Contacts of the helix formed by residues 262 - 273 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B GLU* 2.9 33.5 + - - -
260B HIS 3.5 1.8 + - - -
261B PHE* 1.3 75.9 - - - +
263B SER* 1.3 65.9 + - - +
264B ASP* 3.6 5.7 + - - +
265B LEU* 3.0 17.9 + - - +
266B LYS* 3.0 21.7 + - - +
296B TRP* 3.9 4.7 - - - -
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Residues in contact with SER 263 (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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261B PHE 3.8 1.0 + - - -
262B SER* 1.3 71.7 - - - +
264B ASP* 1.3 63.2 + - - +
266B LYS* 3.3 18.3 + - - +
267B ASP* 3.0 28.1 + - - +
270B ARG* 4.5 2.9 + - - -
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Residues in contact with ASP 264 (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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262B SER* 3.2 8.1 + - - +
263B SER* 1.3 79.3 - - - +
265B LEU* 1.3 65.3 + - - +
267B ASP* 3.5 2.6 + - - -
268B LEU* 3.0 19.8 + - - +
294B HIS* 3.1 14.5 - - - -
295B LYS* 3.1 44.9 - - + +
296B TRP* 4.1 21.4 - - + +
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Residues in contact with LEU 265 (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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140B GLU* 3.5 25.8 - - + +
228B ILE* 3.6 21.3 - - + -
232B ALA* 3.8 22.4 - - + -
261B PHE* 3.8 21.1 - - + -
262B SER* 3.0 23.9 + - - +
264B ASP* 1.3 75.5 - - - +
266B LYS* 1.3 58.9 + - - +
268B LEU* 3.2 5.1 + - + +
269B LEU* 2.9 55.7 + - + +
296B TRP* 3.6 27.3 - - + +
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Residues in contact with LYS 266 (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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257B PHE* 3.5 41.6 - - + -
258B PRO 4.7 2.7 - - - +
259B SER* 5.8 1.2 + - - +
261B PHE* 3.7 26.3 + - + +
262B SER 3.0 17.3 + - - +
263B SER* 3.6 18.6 + - - +
265B LEU* 1.3 77.9 - - - +
267B ASP* 1.3 57.1 + - - +
269B LEU* 3.4 1.7 + - - +
270B ARG* 3.0 56.6 + - - +
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Residues in contact with ASP 267 (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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263B SER 3.0 16.3 + - - +
264B ASP* 3.7 6.3 - - - +
266B LYS* 1.3 73.8 - - - +
268B LEU* 1.3 62.4 + - - +
270B ARG* 3.3 22.1 + - - +
271B ASN* 2.7 45.3 + - - -
294B HIS* 2.7 26.7 + - + +
295B LYS* 3.7 15.4 + - - +
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Residues in contact with LEU 268 (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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228B ILE* 4.1 14.6 - - + -
264B ASP 3.0 15.0 + - - +
265B LEU* 3.5 11.2 - - + +
267B ASP* 1.3 74.9 - - - +
269B LEU* 1.3 64.4 + - + +
271B ASN* 3.0 7.5 + - - +
272B LEU* 3.0 40.4 + - + +
281B PHE* 4.4 11.0 - - + -
291B ILE* 4.5 6.7 - - + -
294B HIS* 3.3 34.6 + - + -
296B TRP* 3.4 37.2 - - + -
297B PHE* 3.6 17.9 - - + -
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Residues in contact with LEU 269 (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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225B GLY* 3.5 28.9 - - - +
228B ILE* 3.7 28.0 - - + -
229B TYR* 4.0 15.3 - - + -
257B PHE* 3.7 22.9 - - + -
261B PHE* 3.6 31.4 - - + -
265B LEU* 2.9 32.0 + - + +
266B LYS 3.9 0.2 - - - +
268B LEU* 1.3 77.3 - - + +
270B ARG* 1.3 53.8 + - - +
272B LEU* 4.4 4.5 - - + +
273B LEU* 2.8 44.3 + - + +
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Residues in contact with ARG 270 (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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257B PHE* 3.8 30.4 - - + -
263B SER 4.5 2.4 + - - -
266B LYS* 3.0 36.6 + - - +
267B ASP* 3.6 35.3 + - - +
268B LEU 3.3 0.2 - - - -
269B LEU* 1.3 76.1 - - - +
271B ASN* 1.3 62.5 + - - +
273B LEU* 3.8 4.5 + - - +
274B GLN* 3.0 32.0 + - - +
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Residues in contact with ASN 271 (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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267B ASP* 2.7 42.2 + - - -
268B LEU* 3.0 8.5 + - - +
270B ARG* 1.3 79.8 - - - +
272B LEU* 1.3 62.3 + - - +
274B GLN* 3.7 6.5 - - - +
279B LYS 4.1 5.4 - - - +
280B ARG* 3.5 8.5 - - - -
281B PHE* 3.0 66.4 + - + -
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Residues in contact with LEU 272 (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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221B TRP* 3.8 15.0 - - + +
222B TRP* 3.7 9.8 - - - -
224B LEU* 4.5 7.6 - - + -
225B GLY* 3.8 24.7 - - - +
228B ILE* 3.7 29.8 - - + -
268B LEU* 3.0 34.4 + - + +
269B LEU* 3.9 5.6 - - + +
271B ASN* 1.3 75.5 - - - +
273B LEU* 1.3 59.4 + - - +
274B GLN 3.2 5.4 + - - -
280B ARG* 3.2 24.6 + - - +
281B PHE* 3.9 27.8 - - + +
291B ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 273 (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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222B TRP* 3.3 54.1 - - + +
225B GLY* 4.1 13.5 - - - +
226B VAL* 3.8 21.5 - - + +
229B TYR* 4.7 3.8 - - + -
237B PRO* 4.3 20.9 - - + -
238B PHE* 4.4 2.5 - - + -
253B GLY* 5.9 1.6 - - - -
255B VAL* 4.4 31.3 - - + +
257B PHE* 5.1 0.9 - - + -
269B LEU* 2.8 33.7 + - + +
270B ARG* 3.9 8.2 - - - +
272B LEU* 1.3 69.2 - - - +
274B GLN* 1.3 61.4 + - - +
275B VAL* 3.5 4.2 + - - +
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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