Contacts of the helix formed by residues 374 - 392 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B CYS* 3.7 18.8 - - - +
239B ASP* 5.3 3.1 - - - +
240B HIS* 3.4 27.8 + - + +
371B LEU* 2.9 20.1 + - - +
372B ASN 3.4 0.5 - - - +
373B GLY* 1.3 74.4 - - - +
375B PRO* 1.3 71.6 - - - +
376B LEU* 2.8 29.6 - - - +
377B PHE* 2.9 30.4 + - + +
378B SER* 3.6 4.7 + - - -
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Residues in contact with PRO 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 5.1 1.7 - - - +
373B GLY 3.0 9.6 - - - +
374B ASN* 1.3 90.5 - - - +
376B LEU* 1.3 60.8 + - - +
378B SER* 3.4 10.0 + - - +
379B LYS* 3.2 19.9 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.5 27.8 - - + +
235B GLN* 3.6 38.1 - - + +
236B CYS* 3.5 19.3 - - - +
239B ASP* 4.0 11.0 - - - +
374B ASN* 2.8 22.1 - - - +
375B PRO* 1.3 75.8 - - + +
377B PHE* 1.3 58.0 + - - +
379B LYS* 3.3 20.6 + - + +
380B ALA* 2.9 25.1 + - - +
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Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLN* 3.1 50.7 - - + -
190B GLN* 4.5 2.7 - - - -
227B TRP* 3.7 25.1 - + - -
233B LEU* 4.2 2.9 - - + -
236B CYS* 3.6 15.2 - - - -
338B THR* 3.4 30.3 - - + -
371B LEU* 3.7 28.3 - - + +
372B ASN 4.3 1.3 - - - +
374B ASN* 2.9 17.5 + - + +
376B LEU* 1.3 77.2 - - - +
378B SER* 1.3 60.0 + - - +
380B ALA* 3.0 11.6 + - + +
381B LEU* 2.9 52.0 + - + +
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS 4.2 1.2 + - - -
139B GLN* 3.4 27.4 + - - +
142B GLY* 3.8 26.2 - - - -
143B MET* 4.0 3.4 - - - -
146B LEU* 3.7 6.8 - - - +
373B GLY 5.7 0.7 + - - -
374B ASN 3.6 4.0 + - - -
375B PRO* 3.4 12.3 + - - +
377B PHE* 1.3 78.8 - - - +
379B LYS* 1.3 57.4 + - - +
381B LEU* 3.3 13.4 + - - +
382B ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.5 19.0 - - + +
150B LEU* 6.2 2.0 - - - +
232B LEU* 3.8 18.2 - - + -
375B PRO 3.2 13.0 + - - +
376B LEU* 3.3 23.3 - - + +
377B PHE 3.1 0.2 - - - -
378B SER* 1.3 74.9 - - - +
380B ALA* 1.3 65.2 + - - +
382B ALA* 3.3 1.1 + - - -
383B ASP* 2.9 44.3 + - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 5.3 1.1 - - + -
230B HIS* 4.2 6.5 - - - +
232B LEU* 3.6 29.4 - - + +
233B LEU* 4.3 11.9 - - + +
376B LEU 2.9 14.0 + - - +
377B PHE* 3.0 22.6 + - + +
379B LYS* 1.3 77.7 - - - +
381B LEU* 1.3 62.6 + - - +
383B ASP* 3.3 1.9 + - - +
384B LEU* 3.0 33.4 + - + +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 4.0 14.1 - - + -
139B GLN* 3.8 39.9 - - + +
143B MET* 3.9 16.2 - - + -
188B PHE* 3.6 26.4 - - + -
190B GLN* 3.7 16.4 - - - +
227B TRP* 4.1 10.3 - - + -
377B PHE* 2.9 37.6 + - + +
378B SER* 3.5 7.4 - - - +
380B ALA* 1.3 77.2 - - - +
382B ALA* 1.3 61.5 + - - +
384B LEU* 3.3 3.6 + - - +
385B VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B MET* 3.9 14.5 - - - +
146B LEU* 3.7 21.5 - - + -
147B LEU* 3.4 14.2 - - + +
150B LEU* 3.6 21.1 - - + -
378B SER 2.9 15.6 + - - +
379B LYS 3.8 3.6 - - - +
381B LEU* 1.3 76.1 - - - +
383B ASP* 1.3 59.5 + - - +
385B VAL* 3.4 0.6 + - - -
386B HIS* 2.8 30.3 + - - +
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Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.9 20.6 - - - +
230B HIS* 4.2 15.3 - - + +
231B HIS* 4.9 5.2 + - + -
232B LEU* 3.3 20.4 - - - +
379B LYS* 2.9 36.0 + - - +
380B ALA 3.7 3.1 - - - +
382B ALA* 1.3 72.7 - - - +
384B LEU* 1.3 60.8 + - - +
386B HIS* 3.6 7.0 + - - +
387B SER* 2.9 37.4 + - - +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 3.8 18.6 - - + -
224B ILE* 3.8 13.2 - - + +
226B ARG 5.4 0.2 - - - +
227B TRP* 3.3 58.1 - - + -
230B HIS* 3.4 29.4 - - + -
380B ALA* 3.0 23.9 + - + +
381B LEU* 3.6 4.3 - - - +
383B ASP* 1.3 77.3 - - - +
385B VAL* 1.3 62.0 + - - +
387B SER* 4.0 4.7 - - - -
388B HIS* 3.0 24.6 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.4 10.3 - - + -
143B MET* 4.1 11.2 - - - -
147B LEU* 3.6 24.2 - - + -
186B ILE* 4.1 15.0 - - + -
188B PHE* 3.5 28.5 - - + -
224B ILE* 3.8 12.1 - - + -
381B LEU 3.0 17.2 + - - +
382B ALA 3.8 3.4 - - - +
384B LEU* 1.3 76.5 - - - +
386B HIS* 1.3 62.6 + - - +
388B HIS* 3.3 1.7 + - - +
389B ILE* 3.0 42.4 + - + +
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Residues in contact with HIS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.1 8.3 - - + +
150B LEU* 3.4 41.3 + - + +
151B SER* 3.9 23.0 - - - -
382B ALA 2.8 18.8 + - - +
383B ASP* 3.6 9.2 + - - +
384B LEU 3.2 0.2 - - - -
385B VAL* 1.3 77.8 - - - +
387B SER* 1.3 56.7 + - - +
389B ILE* 3.1 8.0 + - + +
390B GLN* 2.9 64.8 + - + +
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS* 5.7 1.4 + - - -
383B ASP* 2.9 19.4 + - - +
384B LEU* 4.0 4.9 - - - -
386B HIS* 1.3 77.4 + - - +
388B HIS* 1.3 61.5 + - - +
390B GLN* 3.8 8.6 - - - +
391B SER* 3.0 27.3 + - - -
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.1 22.7 - - + +
222B SER* 2.7 30.2 + - - -
223B THR 3.3 18.8 + - - -
224B ILE* 3.4 21.5 - - + +
384B LEU 3.0 19.1 + - - +
385B VAL 3.4 4.7 - - - +
386B HIS 3.2 0.2 - - - -
387B SER* 1.3 77.6 - - - +
389B ILE* 1.3 63.0 + - - +
391B SER* 3.2 16.2 + - - -
392B ASN* 3.3 8.7 + - - -
393B GLU* 3.0 63.2 + - + +
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Residues in contact with ILE 389 (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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69B THR* 4.6 2.5 - - + -
147B LEU* 5.4 0.7 - - + -
151B SER* 4.5 9.6 - - - +
154B THR* 3.8 35.7 - - + +
157B HIS* 4.5 5.8 - - - +
184B ARG* 3.7 35.4 + - - +
186B ILE* 3.9 21.3 - - + -
385B VAL* 3.0 35.4 + - + +
386B HIS* 3.1 9.6 + - + +
388B HIS* 1.3 79.2 - - - +
390B GLN* 1.3 66.8 + - + +
391B SER 3.5 0.3 + - - -
392B ASN* 3.5 15.3 + - - +
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Residues in contact with GLN 390 (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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151B SER* 5.5 1.2 + - - -
153B ASN* 5.8 2.4 + - - -
386B HIS* 2.9 56.0 + - + +
387B SER* 3.8 8.5 - - - +
388B HIS 3.3 0.2 - - - -
389B ILE* 1.3 84.2 - - - +
391B SER* 1.3 58.3 + - - +
392B ASN* 3.6 5.5 + - - +
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Residues in contact with SER 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B SER 3.0 18.3 + - - -
388B HIS* 3.2 10.0 + - - -
390B GLN* 1.3 75.7 - - - +
392B ASN* 1.3 68.5 + - - +
393B GLU* 3.0 20.1 + - - +
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Residues in contact with ASN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 5.5 6.3 + - - +
388B HIS 3.3 6.8 + - - -
389B ILE* 3.5 11.6 + - - +
390B GLN 3.4 7.6 - - - +
391B SER* 1.3 80.1 - - - +
393B GLU* 1.3 65.8 + - - +
394B LEU* 3.5 11.3 + - - +
423B LEU* 4.1 33.0 + - - +
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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