Contacts of the helix formed by residues 360 - 373 (chain A) in PDB entry 4OE5
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 LEU 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A VAL* 3.9 15.5 - - + -
324A HIS 3.5 17.7 - - - +
325A ARG* 3.3 34.5 - - - +
327A ALA* 4.3 11.4 - - + +
329A VAL* 3.9 25.4 - - + -
332A VAL* 6.0 0.2 - - + -
357A PRO* 3.2 12.3 + - + +
359A SER* 1.3 83.6 + - - +
361A TRP* 1.3 60.0 + - - +
362A PRO* 3.5 1.8 - - - -
363A GLN* 3.2 11.1 + - + +
364A ILE* 2.9 39.8 + - + +
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Residues in contact with TRP 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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356A VAL* 3.5 16.6 - - + -
357A PRO 3.2 12.6 + - - +
358A HIS* 3.4 12.5 + + - +
360A LEU* 1.3 75.6 - - - +
362A PRO* 1.4 65.2 - - + +
364A ILE* 4.1 15.7 - - + -
365A LYS* 2.5 86.0 + - + +
368A LEU* 4.2 9.4 - - + -
369A LEU* 6.2 0.2 - - + -
416A LEU* 3.7 27.4 - - + -
435A GLU* 3.9 18.7 + - - -
455A VAL* 3.8 23.8 - - + -
457A VAL* 3.7 33.0 - - + +
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Residues in contact with PRO 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 HIS 3.5 14.8 - - - +
359A SER 4.0 6.5 - - - +
360A LEU 3.6 3.6 - - - -
361A TRP* 1.4 93.8 - - + +
363A GLN* 1.3 61.4 + - - +
365A LYS* 3.9 6.1 - - + +
366A GLY* 3.1 21.0 + - - -
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Residues in contact with GLN 363 (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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329A VAL* 4.5 18.6 - - + -
359A SER 5.8 0.4 - - - +
360A LEU* 3.2 14.1 + - + +
362A PRO* 1.3 76.4 - - - +
364A ILE* 1.3 64.0 + - - +
366A GLY* 4.0 0.7 - - - -
367A ARG* 3.2 32.0 + - + +
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Residues in contact with ILE 364 (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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323A VAL* 4.2 12.1 - - + -
329A VAL* 4.2 24.0 - - + -
332A VAL* 4.0 30.1 - - + -
333A VAL* 4.2 3.4 - - + +
354A LEU* 4.7 0.9 - - + -
356A VAL* 4.1 22.9 - - + -
360A LEU* 2.9 41.8 + - + +
361A TRP* 3.8 13.5 - - + +
363A GLN* 1.3 71.2 - - - +
365A LYS* 1.3 57.8 + - - +
367A ARG* 3.4 2.1 + - - +
368A LEU* 2.9 50.7 + - + +
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TRP* 2.5 67.3 + - + +
362A PRO* 3.9 5.4 - - + +
364A ILE* 1.3 73.3 - - - +
366A GLY* 1.3 62.2 + - - +
368A LEU* 3.2 4.1 + - - +
369A LEU* 3.1 44.6 + - + +
416A LEU* 3.9 29.8 - - + +
435A GLU* 5.1 3.0 + - - -
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Residues in contact with GLY 366 (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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362A PRO 3.1 16.7 + - - -
363A GLN* 4.0 1.3 - - - -
365A LYS* 1.3 76.6 - - - +
367A ARG* 1.3 61.9 + - - +
369A LEU* 3.4 6.9 + - - +
370A GLU* 3.1 34.1 + - - +
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Residues in contact with ARG 367 (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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329A VAL* 4.2 8.5 - - + -
330A GLU* 2.7 41.4 + - - +
333A VAL* 3.7 21.2 - - + +
363A GLN* 3.2 19.7 + - + +
366A GLY* 1.3 72.8 - - - +
368A LEU* 1.3 65.1 + - - +
370A GLU* 2.9 34.3 + - - +
371A GLU* 2.7 64.9 + - - +
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Residues in contact with LEU 368 (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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332A VAL* 6.4 0.2 - - + -
333A VAL* 4.1 21.3 - - + +
336A THR* 4.8 12.1 - - + -
337A LEU* 3.8 34.0 - - + +
354A LEU* 3.9 18.2 - - + -
361A TRP* 4.2 14.8 - - + -
364A ILE* 2.9 39.9 + - + +
365A LYS 3.6 4.7 - - - +
367A ARG* 1.3 75.2 - - - +
369A LEU* 1.3 66.3 + - + +
371A GLU* 3.9 1.0 - - - +
372A HIS* 2.9 30.7 + - - +
416A LEU* 6.3 0.2 - - + -
433A ILE* 4.5 13.8 - - + +
453A LEU* 5.1 2.2 - - + -
455A VAL* 5.1 4.9 - - + -
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Residues in contact with LEU 369 (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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361A TRP* 6.2 0.2 - - + -
365A LYS* 3.1 46.4 + - + +
366A GLY* 4.0 5.2 - - - +
367A ARG 3.2 0.4 - - - -
368A LEU* 1.3 85.1 - - + +
370A GLU* 1.3 65.4 + - + +
372A HIS* 3.4 5.9 + - - +
373A SER* 3.2 22.5 + - - -
416A LEU* 4.3 37.2 - - + +
417A ALA* 4.4 13.2 - - + -
433A ILE* 4.7 6.5 - - + -
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Residues in contact with GLU 370 (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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366A GLY* 3.1 17.7 + - - +
367A ARG* 2.9 43.8 + - - +
369A LEU* 1.3 76.6 - - + +
371A GLU* 1.3 62.1 + - - +
373A SER* 2.7 25.0 + - - -
374A ARG* 3.8 9.5 + - - +
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Residues in contact with GLU 371 (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 VAL* 3.9 12.3 - - + -
334A SER* 6.3 0.7 - - - -
337A LEU* 3.4 24.0 - - + -
367A ARG* 2.7 53.2 + - - +
370A GLU* 1.3 74.1 - - - +
372A HIS* 1.3 66.0 + - - +
374A ARG* 3.0 36.5 + - - +
375A ILE* 3.7 9.4 + - - +
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Residues in contact with HIS 372 (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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337A LEU* 4.3 2.8 - - + +
341A PHE* 4.7 3.6 - + - -
368A LEU 2.9 21.2 + - - +
369A LEU* 3.6 9.5 + - - +
370A GLU 3.3 0.2 - - - -
371A GLU* 1.3 76.9 - - - +
373A SER* 1.3 67.3 + - - +
375A ILE* 3.1 30.4 + - + +
417A ALA* 3.7 25.0 - - + +
418A GLY* 3.8 9.9 - - - -
430A GLU* 5.8 1.8 - - + -
431A PRO* 2.7 47.1 + - + +
433A ILE* 3.8 26.9 - - + -
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Residues in contact with SER 373 (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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369A LEU 3.2 10.2 + - - -
370A GLU* 2.7 23.7 + - - -
372A HIS* 1.3 83.1 + - - +
374A ARG* 1.3 60.9 + - - +
375A ILE 3.4 3.0 + - - +
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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