Contacts of the helix formed by residues 277 - 291 (chain D) in PDB entry 2E52
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 MET 277 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C TRP* 3.4 40.4 - - + +
255C GLN* 4.2 6.7 - - + -
256C ILE* 3.4 28.7 - - + -
259C ILE* 3.5 27.4 - - + -
272D LEU* 3.8 33.0 + - + +
275D ILE* 3.4 25.3 - - + -
276D ASN* 1.3 75.4 - - - +
278D SER* 1.3 63.6 + - - +
280D LYS* 3.2 11.0 + - - +
281D ILE* 2.9 33.4 + - - +
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Residues in contact with SER 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 5.2 6.7 - - - -
272D LEU 5.6 0.9 + - - -
276D ASN* 4.6 6.1 + - - -
277D MET* 1.3 85.8 + - - +
279D SER* 1.3 59.0 + - - +
281D ILE* 3.5 11.2 + - - +
282D GLU* 2.9 33.8 + - - +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ASN* 3.3 29.7 + - - -
277D MET 3.2 0.4 - - - -
278D SER* 1.3 78.4 + - - +
280D LYS* 1.3 60.7 + - - +
282D GLU* 3.2 15.7 + - - +
283D THR* 2.9 35.8 + - - -
9F T 4.1 14.6 + - - -
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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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51C GLU* 4.1 0.4 - - - +
115C SER* 3.7 27.3 + - - +
252C TRP* 3.5 46.0 - - + +
275D ILE* 3.3 25.6 + - - -
276D ASN* 3.4 11.8 + - + +
277D MET* 3.2 10.3 + - - +
279D SER* 1.3 78.1 - - - +
281D ILE* 1.3 62.1 + - - +
283D THR* 3.2 6.9 + - - -
284D ILE* 3.0 28.0 + - - +
7F C 5.1 1.2 + - - -
8F T 3.9 24.9 + - - +
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Residues in contact with ILE 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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249C LYS* 4.1 20.9 - - + +
252C TRP* 3.9 28.0 - - + -
253C LYS* 4.1 36.6 - - + +
256C ILE* 4.6 13.2 - - + -
277D MET 2.9 23.3 + - - +
278D SER* 3.8 8.1 - - - +
280D LYS* 1.3 75.3 - - - +
282D GLU* 1.3 60.1 + - + +
284D ILE* 3.3 10.3 + - + +
285D ASP* 3.0 39.9 + - - +
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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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278D SER* 2.9 21.4 - - - +
279D SER* 3.2 14.7 + - - +
281D ILE* 1.3 75.8 - - + +
283D THR* 1.3 61.1 + - - +
285D ASP* 3.4 7.7 + - - +
286D SER* 2.9 30.8 + - - -
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Residues in contact with THR 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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114C LEU 3.8 4.5 - - - +
115C SER 3.4 31.4 + - - +
116C ARG 3.7 12.8 - - - +
117C THR* 4.1 17.7 - - + +
279D SER* 2.9 19.7 + - - -
280D LYS* 3.2 10.2 + - - -
282D GLU* 1.3 77.2 - - - +
284D ILE* 1.3 52.2 + - - +
286D SER* 3.2 6.8 + - - -
287D PHE* 2.8 35.8 + - + +
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Residues in contact with ILE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.8 30.3 - - + +
114C LEU* 3.6 35.2 - - + -
115C SER* 3.6 1.8 - - - +
245C SER* 3.9 25.4 - - - +
248C GLU* 4.4 6.7 - - + +
249C LYS* 3.7 35.0 - - + +
252C TRP* 4.7 3.6 - - + -
280D LYS 3.0 21.4 + - - +
281D ILE* 3.3 7.6 + - - +
283D THR* 1.3 75.5 - - - +
285D ASP* 1.3 62.0 + - - +
287D PHE* 3.3 3.6 + - - +
288D ILE* 3.0 30.4 + - + +
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Residues in contact with ASP 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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249C LYS* 2.8 34.9 + - - +
281D ILE* 3.0 31.3 + - - +
282D GLU* 3.8 7.2 - - - +
284D ILE* 1.3 76.7 - - - +
286D SER* 1.3 56.5 + - - +
288D ILE* 3.4 6.2 + - - +
289D LYS* 3.0 31.1 + - - +
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Residues in contact with SER 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 GLU 2.9 18.5 + - - -
283D THR* 3.6 7.9 - - - -
285D ASP* 1.3 73.1 - - - +
287D PHE* 1.3 65.8 + - - +
289D LYS* 3.5 8.8 + - - +
290D GLY* 3.0 20.6 + - - -
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Residues in contact with PHE 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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114C LEU* 3.6 42.0 - - + +
119C LYS* 5.5 1.6 - - - -
144C PRO* 6.2 0.2 - - + -
146C PHE* 3.4 41.5 - - + -
147C GLN* 3.6 34.1 - - + -
241C ILE* 3.9 20.2 - - + -
283D THR* 2.8 22.6 + - + +
284D ILE 3.5 4.0 - - - +
286D SER* 1.3 73.1 - - - +
288D ILE* 1.3 71.4 + - + +
290D GLY* 3.2 3.7 + - - -
291D ILE* 3.1 39.3 + - + +
296D ARG* 4.8 2.5 + - - -
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Residues in contact with ILE 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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114C LEU* 5.0 0.7 - - + -
241C ILE* 3.7 29.6 - - + -
242C GLU* 4.0 32.8 - - + +
245C SER* 3.7 30.7 - - - +
249C LYS* 6.1 0.4 - - - -
284D ILE* 3.0 19.1 + - + +
285D ASP* 3.9 7.2 - - - +
287D PHE* 1.3 80.5 - - + +
289D LYS* 1.3 66.0 + - - +
291D ILE* 3.4 10.3 - - + +
292D LYS* 3.3 35.7 + - + +
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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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285D ASP 3.0 17.7 + - - +
286D SER* 3.7 8.3 - - - +
288D ILE* 1.3 77.2 - - - +
290D GLY* 1.3 63.6 + - - +
292D LYS* 3.4 19.6 + - - +
293D SER* 3.8 5.9 + - - -
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Residues in contact with GLY 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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286D SER 3.0 14.5 + - - -
287D PHE* 3.2 4.7 + - - -
289D LYS* 1.3 77.9 - - - +
291D ILE* 1.3 60.8 + - - +
292D LYS 3.1 0.2 - - - -
293D SER* 3.2 17.3 + - - -
296D ARG* 3.3 30.2 - - - +
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Residues in contact with ILE 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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146C PHE* 3.5 35.8 - - + -
238C ILE* 3.3 46.7 - - + +
241C ILE* 3.8 39.3 - - + -
242C GLU* 5.8 0.2 - - + -
287D PHE* 3.1 24.8 + - + +
288D ILE* 3.4 25.1 - - + +
290D GLY* 1.3 74.4 - - - +
292D LYS* 1.3 60.8 + - + +
293D SER 3.3 7.5 + - - +
296D ARG* 3.8 22.4 - - - +
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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