Contacts of the helix formed by residues 280 - 293 (chain D) in PDB entry 3MSS
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 VAL 280 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D LEU* 3.6 36.8 - - + +
281D GLU* 1.3 63.6 + - + +
282D GLU* 3.3 7.3 - - - +
283D PHE* 3.3 5.4 + - - +
284D LEU* 2.9 40.4 + - + +
311D PHE* 3.8 24.2 - - + -
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Residues in contact with GLU 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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280D VAL* 1.3 78.0 - - + +
282D GLU* 1.3 65.7 + - - +
284D LEU* 3.9 10.2 - - - +
285D LYS* 3.0 29.8 + - + +
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Residues in contact with GLU 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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280D VAL 3.3 3.5 - - - +
281D GLU* 1.3 81.2 - - - +
283D PHE* 1.3 65.7 + - - +
285D LYS* 3.4 28.0 + - - +
286D GLU* 3.0 23.2 + - - +
386D ARG* 5.4 11.2 - - - +
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Residues in contact with PHE 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 LYS* 3.7 38.1 - - + -
272D THR 4.0 17.0 - - - -
273D LEU* 3.7 31.4 - - + -
280D VAL* 3.5 10.4 - - - +
281D GLU 3.3 0.4 - - - -
282D GLU* 1.3 80.5 - - - +
284D LEU* 1.3 66.6 + - + +
286D GLU* 3.3 9.6 + - - +
287D ALA* 3.1 24.9 + - - +
306D THR* 4.3 4.9 - - + -
311D PHE* 3.2 49.4 - + + -
312D TYR 4.2 2.5 - - - -
313D ILE* 3.7 31.2 - - + +
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Residues in contact with LEU 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 VAL* 2.9 33.8 + - + +
281D GLU* 4.1 9.2 - - - +
283D PHE* 1.3 84.9 - - + +
285D LYS* 1.3 56.0 + - - +
287D ALA* 3.4 6.8 + - - +
288D ALA* 3.0 27.5 + - - +
306D THR* 4.3 20.4 - - + +
311D PHE* 3.6 33.7 - - + -
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Residues in contact with LYS 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 GLU* 3.0 20.8 + - + +
282D GLU* 3.6 25.2 + - - +
284D LEU* 1.3 74.5 - - - +
286D GLU* 1.3 64.5 + - - +
288D ALA* 3.4 7.1 + - + +
289D VAL* 3.0 36.1 + - + +
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Residues in contact with GLU 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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1D STI 2.9 57.6 + - + -
271D LYS* 2.8 32.7 + - - +
282D GLU 3.0 13.1 + - - +
283D PHE* 3.3 12.5 + - - +
285D LYS* 1.3 72.7 - - - +
287D ALA* 1.3 68.0 + - - +
289D VAL* 3.4 7.1 + - - +
290D MET* 3.0 27.9 + - - +
313D ILE* 4.3 6.3 - - + +
381D ASP 4.0 5.0 - - - +
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Residues in contact with ALA 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 PHE 3.1 13.3 + - - +
284D LEU* 3.6 11.9 - - - +
285D LYS 3.3 0.2 - - - -
286D GLU* 1.3 79.2 - - - +
288D ALA* 1.3 60.4 + - - +
290D MET* 3.3 6.0 + - - +
291D LYS* 3.3 32.9 + - - +
301D LEU* 4.8 1.3 - - - +
304D VAL* 4.3 15.4 - - + +
306D THR* 4.7 11.0 - - + -
313D ILE* 3.8 23.7 - - + +
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Residues in contact with ALA 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 LEU 3.0 17.0 + - - +
285D LYS* 3.8 8.3 - - + +
286D GLU 3.3 0.4 - - - -
287D ALA* 1.3 74.3 - - - +
289D VAL* 1.3 64.4 + - - +
291D LYS* 3.3 28.4 + - + +
292D GLU* 3.6 14.7 - - - +
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Residues in contact with VAL 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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1D STI 3.7 47.6 - - + +
285D LYS* 3.0 35.2 + - + +
286D GLU* 3.7 6.3 - - - +
288D ALA* 1.3 75.9 - - + +
290D MET* 1.4 59.7 + - - +
292D GLU* 2.9 28.3 + - - +
293D ILE* 3.5 11.3 + - + +
359D PHE* 4.3 19.7 - - + -
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Residues in contact with MET 290 (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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1D STI 3.3 71.6 - - + +
235D TRP* 5.5 1.2 - - - -
286D GLU* 3.0 25.8 + - - +
287D ALA 3.3 4.9 + - - +
289D VAL* 1.4 76.3 - - - +
291D LYS* 1.3 61.4 + - - +
292D GLU 3.3 0.5 + - - -
293D ILE* 3.3 28.3 - - + +
299D VAL* 4.7 8.1 - - + +
301D LEU* 4.0 32.7 - - + +
313D ILE* 3.9 14.6 - - + -
315D THR* 3.6 21.5 - - + -
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Residues in contact with LYS 291 (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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233D ASP* 2.9 28.4 + - - +
235D TRP* 3.4 53.3 + - + +
287D ALA* 3.3 24.4 + - - +
288D ALA* 3.5 16.7 - - - +
289D VAL 3.2 0.8 - - - -
290D MET* 1.3 77.0 - - - +
292D GLU* 1.3 65.3 + - - +
293D ILE 3.5 1.1 - - - +
301D LEU* 3.8 12.8 - - + -
304D VAL* 4.2 20.9 - - - +
306D THR* 5.0 4.2 + - - -
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Residues in contact with GLU 292 (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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288D ALA 3.6 16.9 - - - +
289D VAL* 2.9 13.3 + - - +
291D LYS* 1.3 86.5 - - - +
293D ILE* 1.3 61.8 + - - +
294D LYS 4.1 0.2 + - - -
353D TYR* 3.7 8.1 + - - -
357D LYS* 4.3 11.4 + - + +
359D PHE* 4.2 20.0 - - + -
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Residues in contact with ILE 293 (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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1D STI 3.6 41.5 - - + -
289D VAL* 3.7 17.3 - - + +
290D MET* 3.3 26.1 + - + +
291D LYS 4.8 0.9 - - - +
292D GLU* 1.3 83.9 - - - +
294D LYS* 1.3 64.0 + - - +
298D LEU* 4.3 14.1 - - + -
299D VAL 5.7 2.7 - - - +
301D LEU* 5.9 1.6 + - - +
353D TYR* 3.5 17.7 - - + +
354D LEU* 4.4 9.6 - - + -
359D PHE* 3.5 34.3 - - + -
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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