Contacts of the helix formed by residues 349 - 364 (chain A) in PDB entry 3PM0
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 TYR 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A LEU* 2.8 40.1 + - + +
346A PHE 3.5 4.5 - - - +
348A ARG* 1.3 95.2 - - + +
350A PRO* 1.3 65.8 - - - +
351A ASP 3.1 3.6 - - - -
352A VAL* 3.0 26.5 + - + +
353A GLN 2.9 18.4 + - - -
391A PHE* 3.9 19.5 - + - -
438A GLU 5.3 1.2 + - - -
439A ASN* 5.7 0.2 - - - -
440A PHE* 3.7 39.1 + + + +
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Residues in contact with PRO 350 (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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346A PHE 3.6 8.2 - - - +
347A THR* 3.9 12.8 - - - +
348A ARG 3.4 8.1 - - - +
349A TYR* 1.3 88.6 - - - +
351A ASP* 1.3 57.1 + - - +
353A GLN* 3.3 10.7 + - + +
354A THR* 2.9 31.6 + - - -
493A PHE 6.0 0.4 - - - +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TYR* 3.0 1.6 + - - -
350A PRO* 1.3 77.5 - - - +
352A VAL* 1.3 68.3 + - + +
354A THR* 3.1 9.1 + - - +
355A ARG* 3.0 65.9 + - - +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU 4.7 1.1 - - - +
346A PHE* 4.5 2.9 - - + -
349A TYR* 3.0 33.2 + - + +
351A ASP* 1.3 76.5 - - + +
353A GLN* 1.3 69.1 + - - +
355A ARG* 3.1 6.0 + - - +
356A VAL* 2.8 27.4 + - - +
380A TYR* 3.7 23.1 - - + +
384A PHE* 3.7 32.1 - - + -
440A PHE* 3.9 22.4 - - + +
442A PRO* 4.5 8.3 - - + -
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Residues in contact with GLN 353 (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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346A PHE* 2.8 61.2 + - + +
349A TYR 2.9 1.6 + - - -
350A PRO* 3.4 15.1 - - - +
352A VAL* 1.3 85.7 - - - +
354A THR* 1.3 57.1 + - - +
356A VAL* 4.0 2.9 - - - +
357A GLN* 2.8 44.8 + - + +
492A ASP* 3.7 8.5 - - - +
493A PHE* 2.8 53.1 + - - -
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Residues in contact with THR 354 (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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350A PRO 2.9 15.0 + - - -
351A ASP* 3.1 12.7 + - - +
353A GLN* 1.3 75.9 - - - +
355A ARG* 1.3 56.5 + - + +
357A GLN* 3.3 14.0 + - - +
358A ALA* 2.6 41.7 + - + +
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Residues in contact with ARG 355 (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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351A ASP* 3.0 53.1 + - - +
352A VAL* 5.0 4.0 - - - +
354A THR* 1.3 76.6 - - + +
356A VAL* 1.3 55.4 + - - +
358A ALA* 2.7 25.7 + - - +
359A GLU* 2.8 16.3 + - - +
380A TYR* 3.3 40.4 + - + -
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Residues in contact with VAL 356 (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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346A PHE* 3.7 34.3 - - + -
352A VAL 2.8 22.0 - - - +
353A GLN 4.0 2.5 - - - +
355A ARG* 1.3 73.8 - - - +
357A GLN* 1.3 61.1 + - - +
359A GLU* 3.5 5.3 + - - +
360A LEU* 3.1 33.3 + - + +
380A TYR* 3.3 26.4 - - + -
381A VAL* 4.4 22.1 - - + +
384A PHE* 4.3 13.9 - - + -
484A ILE* 5.8 2.0 - - + -
488A ALA* 4.0 10.1 - - + -
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Residues in contact with GLN 357 (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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353A GLN* 2.8 34.0 + - - +
354A THR* 3.4 15.4 + - + +
356A VAL* 1.3 82.4 - - + +
358A ALA* 1.3 55.2 + - - +
360A LEU* 3.9 5.7 - - - +
361A ASP* 2.4 34.0 + - - +
488A ALA* 3.0 23.6 + - + +
491A CYS 2.6 30.7 + - - -
492A ASP* 2.9 21.3 + - - +
523A ARG* 3.4 21.8 - - - +
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Residues in contact with ALA 358 (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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354A THR* 2.6 24.9 + - + +
355A ARG* 2.7 10.0 + - - +
357A GLN* 1.3 73.4 - - - +
359A GLU* 1.3 60.2 + - - +
360A LEU 3.0 1.3 - - - -
361A ASP* 2.8 24.4 + - - +
362A GLN* 2.9 13.5 + - - +
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Residues in contact with GLU 359 (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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355A ARG 2.8 16.6 + - - +
356A VAL 4.0 2.5 - - - +
358A ALA* 1.3 73.1 - - - +
360A LEU* 1.3 56.0 + - - +
362A GLN* 3.8 13.2 - - - +
363A VAL* 2.9 38.0 + - + +
378A LEU* 3.2 20.3 - - + +
379A PRO* 3.1 14.2 - - + +
380A TYR* 2.8 36.8 + - + +
381A VAL* 2.9 35.0 + - - +
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Residues in contact with LEU 360 (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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356A VAL* 3.1 17.2 + - + +
357A GLN* 3.9 7.0 - - - +
358A ALA 3.0 0.4 - - - -
359A GLU* 1.3 79.7 - - - +
361A ASP* 1.3 59.9 + - - +
364A VAL* 3.0 38.7 + - + +
370A PRO* 4.0 12.6 - - + -
378A LEU* 3.8 30.1 - - + -
381A VAL* 3.9 15.5 - - + -
485A SER* 3.1 36.1 - - - +
488A ALA* 3.9 14.1 - - + -
489A HIS* 3.4 28.3 - - + +
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Residues in contact with ASP 361 (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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357A GLN 2.4 26.7 - - - +
358A ALA* 2.8 9.7 + - - +
360A LEU* 1.3 79.9 - - - +
362A GLN* 1.3 60.1 + - - +
365A GLY* 3.1 28.8 - - - +
366A ARG* 2.4 36.2 + - + +
523A ARG* 2.7 21.5 + - - -
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Residues in contact with GLN 362 (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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358A ALA 2.9 13.9 + - - +
359A GLU* 3.8 14.2 - - - +
361A ASP* 1.3 81.1 - - - +
363A VAL* 1.3 68.5 + - + +
365A GLY* 4.4 1.2 + - - -
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU* 2.9 24.7 + - + +
362A GLN* 1.3 86.9 - - + +
364A VAL* 1.3 66.6 + - + +
365A GLY* 3.6 0.3 + - - -
368A ARG* 4.8 2.6 + - - -
374A ASP* 4.9 6.5 - - + +
377A ASN* 3.1 51.6 - - + +
378A LEU* 3.7 13.0 - - + -
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.0 29.3 + - + +
363A VAL* 1.3 77.6 - - + +
365A GLY* 1.3 76.8 + - - +
367A ASP* 4.5 2.1 + - - +
368A ARG* 3.7 52.5 + - - +
369A LEU 4.5 0.7 - - - -
370A PRO* 3.6 37.7 - - + -
374A ASP* 4.1 20.6 - - + -
378A LEU* 4.5 1.1 - - + -
489A HIS* 3.9 4.0 - - + -
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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
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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