Contacts of the helix formed by residues 376 - 388 (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 ILE 376 (chain D).
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Specific contacts
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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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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU* 3.6 28.7 - - + +
322D PRO* 4.0 18.8 - - + -
323D THR* 4.6 0.9 - - + -
372D PHE* 3.1 50.8 + - + +
373D ILE* 3.9 9.4 - - - -
376D ILE* 1.3 74.0 - - + +
378D HIS* 1.3 62.5 + - - +
380D LEU* 3.2 4.4 + - - +
381D TRP* 2.9 40.7 + - + +
399D LEU* 4.0 14.4 - - + -
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Residues in contact with HIS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D ILE* 2.9 33.9 + - + +
374D ASP* 4.8 3.6 - - - +
377D VAL* 1.3 73.4 - - - +
379D PRO* 1.3 65.2 - - + +
382D GLU* 2.9 58.5 + - + +
396D LEU* 3.8 7.9 - - + +
399D LEU* 3.7 19.9 - - + +
400D GLU* 2.9 42.4 + - + -
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Residues in contact with PRO 379 (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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280D LEU* 3.8 20.4 - - + +
284D LYS* 5.0 6.5 - - - +
373D ILE 3.4 11.7 - - - +
374D ASP 3.4 14.6 - - - +
375D TYR* 3.5 20.0 - - - +
376D ILE 3.6 9.4 - - - +
378D HIS* 1.3 93.8 - - + +
380D LEU* 1.3 55.8 + - - +
382D GLU* 4.2 7.7 - - + +
383D THR* 2.5 34.7 + - - -
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D HIS* 4.0 7.9 - - + -
280D LEU* 4.0 13.7 - - + +
283D LEU* 4.1 8.7 - - + -
312D ASN* 4.0 22.2 - - - +
315D HIS* 3.7 27.4 - - + +
316D CYS* 3.7 35.4 - - - -
319D LEU* 3.9 23.6 - - + -
376D ILE 3.3 15.3 + - - +
377D VAL* 3.2 4.4 + - - +
378D HIS 3.2 0.4 - - - -
379D PRO* 1.3 79.5 - - - +
381D TRP* 1.3 62.2 + - + +
383D THR* 3.2 4.7 + - - -
384D TRP* 2.9 24.8 + - - +
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Residues in contact with TRP 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TRP* 3.6 35.4 - + - -
175D LEU* 3.8 19.7 - - + -
316D CYS* 3.3 33.6 + - + +
319D LEU* 3.2 18.7 + - - +
320D SER* 4.0 2.7 - - - -
323D THR* 3.7 16.3 - - + +
377D VAL* 2.9 39.0 + - + +
380D LEU* 1.3 81.8 - - + +
382D GLU* 1.3 56.0 + - - +
384D TRP* 3.7 30.8 - + + +
385D ALA* 2.7 36.7 + - - +
392D ALA* 4.8 3.4 - - + -
395D ILE* 3.9 24.9 - - + -
396D LEU* 4.1 9.6 - - + +
399D LEU* 4.1 13.5 - - + -
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Residues in contact with GLU 382 (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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378D HIS* 2.9 44.7 + - + +
379D PRO* 4.2 6.8 - - - +
381D TRP* 1.3 75.4 - - - +
383D THR* 1.3 64.1 + - - +
385D ALA* 3.4 1.9 + - - +
386D ASP* 3.1 29.9 + - - +
396D LEU* 3.8 21.5 - - + +
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Residues in contact with THR 383 (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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280D LEU* 3.4 11.8 - - + +
283D LEU* 3.6 25.4 - - + -
284D LYS* 3.7 39.7 - - + +
287D VAL* 3.6 12.2 - - + +
379D PRO 2.5 25.2 + - - -
380D LEU 3.4 4.5 - - - -
381D TRP 3.2 0.4 - - - -
382D GLU* 1.3 78.0 + - - +
384D TRP* 1.3 65.2 + - - +
386D ASP* 3.2 9.7 + - - +
387D LEU* 3.1 16.6 + - - +
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Residues in contact with TRP 384 (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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175D LEU* 4.1 16.3 - - + +
181D LEU* 4.1 11.7 - - + -
283D LEU* 4.0 13.9 - - + +
309D VAL* 3.9 15.7 - - + -
312D ASN* 4.3 4.7 - - + -
313D MET* 3.7 52.7 - - + -
316D CYS* 3.8 25.8 - - - -
380D LEU 2.9 16.5 + - - +
381D TRP* 3.8 25.8 - + - +
383D THR* 1.3 76.8 - - - +
385D ALA* 1.3 65.5 + - - +
387D LEU* 3.0 34.9 + - + +
388D VAL* 3.1 34.6 + - + +
392D ALA* 4.4 4.0 - - + -
503D EDO 3.6 18.0 + - - -
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Residues in contact with ALA 385 (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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381D TRP* 2.7 22.5 + - + +
382D GLU 3.6 5.4 - - - +
384D TRP* 1.3 72.7 - - - +
386D ASP* 1.3 58.4 + - - +
388D VAL* 3.5 1.5 + - - +
389D HIS* 2.9 34.7 + - - +
390D PRO* 5.0 0.5 - - - +
392D ALA* 4.0 31.8 + - + +
393D GLN* 5.2 2.7 - - - +
396D LEU* 4.1 22.4 - - + -
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Residues in contact with ASP 386 (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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287D VAL* 3.8 24.3 - - + +
290D LYS* 3.1 17.3 + - - +
382D GLU* 3.1 22.6 + - - +
383D THR* 3.3 12.7 - - - +
385D ALA* 1.3 77.2 - - - +
387D LEU* 1.3 64.7 + - - +
388D VAL 3.4 0.2 + - - -
389D HIS* 3.4 18.3 + - - +
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Residues in contact with LEU 387 (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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180D ALA* 4.8 2.9 - - - +
181D LEU* 5.7 0.4 - - + -
283D LEU* 4.0 13.7 - - + -
286D MET* 4.0 22.9 - - + -
287D VAL* 3.8 25.1 - - + +
290D LYS* 2.8 28.5 + - + +
298D LEU* 3.8 45.3 - - + +
309D VAL* 4.4 11.9 - - + -
383D THR 3.1 7.4 + - - +
384D TRP* 3.0 39.8 + - + +
386D ASP* 1.3 76.4 - - - +
388D VAL* 1.3 62.9 + - + +
389D HIS 3.4 0.2 - - - -
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Residues in contact with VAL 388 (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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178D THR* 4.1 13.9 - - + -
180D ALA* 3.7 20.2 - - + +
181D LEU* 4.5 8.5 - - + -
290D LYS* 4.6 0.4 - - - -
298D LEU* 5.9 0.2 - - + -
384D TRP* 3.1 46.8 + - + +
385D ALA 4.1 3.6 - - - +
387D LEU* 1.3 85.2 - - + +
389D HIS* 1.3 67.4 + - - +
391D ASP* 2.9 33.1 + - + +
392D ALA* 4.1 8.1 - - + -
503D EDO 3.7 19.1 - - - +
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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