Contacts of the helix formed by residues 364 - 376 (chain D) in PDB entry 4OGB
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 SER 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337D MET* 5.8 2.1 - - - +
357D MET* 6.4 0.2 - - - +
362D ASN 3.5 6.4 + - - -
363D ALA* 1.3 73.7 - - - +
365D VAL* 1.3 64.5 + - - +
366D GLU* 3.4 4.3 + - - -
367D LYS* 3.4 31.7 + - - +
368D SER* 2.8 30.5 + - - -
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Residues in contact with VAL 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D THR* 3.8 19.5 - - + -
334D ASP* 6.1 0.4 - - - +
337D MET* 3.7 47.1 - - + +
341D PHE* 4.2 13.7 - - + -
363D ALA* 3.8 6.2 - - + -
364D SER* 1.3 76.1 - - - +
366D GLU* 1.3 80.1 + - - +
368D SER* 3.4 5.8 + - - -
369D GLN* 3.1 22.6 + - + +
406D TYR* 4.9 4.0 - - + -
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Residues in contact with GLU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D SER* 3.4 1.2 - - - -
365D VAL* 1.3 91.2 + - + +
367D LYS* 1.4 55.4 + - - +
369D GLN* 3.5 4.0 + - - +
370D VAL* 3.1 28.8 + - - +
405D TRP* 5.7 0.2 - - + -
406D TYR* 3.5 39.7 - - + +
409D THR* 3.3 31.7 + - - +
410D ILE* 3.9 11.7 - - + +
411D PRO* 3.8 19.1 - - - +
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Residues in contact with LYS 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D SER* 3.4 24.7 + - - +
366D GLU* 1.4 71.3 - - - +
368D SER* 1.3 60.1 - - - +
369D GLN 3.1 1.6 - - - -
370D VAL* 3.6 3.8 - - - +
371D GLY* 2.7 32.1 + - - -
410D ILE* 3.7 43.7 - - + -
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Residues in contact with SER 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D MET* 5.5 3.9 - - - +
357D MET* 3.5 36.5 - - - +
364D SER* 2.8 28.0 + - - -
365D VAL* 3.6 7.2 - - - -
367D LYS* 1.3 80.7 - - - +
369D GLN* 1.3 55.9 + - - +
371D GLY* 3.3 1.2 + - - -
372D PHE* 2.6 36.4 + - - +
502D 2SR 3.2 11.3 - - - +
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Residues in contact with GLN 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D PRO* 4.7 0.2 - - - +
329D TYR* 2.4 41.9 + - - +
333D THR* 4.0 29.9 + - + +
336D ILE* 4.8 5.5 - - - +
337D MET* 5.0 7.5 - - - -
365D VAL 3.1 16.4 + - - +
366D GLU 3.6 8.7 - - - +
367D LYS 3.1 0.2 - - - -
368D SER* 1.3 76.1 - - - +
370D VAL* 1.3 60.1 + - - +
372D PHE* 3.1 9.5 + - - +
373D ILE* 2.8 37.3 + - - +
406D TYR* 3.9 21.3 - - + -
502D 2SR 2.9 30.0 + - - -
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Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D GLU 3.1 16.7 + - - +
367D LYS* 3.8 8.7 - - - +
369D GLN* 1.3 73.5 - - - +
371D GLY* 1.3 58.4 + - - +
373D ILE* 3.8 5.2 - - - +
374D ASP* 2.8 53.5 + - - +
403D ARG* 3.4 35.0 - - - +
406D TYR* 4.1 2.4 - - + +
407D GLN* 3.6 42.2 - - + +
410D ILE* 4.4 3.4 - - + -
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Residues in contact with GLY 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D LYS 2.7 20.7 + - - -
368D SER* 3.6 1.8 - - - -
370D VAL* 1.3 73.7 - - - +
372D PHE* 1.3 64.1 + - - +
374D ASP* 4.5 1.6 - - - -
375D TYR* 3.0 43.9 + - - +
502D 2SR 4.8 3.8 - - - -
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MET* 4.6 2.5 - - + -
319D LEU* 4.1 12.6 - - + -
322D PRO* 4.6 12.1 - - + -
329D TYR* 5.4 0.2 - - - -
368D SER 2.6 21.6 + - - +
369D GLN* 3.5 15.7 - - - +
371D GLY* 1.3 69.8 - - - +
373D ILE* 1.3 58.4 + - - +
376D ILE* 2.8 55.8 + - + +
377D VAL* 3.1 30.2 + - + -
502D 2SR 3.3 91.2 - + + +
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Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D PRO* 4.1 8.1 - - + -
329D TYR* 3.6 26.7 - - + +
369D GLN* 2.8 20.9 + - + +
370D VAL* 3.8 3.1 - - - +
372D PHE* 1.3 78.1 - - + +
374D ASP* 1.3 65.8 + - - +
375D TYR 3.1 0.9 + - - -
377D VAL* 3.4 9.1 + - + -
378D HIS* 2.9 41.1 + - + +
379D PRO* 3.4 0.2 - - - +
399D LEU* 3.7 35.2 - - + -
403D ARG* 3.7 46.0 - - + +
406D TYR* 5.5 1.1 - - + -
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Residues in contact with ASP 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D VAL* 2.8 32.6 + - - +
371D GLY* 3.9 3.6 - - - +
373D ILE* 1.3 76.5 - - - +
375D TYR* 1.3 77.0 + - + +
378D HIS* 4.8 4.0 - - - +
379D PRO* 3.4 14.9 - - - +
403D ARG* 3.1 44.5 + - - +
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Residues in contact with TYR 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D HIS* 4.8 1.2 + - - -
277D MET* 4.5 10.9 - - - +
371D GLY* 3.0 31.1 + - - +
374D ASP* 1.3 92.3 - - + +
376D ILE* 1.3 72.0 + - + +
379D PRO* 3.5 13.6 - - - +
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Residues in contact with ILE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MET* 4.0 7.9 - - + -
276D HIS* 3.8 25.6 + - + +
277D MET* 4.8 7.2 - - + -
319D LEU* 3.8 20.2 - - + -
372D PHE* 2.8 35.9 + - + +
375D TYR* 1.3 91.5 - - + +
377D VAL* 1.3 66.1 + - - +
378D HIS 3.5 0.9 - - - -
379D PRO* 3.6 2.6 - - - +
380D LEU* 3.3 22.2 + - - +
502D 2SR 3.2 42.4 - - + -
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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