Contacts of the helix formed by residues 275 - 289 (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 LYS 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D SER* 4.6 10.8 - - - -
269D LEU* 3.8 11.2 - - - +
270D ALA* 4.7 7.6 - - - +
272D ASP* 2.8 17.7 + - + +
274D SER* 1.3 90.3 - - - +
276D HIS* 1.3 63.3 + - - +
277D MET 3.4 2.4 + - - -
278D ASN* 3.4 12.6 + - + +
279D LEU* 2.9 26.3 + - + +
509D EDO 3.5 43.7 - - - +
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Residues in contact with HIS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ALA 5.5 0.2 + - - -
272D ASP 3.8 1.6 + - - -
273D MET* 3.1 31.2 + - + +
274D SER 3.4 0.2 - - - -
275D LYS* 1.3 76.3 - - - +
277D MET* 1.3 80.1 + - + +
279D LEU* 3.1 5.5 + - - +
280D LEU* 2.7 55.4 + - + +
315D HIS* 3.0 36.2 + + + +
375D TYR 4.8 0.8 + - - -
376D ILE* 3.8 46.5 + - + +
380D LEU* 4.0 16.8 - - + -
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Residues in contact with MET 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D MET 4.9 0.4 + - - -
274D SER 4.9 3.9 + - - +
275D LYS 3.4 0.6 - - - -
276D HIS* 1.3 99.6 - - + +
278D ASN* 1.3 62.4 + - - +
280D LEU* 3.3 10.2 + - - +
281D ALA* 2.9 28.6 + - - +
375D TYR* 4.5 15.3 - - + +
376D ILE* 4.8 7.2 - - + -
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Residues in contact with ASN 278 (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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274D SER 5.6 3.2 + - - -
275D LYS* 3.4 13.4 + - + +
276D HIS 3.2 0.4 - - - -
277D MET* 1.3 81.3 - - - +
279D LEU* 1.3 65.4 + - - +
281D ALA* 3.3 7.3 + - - +
282D ASP* 3.1 29.8 + - - +
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ALA* 3.4 34.5 - - + +
275D LYS* 2.9 18.4 + - + +
276D HIS* 3.4 8.5 - - - +
278D ASN* 1.3 76.3 - - - +
280D LEU* 1.3 62.4 + - - +
282D ASP* 3.1 7.9 + - + +
283D LEU 3.0 18.7 + - - -
308D GLN* 5.0 3.4 - - + +
311D GLN* 4.1 27.8 - - + +
312D ASN* 3.5 32.7 - - - +
315D HIS* 3.8 30.1 - - + +
509D EDO 4.3 12.8 - - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D HIS* 2.7 43.3 + - + +
277D MET* 3.7 11.9 - - - +
279D LEU* 1.3 70.5 - - - +
281D ALA* 1.3 66.0 + - - +
283D LEU* 3.4 4.8 + - + -
284D LYS* 3.0 38.5 + - + +
312D ASN* 4.6 2.9 - - - +
315D HIS* 6.0 0.2 - - - -
379D PRO* 3.8 33.0 - - + +
380D LEU* 4.0 14.6 - - + -
383D THR* 3.4 34.1 - - + +
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Residues in contact with ALA 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D MET 2.9 16.5 + - - +
278D ASN* 3.7 11.9 - - - +
279D LEU 3.2 0.2 - - - -
280D LEU* 1.3 77.6 - - - +
282D ASP* 1.3 66.2 + - - +
284D LYS* 3.3 12.3 + - - +
285D THR* 3.2 24.3 + - - -
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Residues in contact with ASP 282 (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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278D ASN* 3.1 16.4 + - - +
279D LEU* 3.1 9.8 + - + +
281D ALA* 1.3 79.7 - - - +
283D LEU* 1.3 63.7 + - - +
285D THR* 3.4 10.4 + - - -
286D MET* 3.1 21.3 + - - +
308D GLN* 3.9 25.5 + - + +
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU 3.0 12.3 + - - +
280D LEU* 3.6 9.4 - - + +
282D ASP* 1.3 77.3 - - - +
284D LYS* 1.3 62.3 + - - +
286D MET* 3.1 7.1 + - - +
287D VAL* 3.0 24.1 + - + +
308D GLN* 4.6 10.3 - - - +
309D VAL* 5.5 1.8 - - - -
312D ASN* 3.8 39.6 + - + +
380D LEU* 4.1 13.5 - - + -
383D THR* 3.6 28.5 - - + -
384D TRP* 4.0 18.4 - - + +
387D LEU* 4.0 28.9 - - + -
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Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.0 37.8 + - + +
281D ALA* 3.5 12.3 - - - +
282D ASP 3.3 0.2 - - - -
283D LEU* 1.3 76.8 - - - +
285D THR* 1.3 56.0 + - - +
287D VAL* 3.2 5.7 + - - +
288D GLU* 2.9 44.5 + - - +
379D PRO* 5.0 6.7 - - - +
383D THR* 3.7 31.9 - - + -
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Residues in contact with THR 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ALA 3.2 13.9 + - - -
282D ASP* 3.6 13.1 + - - -
283D LEU 3.3 0.4 - - - -
284D LYS* 1.3 73.9 - - - +
286D MET* 1.3 63.0 + - - +
288D GLU* 3.4 14.8 + - - +
289D THR* 2.8 37.3 + - + +
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Residues in contact with MET 286 (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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282D ASP 3.1 4.9 + - - +
283D LEU* 3.1 11.0 + - - +
285D THR* 1.3 76.0 - - - +
287D VAL* 1.3 60.5 + - - +
289D THR* 3.1 9.0 + - - +
290D LYS* 2.8 30.4 + - - -
298D LEU* 4.7 2.0 - - + -
300D LEU* 3.9 12.3 - - + -
305D ASP* 3.4 42.0 - - + +
308D GLN* 2.3 48.7 - - - +
309D VAL* 3.4 20.4 - - + -
387D LEU* 4.0 21.8 - - + -
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Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LEU* 3.0 17.2 + - + +
284D LYS* 3.6 9.9 - - - +
286D MET* 1.3 77.0 - - - +
288D GLU* 1.3 64.2 + - + +
290D LYS* 3.3 23.4 + - + +
383D THR* 3.6 31.2 - - + +
386D ASP* 3.8 28.7 - - + +
387D LEU* 3.8 24.7 - - + +
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Residues in contact with GLU 288 (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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284D LYS* 2.9 31.1 + - - +
285D THR* 3.8 15.1 + - + +
286D MET 3.2 0.4 - - - -
287D VAL* 1.3 78.7 - - + +
289D THR* 1.3 63.9 + - + +
290D LYS 3.5 0.6 + - - -
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D THR* 2.8 29.1 + - + +
286D MET* 3.3 8.8 + - - +
288D GLU* 1.3 81.5 - - + +
290D LYS* 1.3 66.1 + - - +
291D LYS* 3.4 19.8 + - - +
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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