Contacts of the helix formed by residues 275 - 289 (chain D) in PDB entry 3K75
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 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D ARG* 4.0 13.5 - - - +
274D GLY* 1.3 73.2 - - - -
276D ASP* 1.3 68.8 + - - +
277D ILE* 3.3 6.8 + - - +
278D PHE* 2.7 31.7 + - - +
279D ASN* 2.9 10.5 + - - -
333D ARG 3.1 23.3 - - - -
334D SER* 3.2 16.1 + - - -
335D GLU* 5.4 0.3 - - - +
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Residues in contact with ASP 276 (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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275D SER* 1.3 74.8 - - - +
277D ILE* 1.3 67.1 + - + +
279D ASN* 3.4 8.1 + - - +
280D LYS* 3.1 23.2 + - - +
283D ARG* 5.1 1.4 + - - -
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Residues in contact with ILE 277 (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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275D SER* 2.7 8.6 + - - +
276D ASP* 1.3 77.9 - - + +
278D PHE* 1.3 59.5 + - - +
280D LYS* 3.2 8.8 + - + +
281D ASN* 2.9 45.7 + - - +
334D SER 4.8 1.8 - - - +
335D GLU* 3.5 36.8 - - + +
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Residues in contact with PHE 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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270D LEU* 4.2 7.9 - - + -
274D GLY* 4.5 0.4 - - - -
275D SER* 2.7 31.3 + - - +
277D ILE* 1.3 71.9 - - - +
279D ASN* 1.3 72.1 + - - +
281D ASN* 3.2 8.3 + - + +
282D MET* 2.8 60.9 + - - +
320D PHE* 3.8 17.0 - + - -
325D TRP* 4.1 20.0 - + - -
328D ARG* 4.1 16.4 - - + -
332D ASP 4.9 1.6 - - - -
333D ARG* 3.6 49.1 - - + -
334D SER 4.3 6.6 + - - +
337D HIS* 6.3 0.7 - - - -
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Residues in contact with ASN 279 (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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270D LEU* 3.8 9.8 - - - +
271D TYR* 3.0 43.3 + - + +
274D GLY* 3.1 27.5 - - - -
275D SER 2.9 9.7 + - - +
276D ASP* 3.8 9.6 + - - +
278D PHE* 1.3 86.3 - - - +
280D LYS* 1.3 57.7 + - - +
282D MET* 4.1 4.3 - - - +
283D ARG* 3.1 54.6 + - - +
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Residues in contact with LYS 280 (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 ASP 3.1 14.4 + - - +
277D ILE* 3.5 13.2 - - + +
278D PHE 3.1 0.4 - - - -
279D ASN* 1.3 78.7 - - - +
281D ASN* 1.3 64.5 + - - +
283D ARG* 3.6 15.5 + - - +
284D ALA* 3.2 23.0 + - - +
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Residues in contact with ASN 281 (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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277D ILE* 2.9 37.7 + - - +
278D PHE* 3.2 7.8 + - + +
280D LYS* 1.3 77.5 - - - +
282D MET* 1.3 62.0 + - - +
284D ALA* 3.4 6.8 + - - +
285D HIS* 3.2 22.7 + - - +
325D TRP* 4.4 7.8 - - + -
337D HIS* 3.8 40.6 - - + +
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Residues in contact with MET 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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270D LEU* 3.9 28.5 - - + -
278D PHE* 2.8 48.4 + - + +
279D ASN* 4.1 4.5 - - - +
281D ASN* 1.3 70.9 - - - +
283D ARG* 1.3 61.6 + - + +
285D HIS* 3.3 3.9 + - - +
286D ALA* 2.8 26.4 + - - +
293D ILE* 4.1 7.4 - - + +
319D ILE* 4.2 11.4 - - + -
320D PHE* 3.5 35.9 - - + -
323D ILE* 3.6 23.5 - - + +
325D TRP* 3.5 24.0 - - + -
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Residues in contact with ARG 283 (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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271D TYR* 3.8 32.5 - - - -
276D ASP 5.1 1.2 + - - -
279D ASN* 3.1 42.8 + - - +
280D LYS* 4.0 15.1 - - - +
282D MET* 1.3 76.4 - - + +
284D ALA* 1.3 61.8 + - - +
286D ALA* 3.1 21.4 - - - +
287D LEU* 3.1 16.4 + - + +
293D ILE* 3.3 43.6 + - + +
294D ASN* 4.8 7.9 - - - +
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Residues in contact with ALA 284 (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 LYS 3.2 18.1 + - - +
281D ASN* 3.6 9.0 - - - +
282D MET 3.2 0.2 - - - -
283D ARG* 1.3 75.4 - - - +
285D HIS* 1.3 59.8 + - - +
287D LEU* 3.3 13.7 + - - +
288D GLU* 3.1 22.9 + - - +
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Residues in contact with HIS 285 (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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281D ASN 3.2 10.8 + - - +
282D MET* 3.3 6.3 + - - +
284D ALA* 1.3 75.9 - - - +
286D ALA* 1.3 65.5 + - - +
288D GLU* 3.1 29.2 + - - +
289D LYS* 3.0 43.5 + - + +
323D ILE* 3.5 29.6 + - + -
324D GLN 4.5 1.2 + - - -
325D TRP* 3.2 54.2 + + + -
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Residues in contact with ALA 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 MET 2.8 14.4 + - - +
283D ARG* 3.1 13.0 - - - +
284D ALA 3.2 0.2 - - - -
285D HIS* 1.3 79.1 - - - +
287D LEU* 1.3 61.6 + - - +
289D LYS* 3.1 2.8 + - - +
290D GLY 3.0 7.1 + - - -
291D PHE* 2.8 34.4 + - - +
293D ILE* 3.7 33.0 - - + +
323D ILE* 4.0 14.1 - - + -
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Residues in contact with LEU 287 (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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283D ARG* 3.1 13.8 + - + +
284D ALA* 3.5 11.4 - - - +
286D ALA* 1.3 76.2 - - - +
288D GLU* 1.3 67.7 + - - +
290D GLY* 3.3 9.2 + - - -
291D PHE 3.4 16.6 - - - +
292D THR* 4.5 10.8 - - - +
301D LEU* 3.7 21.2 - - + +
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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 ALA 3.1 13.1 + - - +
285D HIS* 3.1 36.6 + - - +
287D LEU* 1.3 78.1 - - - +
289D LYS* 1.3 65.1 + - + +
290D GLY* 3.1 5.0 + - - -
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Residues in contact with LYS 289 (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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41B LYS* 6.2 2.4 - - - +
285D HIS* 3.0 38.0 + - + +
286D ALA 3.5 2.9 - - - +
288D GLU* 1.3 81.6 - - + +
290D GLY* 1.3 60.3 + - - +
291D PHE* 3.3 23.2 - - + -
323D ILE* 3.5 29.4 - - - +
324D GLN* 3.7 30.3 + - - +
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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