Contacts of the helix formed by residues 382 - 393 (chain B) in PDB entry 2PA5
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 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B LYS* 3.9 38.1 - - + +
358B ILE* 5.7 7.2 - - + -
376B GLN* 4.4 4.8 + - - +
378B PRO* 3.8 6.8 - - - +
379B LEU* 2.7 39.4 + - + +
381B ASN* 1.3 86.5 - - - +
383B TYR* 1.3 62.9 + - - +
384B ARG 3.3 2.2 - - - -
385B ASP* 3.1 23.2 + - - +
386B PHE* 2.9 22.2 + - - +
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Residues in contact with TYR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO* 3.7 15.3 - - + -
379B LEU 2.9 33.6 + - - -
380B GLU* 3.6 40.4 + - + +
382B THR* 1.3 76.1 - - - +
384B ARG* 1.3 63.0 + - - +
386B PHE* 3.2 8.1 + - - +
387B TRP* 3.0 31.3 + - + -
413B GLY* 3.3 7.9 - - - -
414B GLN* 3.1 36.1 + - - +
415B TYR* 3.4 29.6 - - + -
426B PHE* 3.5 28.7 - + + -
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LYS* 6.1 0.4 - - - +
346B LEU* 4.1 8.3 - - - +
347B THR 4.5 6.1 + - - -
348B LYS* 5.2 0.6 - - - +
354B GLN* 3.5 39.5 + - - +
355B THR 4.8 6.9 + - - -
380B GLU 5.2 0.4 + - - -
381B ASN 5.4 1.7 - - - +
382B THR* 3.3 0.8 - - - +
383B TYR* 1.3 78.8 - - - +
385B ASP* 1.3 88.0 + - - +
387B TRP* 3.4 1.8 + - - +
388B LEU* 2.9 56.9 + - + +
426B PHE* 4.0 38.0 - - + +
429B LEU* 4.8 2.6 - - + +
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LYS* 4.4 14.3 + - - +
346B LEU* 3.6 25.7 - - + +
355B THR 5.5 0.4 - - - +
357B TYR 4.2 7.9 - - - +
358B ILE* 3.8 12.9 - - + +
381B ASN 3.9 5.3 - - - +
382B THR* 3.1 31.5 + - - +
384B ARG* 1.3 110.3 + - - +
386B PHE* 1.3 59.4 + - - +
388B LEU* 3.4 1.2 + - - -
389B MET* 2.9 29.3 + - - +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE* 3.7 13.1 - - + +
375B THR* 4.2 11.9 - - + -
376B GLN 5.3 0.2 - - - -
378B PRO* 3.6 27.1 - - + -
382B THR* 2.9 12.8 + - - +
383B TYR* 3.2 9.2 + - - +
385B ASP* 1.3 76.9 - - - +
387B TRP* 1.3 71.3 + + - +
389B MET* 3.2 17.8 + - + +
390B VAL* 2.9 47.0 + - + +
398B ILE* 4.0 22.2 - - + -
415B TYR* 3.4 39.9 - + - -
512B VAL* 3.8 25.1 - - + -
514B HIS* 4.5 4.9 - + - -
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Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TYR* 3.0 27.5 + - - +
384B ARG 4.1 1.8 - - - +
386B PHE* 1.3 82.2 - + - +
388B LEU* 1.3 63.2 + - - +
390B VAL* 3.3 10.0 + - + +
391B TRP* 2.9 23.6 + - - +
398B ILE* 3.9 25.8 - - + -
415B TYR* 2.8 47.2 + + - -
416B TRP* 3.9 10.3 - - + -
426B PHE* 3.4 30.0 - + + -
429B LEU* 3.7 16.7 - - + +
431B VAL* 3.8 23.5 - - + +
447B LEU* 3.6 26.5 - - + -
449B ILE* 3.7 33.7 - - + +
460B VAL* 5.0 1.6 - - + -
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.2 11.2 - - + -
347B THR* 3.9 20.9 - - - +
384B ARG* 2.9 53.4 + - + +
385B ASP 3.7 4.0 - - - +
386B PHE 3.3 0.2 - - - -
387B TRP* 1.3 75.9 - - - +
389B MET* 1.3 57.2 + - - +
391B TRP* 3.3 4.4 + - + +
392B GLU* 2.8 64.3 + - + +
428B PHE* 3.8 32.5 - - + -
429B LEU* 3.6 12.6 - - + +
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Residues in contact with MET 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 3.9 24.5 - - + -
346B LEU* 3.7 14.6 - - + +
358B ILE* 3.9 19.7 - - + -
360B ALA* 3.6 26.5 - - + -
373B ILE* 3.8 25.8 - - + -
375B THR* 4.3 8.1 - - + -
385B ASP 2.9 14.0 + - - +
386B PHE* 3.2 31.6 + - + +
388B LEU* 1.3 76.5 - - - +
390B VAL* 1.3 64.7 + - + +
392B GLU* 4.8 2.9 - - - -
393B GLN* 2.9 31.9 + - + +
512B VAL* 4.4 11.0 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 2.9 49.0 + - + +
387B TRP* 3.6 16.4 - - + +
389B MET* 1.3 73.8 - - + +
391B TRP* 1.3 61.8 + - - +
394B LYS 3.2 1.9 + - - -
395B VAL* 3.1 38.7 + - + +
398B ILE* 4.2 8.3 - - + -
449B ILE* 3.4 28.7 - - + -
458B ARG* 2.9 18.9 + - - +
460B VAL* 4.4 3.8 - - + -
512B VAL* 4.6 14.1 - - + -
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Residues in contact with TRP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B TRP 2.9 16.0 + - - +
388B LEU* 3.7 5.6 - - + +
390B VAL* 1.3 77.7 - - - +
392B GLU* 1.3 74.7 + - + +
394B LYS* 3.1 6.8 + - - +
428B PHE* 5.4 2.5 - + - -
429B LEU* 4.1 13.7 - - + -
449B ILE* 3.7 41.3 - - + +
451B ASN* 3.1 41.1 - - + +
454B GLU* 3.2 25.5 + - - -
456B GLN* 3.6 37.7 - - + -
457B LYS* 4.4 3.1 - - - -
458B ARG* 2.9 58.9 + - + +
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LYS 4.2 4.7 - - - +
346B LEU* 3.7 10.9 - - - +
347B THR* 2.5 56.2 + - - +
388B LEU* 2.8 43.5 + - + +
389B MET* 4.2 2.2 - - - +
391B TRP* 1.3 81.6 - - + +
393B GLN* 1.3 71.5 + - - +
394B LYS* 3.3 16.9 + - - +
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Residues in contact with GLN 393 (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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344B VAL* 4.0 19.4 - - + +
345B LYS 4.4 9.5 + - - -
362B PHE* 3.4 28.5 - - - -
373B ILE* 3.9 28.3 - - + -
389B MET* 2.9 21.0 + - + +
392B GLU* 1.3 86.5 + - + +
394B LYS* 1.3 71.1 + - - +
395B VAL* 3.2 7.6 + - + -
509B PRO* 3.8 2.4 - - - +
510B PRO* 3.7 20.3 - - + +
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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
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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