Contacts of the helix formed by residues 257 - 269 (chain B) in PDB entry 4O14
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 HIS 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B TRP* 3.4 38.0 - - + +
254B GLY* 2.9 10.0 + - - -
256B ASP* 1.3 96.9 + - + +
258B GLU* 1.3 64.2 + - - +
259B LYS* 3.2 3.1 - - - +
260B ASP* 2.9 30.6 + - + +
261B ALA 3.0 17.5 + - - -
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Residues in contact with GLU 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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250B ILE* 3.8 13.6 - - + +
254B GLY 3.9 3.9 + - - -
255B LYS 4.2 2.9 + - - +
256B ASP 3.6 2.4 - - - -
257B HIS* 1.3 76.8 - - - +
259B LYS* 1.3 62.9 + - - +
261B ALA* 3.1 8.4 + - - +
262B PHE* 3.0 56.3 + - + -
278B SER* 3.9 12.5 - - - +
280B SER* 4.1 12.1 + - - -
281B TYR* 3.6 38.1 + - + +
282B ASP 5.1 2.6 + - - +
285B ASN* 4.9 4.3 + - - -
286B ALA* 4.4 4.0 - - - +
290B ILE* 3.5 19.2 - - + +
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Residues in contact with LYS 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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256B ASP 5.3 0.6 + - - +
257B HIS* 3.2 0.9 - - - -
258B GLU* 1.3 79.7 - - - +
260B ASP* 1.3 72.4 + - - +
262B PHE* 3.4 2.3 + - - +
263B GLU* 3.0 48.3 + - - +
290B ILE* 3.9 34.0 - - + +
294B ASP* 3.6 33.8 + - + +
295B LEU* 3.7 13.3 - - + +
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Residues in contact with ASP 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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253B TRP* 4.0 19.8 - - + -
257B HIS* 2.9 40.0 + - + +
259B LYS* 1.3 93.1 + - - +
261B ALA* 1.3 64.8 + - - +
263B GLU* 3.8 7.6 - - - +
264B HIS* 3.0 25.8 + - - +
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Residues in contact with ALA 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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250B ILE* 4.0 25.6 - - + +
253B TRP* 3.4 40.6 - - + +
257B HIS 3.0 8.5 + - - +
258B GLU* 3.3 10.5 - - - +
260B ASP* 1.3 77.5 - - - +
262B PHE* 1.3 63.6 + - - +
264B HIS* 3.3 3.1 + - - +
265B ILE* 3.0 30.5 + - + +
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Residues in contact with PHE 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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250B ILE* 3.8 12.6 - - + -
258B GLU* 3.0 46.0 + - + -
259B LYS 3.6 3.4 - - - +
261B ALA* 1.3 75.8 - - - +
263B GLU* 1.3 57.8 + - - +
265B ILE* 3.3 5.0 + - - +
266B VAL* 2.9 34.9 + - - +
276B VAL* 3.7 22.9 - - + -
277B VAL 3.8 7.6 - - - -
278B SER* 4.0 18.8 - - - -
286B ALA* 4.0 13.9 - - + -
290B ILE* 3.5 25.1 - - + -
291B TRP* 3.3 40.4 - + + -
295B LEU* 3.5 12.6 - - + -
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Residues in contact with GLU 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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259B LYS* 3.0 38.6 + - - +
260B ASP* 3.8 8.2 - - - +
262B PHE* 1.3 77.1 - - - +
264B HIS* 1.3 60.1 + - - +
266B VAL* 3.5 8.0 - - - +
267B THR* 2.7 37.6 + - - +
295B LEU* 3.7 14.9 - - + +
297B HIS* 4.9 4.9 + - - -
298B LEU* 3.7 24.7 - - + +
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Residues in contact with HIS 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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24A LYS 2.9 28.7 + - - -
25A GLN* 3.7 10.1 - - - -
26A TYR 4.0 5.9 + - - -
28A PRO* 4.0 24.2 - - + +
253B TRP* 3.5 29.0 - + + -
260B ASP 3.0 18.2 + - - +
261B ALA 3.6 3.1 - - - +
263B GLU* 1.3 76.5 - - - +
265B ILE* 1.3 55.5 + - - +
267B THR* 3.2 4.8 + - - -
268B GLN* 2.7 58.9 + - + +
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Residues in contact with ILE 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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25A GLN* 3.8 53.4 - - + +
245B ALA* 4.0 4.9 - - + -
249B THR 4.2 8.5 - - - +
250B ILE* 3.5 32.5 - - + -
261B ALA 3.0 20.3 + - - +
262B PHE* 3.8 3.8 - - - +
264B HIS* 1.3 77.4 - - + +
266B VAL* 1.3 58.1 + - - +
268B GLN* 3.3 3.8 + - - -
269B PHE* 3.0 33.6 + - + +
274B VAL* 4.0 22.7 - - + -
276B VAL* 4.1 13.0 - - + -
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Residues in contact with VAL 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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262B PHE 2.9 26.9 + - - +
263B GLU* 3.5 12.3 - - - +
265B ILE* 1.3 73.0 - - - +
267B THR* 1.3 62.6 + - - +
269B PHE 4.5 0.2 - - - +
270B SER* 3.3 13.2 + - - -
274B VAL* 4.2 12.1 - - + -
276B VAL* 4.3 4.0 - - + -
291B TRP* 3.6 31.0 - - + -
295B LEU* 5.4 0.4 - - + -
298B LEU* 4.2 24.2 - - + -
299B ILE* 4.5 6.1 - - + -
302B ARG* 3.1 32.2 + - - +
308B LEU* 4.0 16.4 - - + -
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Residues in contact with THR 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 GLU* 2.7 32.8 + - - +
264B HIS* 3.7 4.7 - - - -
266B VAL* 1.3 77.3 - - - +
268B GLN* 1.3 68.1 + - - +
269B PHE 3.2 0.6 + - - -
270B SER* 3.6 19.5 + - - -
298B LEU* 4.3 11.3 - - - +
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Residues in contact with GLN 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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24A LYS* 3.2 52.2 + - + +
264B HIS* 2.7 45.3 + - + +
265B ILE* 3.6 5.2 - - - +
267B THR* 1.3 77.7 - - - +
269B PHE* 1.3 78.9 + - + +
270B SER* 3.7 1.7 + - - -
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Residues in contact with PHE 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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21A THR* 3.7 25.6 - - - -
24A LYS* 3.9 17.9 - - + -
25A GLN* 3.8 29.6 - - + -
93A ASP* 5.9 1.1 - - - -
95A VAL* 4.2 17.7 - - + -
243B PRO* 3.5 31.4 - - + -
265B ILE* 3.0 28.0 + - + +
266B VAL 3.3 3.7 - - - +
268B GLN* 1.3 90.2 - - + +
270B SER* 1.3 59.0 + - - +
271B SER 3.4 2.9 - - - -
272B VAL* 3.3 19.5 - - + +
274B VAL* 3.9 14.7 - - + +
302B ARG* 2.8 26.2 + - - -
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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