Contacts of the helix formed by residues 262 - 273 (chain L) in PDB entry 3E8E
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 262 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140L GLU* 2.7 35.3 + - - -
260L HIS 3.4 2.1 + - - -
261L PHE* 1.3 77.1 - - - +
263L SER* 1.3 59.2 + - - +
264L ASP* 3.8 5.1 + - - +
265L LEU* 3.1 17.4 + - - +
266L LYS* 3.0 26.9 + - - +
296L TRP* 4.0 4.3 - - - -
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Residues in contact with SER 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L PHE 3.9 0.4 + - - -
262L SER* 1.3 71.5 - - - +
264L ASP* 1.3 64.8 + - - +
266L LYS* 3.5 18.3 + - - +
267L ASP* 2.9 28.6 + - - +
270L ARG* 4.6 3.2 + - - +
295L LYS* 5.8 0.2 - - - -
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Residues in contact with ASP 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L SER* 3.4 4.4 + - - +
263L SER* 1.3 78.5 - - - +
265L LEU* 1.3 65.6 + - - +
267L ASP* 3.3 4.4 + - - -
268L LEU* 3.0 20.4 + - - +
294L HIS* 3.2 10.5 - - - -
295L LYS* 3.1 48.5 - - + +
296L TRP* 4.0 24.0 - - + +
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Residues in contact with LEU 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L GLU* 3.4 27.6 - - + +
228L ILE* 3.7 24.9 - - + -
232L ALA* 3.8 19.5 - - + -
261L PHE* 3.7 22.9 - - + -
262L SER* 3.1 24.1 + - - +
264L ASP* 1.3 77.5 - - - +
266L LYS* 1.3 59.3 + - - +
268L LEU* 3.3 3.9 + - + +
269L LEU* 3.0 46.4 + - + +
296L TRP* 3.5 32.6 - - + +
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Residues in contact with LYS 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLU* 2.9 29.0 + - - -
257L PHE* 3.4 46.1 - - + +
258L PRO 4.6 4.1 + - - +
259L SER* 5.3 4.2 + - - +
261L PHE* 3.6 28.3 + - + +
262L SER 3.0 21.3 + - - +
263L SER* 3.6 17.6 + - - +
265L LEU* 1.3 77.8 - - - +
267L ASP* 1.3 60.7 + - - +
269L LEU* 3.5 1.9 + - - -
270L ARG* 3.1 42.8 + - - +
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Residues in contact with ASP 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L SER 2.9 17.8 + - - +
264L ASP* 3.6 6.3 - - - +
265L LEU 3.3 0.2 - - - -
266L LYS* 1.3 72.0 - - - +
268L LEU* 1.3 65.3 + - - +
270L ARG* 3.2 29.5 + - - +
271L ASN* 2.9 30.3 + - - +
281L PHE* 6.0 0.2 - - - -
294L HIS* 2.7 24.1 + - + +
295L LYS* 3.2 21.3 + - - +
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Residues in contact with LEU 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ILE* 4.3 13.5 - - + -
264L ASP 3.0 8.1 + - - +
265L LEU* 3.5 12.1 - - + +
267L ASP* 1.3 76.5 - - - +
269L LEU* 1.3 59.3 + - + +
271L ASN* 3.3 5.0 + - - +
272L LEU* 3.0 44.2 + - + +
281L PHE* 4.6 11.2 - - + -
291L ILE* 4.6 7.2 - - + -
294L HIS* 3.4 41.4 - - + +
296L TRP* 3.5 39.0 - - + -
297L PHE* 3.8 16.4 - - + -
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Residues in contact with LEU 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L GLY* 3.2 34.1 - - - +
228L ILE* 3.9 20.9 - - + -
229L TYR* 4.0 11.7 - - + +
257L PHE* 3.7 25.5 - - + -
261L PHE* 3.6 32.5 - - + -
265L LEU* 3.0 31.2 + - + +
266L LYS 3.9 0.9 - - - +
267L ASP 3.3 0.2 - - - -
268L LEU* 1.3 74.9 - - + +
270L ARG* 1.3 61.1 + - - +
272L LEU* 4.4 7.0 - - + +
273L LEU* 2.8 38.2 + - + +
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Residues in contact with ARG 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLU* 4.4 16.2 + - - +
257L PHE* 3.8 32.6 - - + -
263L SER* 4.6 2.6 + - - +
266L LYS* 3.1 28.2 + - - +
267L ASP* 3.2 31.5 + - - +
269L LEU* 1.3 76.8 - - - +
271L ASN* 1.3 63.1 + - - +
273L LEU* 3.5 18.5 - - - +
274L GLN* 3.6 13.5 + - - -
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Residues in contact with ASN 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L ASP* 2.9 34.8 + - - +
268L LEU* 3.7 7.5 - - - +
269L LEU 3.3 0.2 - - - -
270L ARG* 1.3 79.7 - - - +
272L LEU* 1.3 59.6 + - - +
274L GLN* 3.5 18.1 - - - +
279L LYS 4.4 3.8 + - - -
280L ARG* 3.5 9.5 - - - -
281L PHE* 3.0 68.5 + - + -
294L HIS* 4.7 0.3 + - - -
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Residues in contact with LEU 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221L TRP* 3.9 14.1 - - + +
222L TRP* 3.7 12.2 - - - -
224L LEU* 4.4 8.1 - - + -
225L GLY* 3.8 32.1 - - - +
228L ILE* 4.2 16.2 - - + -
268L LEU* 3.0 41.4 + - + +
269L LEU* 4.2 4.0 - - + +
271L ASN* 1.3 73.2 - - - +
273L LEU* 1.3 60.1 + - - +
274L GLN 3.1 10.0 + - - -
280L ARG* 3.4 20.6 - - - +
281L PHE* 4.0 24.7 - - + +
291L ILE* 4.0 24.2 - - + -
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Residues in contact with LEU 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L TRP* 3.5 50.4 - - + +
225L GLY* 3.8 13.0 - - - +
226L VAL* 3.6 24.5 - - + +
229L TYR* 4.7 3.8 - - + -
237L PRO* 4.3 18.6 - - + -
238L PHE* 4.5 1.6 - - + -
255L VAL* 4.1 34.2 - - + +
257L PHE* 5.1 0.4 - - + -
269L LEU* 2.8 28.7 + - + +
270L ARG* 3.5 11.3 - - - +
272L LEU* 1.3 71.8 - - - +
274L GLN* 1.3 58.8 + - - +
275L VAL* 3.9 2.9 + - - +
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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