - + -
358B PHE* 3.8 26.8 - - + -
360B LEU* 3.8 32.3 - - + -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 2.6 31.0 + - - +
111B MSE 4.1 10.7 - - + +
272B PRO* 4.7 7.4 - - + -
299B SER* 4.7 1.6 - - - +
300B SER* 4.2 6.7 - - - +
302B THR* 3.3 25.1 + - - +
303B THR 3.1 3.7 + - - -
305B ILE* 1.3 78.8 - - - +
307B THR* 1.3 57.6 + - - +
309B ALA* 3.1 6.2 + - - +
310B GLU* 2.8 67.2 + - + +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.7 5.1 + - + +
303B THR 3.3 10.8 + - - -
304B GLY* 3.2 12.5 + - - -
305B ILE 3.2 0.4 - - - -
306B THR* 1.3 79.4 - - - +
308B CYS* 1.3 56.7 + - - +
310B GLU* 3.4 9.0 + - - +
311B HIS* 2.9 29.0 + - + +
326B ILE* 4.1 19.2 - - + +
327B MSE 4.7 2.3 + - - -
328B TRP* 3.4 38.8 + - + +
341B LEU* 3.9 17.3 - - + -
348B LEU* 4.9 5.8 - - + -
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Residues in contact with CYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLY 2.9 19.1 + - - -
305B ILE 3.2 6.3 + - - +
307B THR* 1.3 73.2 - - - +
309B ALA* 1.3 67.2 + - - +
311B HIS* 3.2 6.8 + - - +
312B HIS* 3.1 31.2 + - + -
336B VAL* 4.8 0.9 - - - -
339B PRO* 4.5 4.3 - - - -
341B LEU* 3.9 23.1 - - - -
351B PHE* 4.3 8.1 - - + -
356B LEU* 3.5 21.8 - - + +
358B PHE* 3.8 32.8 - - + -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B MSE 3.6 42.4 - - + -
272B PRO* 5.3 0.2 - - + -
278B ILE* 4.5 6.9 - - + +
305B ILE 3.0 10.8 + - - +
306B THR 3.1 7.2 + - - +
308B CYS* 1.3 78.8 - - - +
310B GLU* 1.3 63.6 + - + +
312B HIS* 3.4 2.6 + - - +
313B ILE* 3.1 30.7 + - + +
356B LEU* 3.8 15.8 - - + +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 5.6 1.2 - - - +
139B TYR* 5.0 5.6 - - + +
272B PRO* 3.4 26.5 - - + +
297B ILE* 3.8 26.3 - - + +
298B HIS 3.3 18.2 - - - +
299B SER* 3.0 29.6 + - - -
300B SER* 4.8 0.5 + - - -
306B THR* 2.8 44.3 + - + +
307B THR* 3.9 6.7 - - - +
309B ALA* 1.3 70.3 - - + +
311B HIS* 1.3 60.6 + - - +
313B ILE* 3.6 9.2 - - - +
314B GLY* 2.9 25.3 + - - -
325B GLN 4.5 6.4 - - - +
326B ILE* 5.4 0.9 - - - -
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.7 16.0 - - + +
139B TYR* 3.1 28.5 + - - +
307B THR* 2.9 18.7 + - + +
308B CYS* 3.4 9.6 - - - +
309B ALA 3.2 0.2 - - - -
310B GLU* 1.3 78.4 - - - +
312B HIS* 1.3 59.9 + - - +
314B GLY* 3.2 2.4 + - - -
315B LEU* 3.0 40.6 + - + +
348B LEU* 3.2 33.3 + - + +
349B ASP 3.6 3.0 + - - -
350B ALA* 3.5 8.3 - - - -
351B PHE* 3.1 57.3 + + + +
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.9 12.8 - - + -
125B VAL* 4.0 22.2 - - + -
126B HIS* 3.0 47.5 + + - +
129B LEU* 4.7 2.2 - - - +
308B CYS* 3.1 27.3 + - - +
309B ALA 4.0 3.4 - - - +
311B HIS* 1.3 77.8 - - - +
313B ILE* 1.3 66.6 + - - +
315B LEU* 3.4 2.1 + - - +
316B ALA* 3.1 24.9 + - - +
351B PHE* 3.7 28.7 - - + +
353B LYS 4.8 1.1 - - - -
355B GLY 4.0 3.6 - - - -
356B LEU* 3.2 40.3 + - + -
357B GLY* 4.8 0.2 - - - -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 5.3 0.4 - - - -
272B PRO* 4.1 18.2 - - + -
278B ILE* 3.7 47.6 - - + +
281B MSE 3.8 35.7 - - + -
282B MSE 5.2 3.1 - - - -
297B ILE* 4.1 4.3 - - + -
309B ALA* 3.1 23.1 + - + +
310B GLU* 3.6 9.0 - - - +
312B HIS* 1.3 76.0 - - - +
314B GLY* 1.3 63.5 + - - +
316B ALA* 3.3 6.9 + - - +
317B ILE* 3.2 42.9 + - + +
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 2.8 21.9 + - - -
137B VAL* 4.3 7.0 - - - -
297B ILE* 4.7 4.5 - - - -
310B GLU 2.9 15.0 + - - -
311B HIS 3.6 4.0 - - - -
312B HIS 3.2 0.2 - - - -
313B ILE* 1.3 77.7 - - - +
315B LEU* 1.3 58.9 + - - +
317B ILE 3.2 6.9 + - - +
320B LEU* 3.2 32.4 - - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B HIS* 3.4 35.4 - - + +
132B ALA* 3.3 7.4 - - + -
133B HIS* 2.8 28.2 + - - -
134B ARG* 3.6 36.6 + - + +
136B ALA 4.4 4.7 - - - -
137B VAL* 3.5 20.6 - - + +
311B HIS* 3.0 36.9 + - + +
312B HIS* 3.8 4.7 - - - +
314B GLY* 1.3 76.3 - - - +
316B ALA* 1.3 60.5 + - - +
317B ILE 3.5 0.3 + - - -
350B ALA* 3.5 29.8 - - + -
351B PHE 4.3 0.2 - - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B HIS* 4.3 8.7 - - + +
129B LEU* 3.8 33.6 - - + +
131B GLY 3.9 9.8 - - - +
133B HIS* 3.3 17.0 + - - -
282B MSE 3.3 23.8 - - + +
312B HIS 3.1 17.3 + - - +
313B ILE 3.8 4.0 - - - +
314B GLY 3.2 0.4 - - - -
315B LEU* 1.3 78.2 - - - +
317B ILE* 1.3 58.0 + - - +
318B PRO* 3.6 2.1 - - - +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B HIS* 3.9 1.6 - - - -
134B ARG* 2.7 29.1 + - - -
281B MSE 4.3 15.5 - - + +
282B MSE 4.1 12.1 - - + -
285B ALA* 3.9 24.9 - - + -
295B ILE* 4.3 5.4 - - + -
297B ILE* 4.3 0.4 - - + -
313B ILE* 3.2 35.5 + - + +
314B GLY 3.2 1.6 + - - +
316B ALA* 1.3 78.0 - - - +
318B PRO* 1.3 68.7 - - + +
319B ASN* 3.4 36.1 - - - +
320B LEU* 3.7 24.5 - - + +
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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
------------------------------------------------------------
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