Contacts of the helix formed by residues 253 - 264 (chain B) in PDB entry 3N4E
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 THR 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A TYR* 5.2 8.3 - - + +
79B MSE 6.2 2.7 - - - -
87B PRO* 4.8 18.6 - - + -
88B GLU* 4.6 15.4 + - - +
92B THR* 5.0 1.3 - - + -
251B THR* 3.9 2.5 - - - +
252B TYR* 1.3 88.3 - - + +
254B LEU* 1.3 59.4 + - - +
255B GLN* 3.6 14.2 + - - +
256B ALA* 2.9 27.6 + - + +
257B LEU* 3.0 29.1 + - - +
275B MSE 3.6 10.8 - - - +
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Residues in contact with LEU 254 (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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253B THR* 1.3 73.6 - - - +
255B GLN* 1.3 75.4 + - + +
257B LEU* 3.2 6.4 + - - +
258B LYS* 2.9 27.4 + - + +
275B MSE 3.9 6.9 - - + +
283B GLN* 3.7 54.1 - - + +
284B CYS* 4.0 11.4 - - - +
287B LEU* 3.6 25.6 - - + +
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Residues in contact with GLN 255 (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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229A TYR* 3.2 53.1 - - + +
230A HIS* 3.5 30.6 - - + +
253B THR* 3.8 15.4 - - - +
254B LEU* 1.3 94.8 + - + +
256B ALA* 1.3 63.0 + - - +
258B LYS* 3.2 17.8 + - - +
259B ASP* 3.0 27.2 + - - +
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Residues in contact with ALA 256 (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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88B GLU* 5.8 3.4 - - - +
231B VAL* 5.7 0.5 - - - +
251B THR* 3.6 19.3 - - + +
252B TYR 4.9 1.1 - - - +
253B THR* 2.9 21.7 + - + +
255B GLN* 1.3 77.1 - - - +
257B LEU* 1.3 56.6 + - - +
259B ASP* 3.2 10.9 + - - +
260B LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 257 (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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248B GLY* 4.8 1.1 - - - -
251B THR* 3.5 15.0 - - + +
253B THR 3.0 15.0 + - - +
254B LEU 3.4 9.4 - - - +
256B ALA* 1.3 75.3 - - - +
258B LYS* 1.3 65.5 + - - +
260B LEU* 3.2 16.7 + - + +
261B ILE* 3.1 27.0 + - + +
268B VAL* 3.9 36.3 - - + -
270B PRO* 4.2 17.7 - - + -
275B MSE 5.7 0.7 - - + -
284B CYS* 3.6 44.0 - - + +
287B LEU* 4.3 10.8 - - + -
288B ALA 5.9 0.2 - - - +
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Residues in contact with LYS 258 (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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230A HIS* 6.0 2.5 - - - +
231A VAL 5.6 1.6 - - - +
232A GLY* 4.5 18.0 - - - +
254B LEU 2.9 13.6 + - - +
255B GLN* 3.2 20.1 + - - +
257B LEU* 1.3 76.1 - - - +
259B ASP* 1.3 81.3 + - - +
261B ILE* 3.3 9.4 + - - +
262B LEU* 3.0 45.5 + - + +
287B LEU* 3.7 26.6 - - + +
291B HIS* 4.7 9.6 + - + +
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Residues in contact with ASP 259 (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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229A TYR 5.2 2.8 - - - +
231A VAL* 4.4 21.5 + - - +
232A GLY* 5.2 1.9 + - - -
231B VAL* 4.2 8.9 - - + +
255B GLN* 3.0 15.0 + - - +
256B ALA* 3.6 11.3 - - - +
257B LEU 3.2 0.2 - - - -
258B LYS* 1.3 108.5 + - - +
260B LEU* 1.3 58.6 + - - +
262B LEU* 3.4 10.0 + - - +
263B SER* 2.9 29.8 + - - -
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Residues in contact with LEU 260 (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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231B VAL* 4.2 22.6 - - + +
234B MSE 4.4 8.5 - - + -
247B ALA* 3.6 40.6 - - + +
248B GLY* 3.7 11.2 - - - +
251B THR* 3.8 10.8 - - - +
256B ALA 2.9 12.9 + - - +
257B LEU* 3.2 14.6 + - + +
259B ASP* 1.3 76.7 - - - +
261B ILE* 1.3 59.9 + - - +
263B SER* 2.5 24.9 + - - +
265B VAL* 3.4 34.4 + - + -
268B VAL* 4.0 13.7 - - + -
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Residues in contact with ILE 261 (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 LEU* 3.1 19.0 + - + +
258B LYS* 3.4 8.5 - - - +
260B LEU* 1.3 74.4 - - - +
262B LEU* 1.3 59.5 + - + +
264B GLY* 3.1 9.2 + - - -
265B VAL 3.8 6.7 - - - +
266B ARG* 2.7 36.2 + - - +
268B VAL* 4.0 20.4 - - + -
287B LEU* 4.1 28.7 - - + +
288B ALA* 4.6 3.1 - - - -
291B HIS* 3.7 38.8 - - + +
293B VAL* 3.9 24.7 - - + -
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Residues in contact with LEU 262 (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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258B LYS* 3.0 40.1 + - + +
259B ASP* 3.4 15.5 + - - +
261B ILE* 1.3 74.5 - - + +
263B SER* 1.3 64.9 + - - +
264B GLY* 3.3 1.4 + - - -
266B ARG* 5.2 2.2 + - - +
291B HIS* 4.1 25.8 - - + +
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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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231B VAL* 3.6 30.5 + - - +
232B GLY* 4.8 5.4 - - - +
235B GLY* 3.2 28.5 + - - +
236B GLU* 4.0 0.9 + - - -
239B GLN* 4.6 2.9 - - - +
259B ASP 2.9 13.6 + - - -
260B LEU* 2.5 22.3 + - - -
262B LEU* 1.3 77.3 - - - +
264B GLY* 1.3 55.6 + - - +
265B VAL* 3.8 4.3 - - - +
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Residues in contact with GLY 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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235B GLY 3.9 4.0 - - - -
238B ALA* 3.3 15.6 - - - +
239B GLN* 2.8 34.5 + - - -
261B ILE 3.1 9.1 + - - -
262B LEU 3.1 1.5 - - - -
263B SER* 1.3 79.6 + - - +
265B VAL* 1.3 67.1 + - - +
266B ARG* 3.5 12.1 + - - +
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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