Contacts of the helix formed by residues 385 - 395 (chain A) in PDB entry 4PYP
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 PRO 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A SER* 3.7 12.1 - - - +
328A VAL* 4.1 9.9 - - + -
380A GLU* 3.1 25.6 - - + +
381A VAL 4.0 5.8 - - - +
382A GLY 3.0 13.2 - - - +
384A GLY* 1.3 86.7 - - - +
386A ILE* 1.3 67.5 + - + +
387A PRO 3.5 0.2 - - - -
388A TRP* 3.1 15.1 + - - +
389A PHE* 3.3 32.5 + - + -
601A BNG 4.3 25.5 - - + +
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Residues in contact with ILE 386 (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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328A VAL* 4.8 3.4 - - + -
333A ARG* 3.1 48.9 - - + +
336A LEU* 4.1 21.8 - - + -
337A HIS* 3.6 28.5 - - + +
381A VAL 4.4 1.6 - - - +
382A GLY 3.4 14.5 + - - +
385A PRO* 1.3 81.4 - - + +
387A PRO* 1.3 70.1 - - + +
388A TRP 3.1 0.5 + - - -
389A PHE* 3.2 10.4 + - + +
390A ILE* 3.1 43.0 + - + +
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Residues in contact with PRO 387 (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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278A LEU* 3.3 51.2 - - + +
279A GLN* 3.8 14.0 + - - +
282A GLN* 4.3 9.9 - - + +
337A HIS* 4.1 7.6 - - + +
383A PRO* 3.3 32.1 - - + +
384A GLY 4.3 3.4 - - - +
386A ILE* 1.3 93.8 - - + +
388A TRP* 1.3 62.6 + - - +
390A ILE* 4.1 1.9 - - - +
391A VAL* 3.3 21.8 + - - +
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Residues in contact with TRP 388 (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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137A THR* 6.1 4.9 - - + -
279A GLN* 3.4 28.0 - - - -
282A GLN* 4.0 23.3 - - - +
384A GLY 4.3 5.2 - - - -
385A PRO 3.1 7.7 + - - +
387A PRO* 1.3 75.2 - - - +
389A PHE* 1.3 67.7 + - - +
390A ILE 2.8 2.1 + - - -
391A VAL* 2.9 18.2 + - + +
392A ALA* 3.6 7.9 + - - +
404A ILE* 4.2 27.1 - - + +
407A ALA* 3.9 16.2 - - + -
408A GLY* 3.7 22.4 - - - -
411A ASN* 3.9 16.0 - - + +
601A BNG 3.8 42.6 + - + +
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Residues in contact with PHE 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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161A GLN* 6.2 0.4 - - - -
328A VAL* 3.7 31.0 - - + -
333A ARG* 4.1 30.7 - - - -
385A PRO* 3.3 31.7 + - + -
386A ILE* 3.2 15.2 + - + +
388A TRP* 1.3 77.5 - - - +
390A ILE* 1.3 59.6 + - - +
392A ALA* 3.5 8.8 + - + +
393A GLU* 2.9 32.9 + - - +
601A BNG 3.5 32.4 - - + +
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Residues in contact with ILE 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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274A ILE* 4.7 3.4 - - + -
278A LEU* 3.6 38.6 - - + -
333A ARG* 3.8 24.2 - - + +
334A ARG* 5.2 2.9 - - + -
337A HIS* 5.6 0.4 - - + -
386A ILE* 3.1 32.6 + - + +
387A PRO 4.4 0.9 - - - +
388A TRP 2.8 2.8 + - - -
389A PHE* 1.3 72.5 - - - +
391A VAL* 1.3 55.9 + - + +
393A GLU* 3.1 8.8 + - - +
394A LEU* 2.7 54.8 + - + +
452A VAL* 4.9 13.5 - - + -
453A PRO* 5.2 7.9 - - + +
455A THR* 4.0 8.7 - - + +
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Residues in contact with VAL 391 (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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275A ALA* 3.4 29.4 - - + +
387A PRO 3.3 18.8 - - - +
388A TRP* 2.9 8.9 + - + +
390A ILE* 1.3 77.3 - - + +
392A ALA* 1.3 62.5 + - - +
393A GLU 3.0 0.2 - - - -
394A LEU* 3.0 16.3 + - - +
395A PHE* 3.1 18.6 + - + +
400A ARG* 4.2 0.6 - - - +
403A ALA* 3.8 35.4 - - + +
404A ILE* 4.0 19.7 - - + -
407A ALA* 4.4 13.5 - - + -
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Residues in contact with ALA 392 (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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388A TRP 3.6 5.8 + - - +
389A PHE* 3.5 12.2 + - + +
390A ILE 3.3 0.8 - - - -
391A VAL* 1.3 78.2 - - - +
393A GLU* 1.3 60.9 + - + +
395A PHE 3.3 15.1 - - - +
400A ARG* 3.4 32.2 + - - +
404A ILE* 4.9 7.0 - - + +
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Residues in contact with GLU 393 (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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333A ARG* 3.6 24.4 + - - -
389A PHE* 2.9 26.2 + - - +
390A ILE* 3.1 5.5 + - - +
391A VAL 3.0 0.4 - - - -
392A ALA* 1.3 83.5 - - + +
394A LEU* 1.3 64.8 + - - +
395A PHE 3.3 2.9 + - - -
455A THR* 3.2 45.1 + - + +
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Residues in contact with LEU 394 (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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268A TYR* 5.8 0.9 - - - -
271A PRO* 3.1 49.4 - - + +
274A ILE* 4.0 23.3 - - + -
275A ALA* 4.5 2.9 - - + +
390A ILE* 2.7 28.6 + - + +
391A VAL* 3.0 3.3 + - - +
393A GLU* 1.3 78.5 - - - +
395A PHE* 1.3 81.9 + - + +
453A PRO* 4.9 13.5 - - + -
455A THR* 4.0 22.2 - - + -
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Residues in contact with PHE 395 (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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262A LEU* 4.0 21.8 - - + -
268A TYR* 4.0 18.2 - + - -
271A PRO* 3.9 13.2 - - + -
272A ILE* 3.8 32.1 - - + -
275A ALA* 4.3 11.0 - - + -
391A VAL* 3.1 15.3 + - + +
392A ALA 3.3 6.4 - - - +
393A GLU 3.3 2.3 - - - -
394A LEU* 1.3 107.4 - - + +
396A SER* 1.3 60.4 + - - +
399A PRO* 3.7 22.2 - - + -
400A ARG* 2.9 45.7 + - - +
403A ALA* 3.4 24.5 - - + -
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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
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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