Contacts of the helix formed by residues 323 - 336 (chain A) in PDB entry 2PGE
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 SER 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 19.7 - - - +
34A PHE* 3.6 7.3 - - - -
47A GLU* 2.5 35.7 + - - -
322A GLU* 1.3 78.7 - - - +
324A ASN* 1.3 62.1 + - - +
325A LEU* 3.0 15.1 + - - +
326A GLY 3.2 1.0 + - - -
327A LEU* 2.9 21.6 + - - +
354A ASN* 3.4 19.1 - - - +
355A LEU* 3.9 13.2 - - - +
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Residues in contact with ASN 324 (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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323A SER* 1.3 72.7 - - - +
325A LEU* 1.3 62.0 + - - +
327A LEU* 3.8 23.0 - - - +
328A ALA* 3.1 23.2 + - - +
347A THR* 4.7 14.3 - - - +
348A GLY 5.6 0.5 + - - -
354A ASN* 2.9 31.6 + - - +
355A LEU* 2.7 32.5 + - + +
356A PRO* 5.0 0.2 - - - +
357A SER* 3.5 30.3 + - - +
359A LEU* 4.2 4.5 - - + +
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Residues in contact with LEU 325 (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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34A PHE* 4.1 9.9 - - + -
45A GLN* 4.0 22.7 - - + +
46A GLY 3.8 34.1 - - - +
47A GLU* 3.7 5.8 - - + +
127A MET* 4.0 6.7 - - + -
138A GLN* 3.8 26.5 - - + +
140A TRP* 3.7 31.9 - - + -
323A SER* 3.0 11.4 + - - +
324A ASN* 1.3 75.9 - - - +
326A GLY* 1.3 66.9 + - - +
328A ALA* 3.2 5.8 + - - +
329A ALA* 3.1 17.7 + - - +
355A LEU* 3.9 20.0 - - + +
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Residues in contact with GLY 326 (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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47A GLU* 3.0 17.1 + - - -
123A PHE* 5.2 1.8 - - - -
127A MET* 3.9 19.9 - - - +
322A GLU* 4.1 14.6 - - - -
323A SER 3.2 1.3 + - - -
325A LEU* 1.3 79.6 - - - +
327A LEU* 1.3 61.7 + - - +
329A ALA* 3.3 2.6 + - - +
330A ILE* 3.0 30.7 + - - +
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Residues in contact with LEU 327 (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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319A SER* 4.0 26.7 - - - -
322A GLU* 4.2 7.7 - - + +
323A SER 2.9 17.6 + - - +
324A ASN* 3.9 19.5 - - - +
326A GLY* 1.3 76.2 - - - +
328A ALA* 1.3 57.9 + - - +
330A ILE* 3.3 5.7 + - + +
331A ALA* 2.9 29.5 + - + +
345A LEU* 4.3 11.4 - - + -
346A GLY* 3.7 41.1 - - - +
347A THR* 4.2 5.6 - - - -
348A GLY 5.2 0.9 - - - +
359A LEU* 3.8 20.4 - - + -
366A LEU* 5.5 1.8 - - + -
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Residues in contact with ALA 328 (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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138A GLN* 5.6 2.9 - - - +
140A TRP* 3.8 16.2 - - + -
324A ASN 3.1 19.5 + - - +
325A LEU 3.5 4.9 - - - +
327A LEU* 1.3 76.8 - - - +
329A ALA* 1.3 61.6 + - - +
331A ALA* 3.3 3.9 + - - +
332A GLN* 2.9 37.1 + - - +
357A SER* 6.1 0.9 - - - -
359A LEU* 3.9 21.7 - - + +
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Residues in contact with ALA 329 (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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123A PHE* 5.1 0.2 - - + -
127A MET* 3.8 22.7 - - + -
140A TRP* 3.6 35.1 - - + -
141A PHE* 4.1 2.9 - - - -
298A PHE* 3.5 23.3 - - + -
325A LEU 3.1 3.6 + - - +
326A GLY 3.6 7.2 - - - +
328A ALA* 1.3 78.8 - - - +
330A ILE* 1.3 63.0 + - - +
332A GLN* 3.3 4.1 + - - +
333A TRP* 3.1 17.5 + - - +
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Residues in contact with ILE 330 (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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123A PHE* 4.0 13.9 - - + -
292A PRO* 4.4 16.2 - - + -
298A PHE* 3.8 19.7 - - + -
317A ILE* 4.0 14.6 - - + -
318A THR 4.5 2.5 - - - +
319A SER* 4.6 7.2 - - - -
322A GLU* 3.3 35.9 - - - +
326A GLY 3.0 20.9 + - - +
327A LEU* 3.8 5.8 - - - +
329A ALA* 1.3 73.2 - - - +
331A ALA* 1.3 57.6 + - - +
333A TRP* 3.4 1.8 + - + +
334A THR* 2.6 42.5 + - - +
345A LEU* 3.6 24.5 - - + -
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Residues in contact with ALA 331 (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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145A PHE* 3.9 16.8 - - + -
152A ILE* 3.3 10.4 - - + +
327A LEU* 2.9 18.9 + - + +
328A ALA* 3.8 6.5 - - - +
330A ILE* 1.3 73.8 - - - +
332A GLN* 1.3 66.9 + - - +
334A THR 3.3 0.2 + - - -
335A ALA* 3.0 20.6 + - - +
345A LEU* 3.8 14.6 - - + +
359A LEU* 5.0 2.9 - - + -
366A LEU* 3.9 27.8 - - + -
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Residues in contact with GLN 332 (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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138A GLN 3.1 22.0 + - - -
139A GLU* 3.6 0.8 - - - +
140A TRP* 2.9 41.0 + - - +
141A PHE* 3.1 24.1 + - + +
143A SER* 4.7 1.2 + - - -
145A PHE* 4.0 16.6 - - + -
146A THR* 3.6 29.0 - - + +
328A ALA* 2.9 26.0 + - - +
329A ALA 3.7 4.3 - - - +
331A ALA* 1.3 77.0 - - - +
333A TRP* 1.3 61.9 + - - +
335A ALA* 3.6 10.7 + - - +
336A LEU* 3.6 14.2 - - - +
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Residues in contact with TRP 333 (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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100A LEU* 4.3 7.2 - - + +
141A PHE* 3.5 39.4 - + + -
290A LEU* 5.0 1.6 - - + -
292A PRO* 3.9 17.5 - - + -
298A PHE* 3.3 38.9 + + + +
301A ALA* 3.4 20.2 - - + -
302A GLY* 3.7 15.5 - - - -
305A ILE* 3.8 17.3 - - + -
317A ILE* 3.5 35.2 - - + -
329A ALA 3.1 12.4 + - - +
330A ILE 3.6 1.8 - - - +
331A ALA 3.2 0.2 - - - -
332A GLN* 1.3 75.6 - - - +
334A THR* 1.3 68.7 + - - +
336A LEU* 3.0 33.0 + - + +
337A TYR* 3.6 36.1 + + - -
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Residues in contact with THR 334 (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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152A ILE* 4.4 3.4 - - + -
317A ILE* 3.6 35.5 - - + +
330A ILE 2.6 22.4 + - - -
331A ALA 3.3 4.7 + - - -
333A TRP* 1.3 78.1 - - - +
335A ALA* 1.3 62.2 + - - +
337A TYR* 3.0 20.2 + - + +
339A PRO* 3.6 11.5 - - + +
343A GLN* 3.6 37.9 - - + +
345A LEU* 3.7 18.1 - - + +
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Residues in contact with ALA 335 (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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143A SER* 4.2 6.5 - - - +
145A PHE* 3.5 33.9 - - + -
150A LYS* 5.9 2.1 - - + +
152A ILE* 3.8 13.9 - - + +
331A ALA 3.0 16.8 + - - +
332A GLN 3.7 7.2 - - - +
333A TRP 3.2 0.2 - - - -
334A THR* 1.3 76.2 - - - +
336A LEU* 1.3 61.3 + - - +
337A TYR 3.1 0.2 - - - -
338A GLN* 3.1 21.2 + - - +
339A PRO* 4.5 3.4 - - - -
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Residues in contact with LEU 336 (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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96A TYR* 3.8 28.5 - - + -
141A PHE* 3.6 33.9 - - + -
142A ALA 4.3 5.6 - - - +
143A SER* 4.2 21.3 - - - -
332A GLN 3.6 10.3 - - - +
333A TRP* 3.0 27.4 + - + +
335A ALA* 1.3 77.0 - - - +
337A TYR* 1.3 64.3 + - + +
338A GLN* 3.2 7.7 + - - +
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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