Contacts of the helix formed by residues 277 - 291 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A TRP* 3.6 64.4 - - + +
256A ILE* 3.7 31.0 - - + -
259A ILE* 4.2 7.4 - - + -
272B LEU* 3.9 30.3 + - + +
275B ILE* 3.4 11.9 - - + +
276B ASN* 1.3 76.9 - - - +
278B SER* 1.3 65.7 + - - +
280B LYS* 3.1 11.2 + - - +
281B ILE* 3.0 32.1 + - + +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 3.2 9.6 + - - -
277B MET* 1.3 81.7 - - - +
279B SER* 1.3 59.0 + - - +
281B ILE* 3.4 10.1 + - - +
282B GLU* 2.9 33.1 + - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 5.7 1.6 - - - +
276B ASN* 3.1 32.3 + - - -
278B SER* 1.3 79.7 + - - +
280B LYS* 1.3 59.6 + - - +
282B GLU* 3.2 24.4 + - - +
283B THR* 2.8 38.4 + - - -
9E T 3.9 15.5 + - - -
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 4.0 5.8 - - - +
115A SER* 3.8 21.3 + - - +
252A TRP* 3.6 45.3 - - + +
275B ILE* 3.6 29.0 + - - +
276B ASN 3.3 7.7 + - - +
277B MET* 3.1 12.7 + - - +
279B SER* 1.3 78.1 - - - +
281B ILE* 1.3 57.3 + - - +
283B THR* 3.3 5.7 + - - -
284B ILE* 3.0 33.2 + - - +
7E C 5.1 1.2 + - - -
8E T 3.9 23.5 + - - +
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS* 4.1 27.8 - - + +
252A TRP* 3.9 33.4 - - + -
253A LYS* 5.3 1.1 - - - +
277B MET* 3.0 28.1 + - + +
278B SER* 3.8 9.2 - - - +
279B SER 3.3 0.2 - - - -
280B LYS* 1.3 74.4 - - - +
282B GLU* 1.3 58.2 + - - +
284B ILE* 3.3 7.4 + - + +
285B ASP* 2.9 42.0 + - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B SER* 2.9 16.2 + - - +
279B SER* 3.2 37.3 + - - +
281B ILE* 1.3 74.8 - - - +
283B THR* 1.3 59.2 + - - +
285B ASP* 3.9 6.9 - - - +
286B SER* 2.9 31.4 + - - -
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 3.8 4.0 - - - +
115A SER* 3.4 26.9 - - - +
116A ARG 3.6 16.4 - - - +
117A THR* 4.0 18.7 - - + +
119A LYS* 5.8 0.2 - - - +
279B SER* 2.8 27.7 + - - -
280B LYS* 3.5 5.9 - - - -
282B GLU* 1.3 72.3 - - - +
284B ILE* 1.3 64.0 + - - +
286B SER* 3.4 5.7 + - - -
287B PHE* 2.9 24.4 + - + +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 4.0 25.6 - - + +
114A LEU* 3.6 36.3 - - + -
115A SER* 3.6 1.3 - - - +
245A SER* 4.0 23.8 - - - +
248A GLU* 4.4 10.8 - - + +
249A LYS* 3.9 34.1 - - + +
252A TRP* 5.0 3.8 - - + -
280B LYS 3.0 22.7 + - - +
281B ILE* 3.3 8.0 + - + +
283B THR* 1.3 76.8 - - - +
285B ASP* 1.3 56.9 + - - +
287B PHE* 3.2 4.3 + - - +
288B ILE* 3.0 31.2 + - + +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS* 3.0 35.1 + - - +
281B ILE* 2.9 31.5 + - - +
282B GLU* 3.9 6.6 - - - +
284B ILE* 1.3 76.8 - - - +
286B SER* 1.3 58.0 + - - +
288B ILE* 3.4 5.9 + - - +
289B LYS* 2.9 30.2 + - - +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU 2.9 20.0 + - - -
283B THR* 3.8 5.8 - - - -
285B ASP* 1.3 73.6 - - - +
287B PHE* 1.3 60.5 + - - +
289B LYS* 3.8 8.2 - - - +
290B GLY* 3.0 25.8 + - - -
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.7 36.1 - - + +
119A LYS* 5.4 1.6 - - - -
144A PRO* 6.2 0.7 - - + -
146A PHE* 3.5 33.4 - - + -
147A GLN* 3.5 35.2 - - + -
241A ILE* 3.9 20.0 - - + -
283B THR* 2.9 19.0 + - + +
284B ILE 3.5 4.7 - - - +
286B SER* 1.3 78.0 - - - +
288B ILE* 1.3 75.1 + - + +
290B GLY* 3.2 2.8 + - - -
291B ILE* 3.0 48.2 + - + +
296B ARG* 4.8 2.6 + - - -
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 5.0 0.9 - - + -
241A ILE* 3.7 31.9 - - + +
242A GLU* 3.9 32.8 - - + +
245A SER* 3.7 30.1 - - - +
249A LYS* 6.0 2.9 - - - +
284B ILE* 3.0 23.5 + - + +
285B ASP* 3.9 7.6 - - - +
287B PHE* 1.3 84.2 - - + +
289B LYS* 1.3 61.8 + - - +
291B ILE* 3.5 14.7 - - + +
292B LYS* 3.1 32.2 - - + +
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ASP 2.9 18.4 + - - +
286B SER* 3.8 8.7 - - - +
288B ILE* 1.3 76.5 - - - +
290B GLY* 1.3 62.4 + - - +
292B LYS* 3.3 21.5 + - - +
293B SER* 3.9 4.7 + - - -
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B SER 3.0 15.5 + - - -
287B PHE* 3.2 4.7 + - - -
289B LYS* 1.3 76.5 - - - +
291B ILE* 1.3 59.5 + - - +
292B LYS 3.2 1.4 + - - -
293B SER* 3.3 22.4 + - - -
296B ARG* 3.4 25.4 + - - +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 3.6 34.1 - - + -
238A ILE* 3.3 49.5 - - + +
241A ILE* 3.8 37.7 - - + -
242A GLU* 5.8 0.4 - - + -
287B PHE* 3.0 24.8 + - + +
288B ILE* 3.5 24.2 - - + +
289B LYS 3.4 0.2 - - - -
290B GLY* 1.3 75.1 - - - +
292B LYS* 1.3 60.7 + - + +
293B SER 3.3 7.2 + - - +
296B ARG* 3.8 22.3 - - - +
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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