Contacts of the helix formed by residues 262 - 273 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140P GLU* 2.7 37.3 + - - -
260P HIS 3.3 2.0 + - - -
261P PHE* 1.3 77.9 - - - +
263P SER* 1.3 64.3 + - - +
264P ASP* 3.9 5.0 + - - +
265P LEU* 3.1 15.6 + - - +
266P LYS* 3.0 21.7 + - - +
296P TRP* 4.2 2.8 - - - -
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Residues in contact with SER 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P PHE 3.8 0.6 + - - -
262P SER* 1.3 72.6 - - - +
264P ASP* 1.3 68.6 + - - +
266P LYS* 3.3 19.7 + - - +
267P ASP* 3.0 23.4 + - - +
270P ARG* 4.5 3.1 + - - +
295P LYS* 5.9 0.2 - - - -
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Residues in contact with ASP 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262P SER* 3.4 4.8 + - - +
263P SER* 1.3 77.6 - - - +
265P LEU* 1.3 65.6 + - - +
267P ASP* 3.3 3.5 + - - -
268P LEU* 3.2 7.1 + - - +
294P HIS* 3.1 26.8 - - - -
295P LYS* 3.6 40.5 - - + +
296P TRP* 4.0 23.9 - - + +
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Residues in contact with LEU 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P GLU* 3.4 31.9 - - + +
228P ILE* 3.6 23.1 - - + -
232P ALA* 3.9 16.6 - - + -
261P PHE* 3.9 22.0 - - + -
262P SER* 3.1 21.5 + - - +
264P ASP* 1.3 78.9 - - - +
266P LYS* 1.3 64.1 + - - +
268P LEU* 3.3 3.3 + - + +
269P LEU* 3.1 40.5 + - + +
296P TRP* 3.5 27.2 - - + +
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Residues in contact with LYS 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P PHE* 3.4 38.6 - - + -
258P PRO 4.5 2.8 + - - +
259P SER* 5.4 2.8 + - - +
261P PHE* 3.4 42.8 + - + +
262P SER 3.0 9.0 + - - +
263P SER* 3.6 17.7 + - - +
264P ASP 3.3 0.2 - - - -
265P LEU* 1.3 77.9 - - - +
267P ASP* 1.3 61.2 + - - +
269P LEU* 3.4 4.8 + - - -
270P ARG* 3.0 51.4 + - - +
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Residues in contact with ASP 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263P SER 3.0 13.8 + - - +
264P ASP* 3.3 9.6 + - - +
266P LYS* 1.3 76.0 - - - +
268P LEU* 1.3 62.8 + - - +
270P ARG* 3.3 18.7 + - - +
271P ASN* 2.8 37.7 + - - +
294P HIS* 2.7 21.0 + - + +
295P LYS* 2.9 20.1 + - - +
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Residues in contact with LEU 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228P ILE* 3.7 20.0 - - + -
264P ASP 3.2 5.0 + - - +
265P LEU* 3.3 8.3 + - + +
267P ASP* 1.3 78.7 - - - +
269P LEU* 1.3 63.9 + - + +
271P ASN* 3.1 5.2 + - - +
272P LEU* 2.9 64.1 + - + +
281P PHE* 4.4 12.1 - - + -
291P ILE* 4.6 12.6 - - + -
294P HIS* 3.3 39.6 + - + +
296P TRP* 4.4 15.0 - - + -
297P PHE* 4.6 9.2 - - + -
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Residues in contact with LEU 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225P GLY* 3.3 33.4 - - - +
228P ILE* 3.8 20.6 - - + -
229P TYR* 4.3 11.4 - - + -
257P PHE* 3.7 24.4 - - + -
261P PHE* 3.7 26.7 - - + -
265P LEU* 3.1 35.6 + - + +
266P LYS 3.9 0.7 - - - +
268P LEU* 1.3 80.7 - - + +
270P ARG* 1.3 60.4 + - - +
272P LEU* 4.3 2.7 - - - +
273P LEU* 2.8 39.0 + - + +
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Residues in contact with ARG 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257P PHE* 3.7 32.5 - - + -
263P SER* 4.5 2.8 + - - +
266P LYS* 3.0 49.5 + - - +
267P ASP* 3.3 19.0 + - - +
269P LEU* 1.3 76.4 - - - +
271P ASN* 1.3 63.5 + - - +
273P LEU* 3.6 17.2 - - - +
274P GLN* 3.8 12.0 + - - +
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Residues in contact with ASN 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P ASP* 2.8 34.4 + - - +
268P LEU 3.1 8.8 + - - +
270P ARG* 1.3 78.4 - - - +
272P LEU* 1.3 59.0 + - - +
274P GLN* 3.2 32.4 - - - +
279P LYS 4.5 2.2 + - - -
280P ARG* 3.4 0.7 - - - -
281P PHE* 3.2 68.4 + - + -
294P HIS* 4.5 0.2 + - - -
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Residues in contact with LEU 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221P TRP 3.9 14.8 - - - +
222P TRP* 3.7 17.3 - - - -
224P LEU* 4.4 8.3 - - + -
225P GLY* 3.7 31.4 - - - +
228P ILE* 3.9 10.3 - - + -
268P LEU* 2.9 49.0 + - + +
269P LEU* 4.1 3.4 - - + +
271P ASN* 1.3 70.9 - - - +
273P LEU* 1.3 60.4 + - - +
274P GLN 3.0 9.9 + - - -
280P ARG* 3.6 17.0 - - - +
281P PHE* 4.2 12.3 - - + +
291P ILE* 3.9 34.5 - - + -
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Residues in contact with LEU 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222P TRP* 3.3 58.2 - - + +
225P GLY* 3.8 13.9 - - - +
226P VAL* 3.7 23.1 - - + +
229P TYR* 4.9 3.6 - - + -
237P PRO* 4.3 19.7 - - + -
238P PHE* 4.7 1.3 - - + -
253P GLY 4.9 8.7 - - - +
255P VAL* 4.2 29.4 - - + +
257P PHE* 5.0 1.3 - - + -
269P LEU* 2.8 30.9 + - + +
270P ARG* 3.6 9.6 - - - +
272P LEU* 1.3 68.4 - - - +
274P GLN* 1.3 56.5 + - - +
275P VAL* 3.8 2.1 + - - +
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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