Contacts of the helix formed by residues 374 - 392 (chain A) in PDB entry 2PO5
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 ASN 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A CYS* 4.1 14.7 - - - +
239A ASP* 5.3 4.0 - - - +
240A HIS* 3.3 29.8 + - + +
371A LEU* 2.9 18.5 + - - +
372A ASN 3.4 1.0 - - - +
373A GLY* 1.3 74.5 - - - +
375A PRO* 1.3 69.3 - - - +
376A LEU* 2.8 30.0 - - - +
377A PHE* 2.8 32.1 + - + +
378A SER* 3.5 5.4 + - - -
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Residues in contact with PRO 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 5.3 1.4 - - - +
373A GLY 3.0 9.8 - - - +
374A ASN* 1.3 91.4 - - - +
376A LEU* 1.3 59.7 + - - +
378A SER* 3.4 11.0 + - - +
379A LYS* 3.1 20.3 + - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.8 24.4 - - + +
235A GLN* 3.5 39.9 - - + +
236A CYS* 3.6 20.9 - - - +
239A ASP* 4.0 12.3 - - - +
374A ASN* 2.8 17.4 - - - +
375A PRO* 1.3 78.3 - - - +
377A PHE* 1.3 58.5 + - - +
379A LYS* 3.3 23.2 + - + +
380A ALA* 2.9 25.5 + - - +
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Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 3.1 49.1 - - + -
190A GLN* 4.5 2.2 - - - -
227A TRP* 3.7 25.1 - + - -
233A LEU* 4.3 3.6 - - + -
236A CYS* 3.5 13.9 - - - -
338A THR* 3.4 35.9 - - + -
371A LEU* 3.7 25.8 - - + -
372A ASN 4.2 2.7 - - - +
374A ASN* 2.8 18.3 + - + +
376A LEU* 1.3 76.7 - - - +
378A SER* 1.3 65.9 + - - +
380A ALA* 2.9 20.4 + - + +
381A LEU* 2.9 33.1 + - + +
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS 4.3 0.9 + - - -
139A GLN* 3.6 24.4 + - - +
142A GLY* 4.0 25.8 - - - -
143A MET* 4.1 3.6 - - - -
146A LEU* 3.8 5.1 - - - +
373A GLY* 5.6 2.1 + - - -
374A ASN 3.5 5.0 + - - -
375A PRO* 3.4 12.8 + - - +
377A PHE* 1.3 78.4 - - - +
379A LYS* 1.3 62.9 + - - +
381A LEU* 3.2 13.8 + - - +
382A ALA* 3.0 23.7 + - - +
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.5 19.7 - - + +
232A LEU* 3.8 22.9 - - + +
375A PRO 3.1 13.9 + - - +
376A LEU* 3.3 24.0 - - + +
377A PHE 3.1 0.2 - - - -
378A SER* 1.3 79.1 - - - +
380A ALA* 1.3 56.3 + - - +
382A ALA* 3.3 1.4 + - - +
383A ASP* 2.9 30.8 + - + +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TRP* 5.3 4.3 - - + -
230A HIS* 4.2 7.1 - - + +
232A LEU* 3.6 31.9 - - + -
233A LEU* 4.3 11.9 - - + +
376A LEU 2.9 9.4 + - - +
377A PHE* 2.9 22.9 + - + +
379A LYS* 1.3 77.6 - - - +
381A LEU* 1.3 62.9 + - - +
383A ASP* 3.3 2.3 + - - +
384A LEU* 3.0 29.7 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.0 14.4 - - + -
139A GLN* 3.8 39.5 - - + +
143A MET* 3.9 15.5 - - + -
188A PHE* 3.6 27.3 - - + -
190A GLN* 3.5 18.6 - - - +
227A TRP* 4.2 9.2 - - + -
377A PHE* 2.9 36.6 + - + +
378A SER* 3.2 7.4 + - - +
380A ALA* 1.3 77.8 - - - +
382A ALA* 1.3 63.2 + - - +
384A LEU* 3.3 2.5 + - - +
385A VAL* 3.1 28.2 + - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 4.0 17.8 - - - +
146A LEU* 3.7 31.6 - - + -
147A LEU* 3.5 10.4 - - + +
150A LEU* 3.9 13.2 - - + -
378A SER 3.0 16.5 + - - +
379A LYS 3.7 4.0 - - - +
381A LEU* 1.3 77.6 - - - +
383A ASP* 1.3 56.8 + - - +
385A VAL 3.4 0.3 + - - -
386A HIS* 2.9 30.3 + - - +
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 4.5 4.8 - - - +
230A HIS* 2.6 32.4 + - + +
231A HIS* 4.2 8.2 - - - -
232A LEU* 4.5 8.1 - - + -
379A LYS* 2.9 19.6 + - + +
380A ALA 3.7 4.0 - - - +
382A ALA* 1.3 75.8 - - - +
384A LEU* 1.3 57.7 + - - +
386A HIS* 3.4 10.4 + - - +
387A SER* 2.8 46.0 + - - -
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 3.7 20.4 - - + -
224A ILE* 3.9 13.1 - - + +
226A ARG 5.4 0.4 - - - +
227A TRP* 3.4 57.7 - - + -
230A HIS* 3.4 30.5 - - + -
380A ALA 3.0 15.7 + - - +
381A LEU* 3.6 6.3 - - - +
382A ALA 3.3 0.2 - - - -
383A ASP* 1.3 78.3 - - - +
385A VAL* 1.3 62.4 + - - +
387A SER* 3.4 5.4 + - - -
388A HIS* 2.9 25.1 + - - +
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.2 9.6 - - + -
143A MET* 3.9 13.9 - - - -
147A LEU* 3.6 22.4 - - + -
157A HIS* 5.5 0.2 - - + -
186A ILE* 3.9 16.4 - - + -
188A PHE* 3.6 27.1 - - + -
224A ILE* 3.8 10.8 - - + -
381A LEU 3.1 17.1 + - - +
382A ALA 3.8 3.4 - - - +
384A LEU* 1.3 75.4 - - - +
386A HIS* 1.3 64.1 + - - +
388A HIS* 3.2 3.0 + - - +
389A ILE* 2.9 41.1 + - + +
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 4.0 6.3 - - + +
150A LEU* 3.5 47.0 + - + +
151A SER* 3.8 24.5 - - - -
382A ALA 2.9 18.4 + - - +
383A ASP* 3.6 10.7 + - - +
385A VAL* 1.3 76.5 - - - +
387A SER* 1.3 59.3 + - - +
389A ILE* 3.2 8.1 + - + +
390A GLN* 2.6 62.9 + - + +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASP* 2.8 34.9 + - - -
384A LEU* 3.8 5.8 - - - -
386A HIS* 1.3 75.3 + - - +
388A HIS* 1.3 61.4 + - - +
390A GLN* 3.9 10.3 + - - +
391A SER* 3.1 27.2 + - - -
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 4.0 7.6 + - - -
186A ILE* 4.1 23.2 - - + +
222A SER* 2.6 31.4 + - - -
223A THR 3.2 16.3 + - - -
224A ILE* 3.6 21.6 - - + +
384A LEU 2.9 18.7 + - - +
385A VAL 3.4 4.0 - - - +
387A SER* 1.3 78.1 - - - +
389A ILE* 1.3 62.8 + - - +
391A SER* 3.1 17.1 + - - -
392A ASN* 3.3 8.3 + - - -
393A GLU* 2.9 60.6 + - + +
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Residues in contact with ILE 389 (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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69A THR* 4.6 5.8 - - + -
147A LEU* 5.3 0.9 - - + -
151A SER* 4.6 8.5 - - - +
154A THR* 3.8 42.2 - - + +
157A HIS* 4.5 6.7 - - - +
184A ARG* 4.4 16.2 - - - +
186A ILE* 3.9 20.4 - - + -
385A VAL* 2.9 34.5 + - + +
386A HIS* 3.6 10.5 - - + +
388A HIS* 1.3 78.4 - - - +
390A GLN* 1.3 65.3 + - + +
391A SER 3.3 0.7 + - - -
392A ASN* 3.4 16.1 + - - +
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Residues in contact with GLN 390 (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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386A HIS* 2.6 57.6 + - + +
387A SER* 4.0 9.0 - - - +
388A HIS 3.4 0.2 - - - -
389A ILE* 1.3 79.7 - - + +
391A SER* 1.3 59.6 + - - +
392A ASN* 3.4 7.5 - - - +
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER 3.1 14.0 + - - -
388A HIS* 3.1 14.2 + - - -
389A ILE 3.2 0.2 - - - -
390A GLN* 1.3 77.7 - - - +
392A ASN* 1.3 69.8 + - - +
393A GLU* 3.0 21.3 + - - +
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Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 6.3 0.2 - - - +
388A HIS 3.3 6.0 + - - -
389A ILE* 3.4 11.3 + - - +
390A GLN 3.9 8.7 - - - +
391A SER* 1.3 81.3 + - - +
393A GLU* 1.3 65.6 + - - +
394A LEU* 3.5 12.4 + - - +
423A LEU* 4.4 28.5 + - - +
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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