Contacts of the helix formed by residues 251 - 260 (chain B) in PDB entry 4JOQ
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 MSE 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLY* 4.6 7.9 - - - +
199B ARG* 4.0 7.2 - - - +
224B ASP* 2.7 23.4 + - + +
225B ASP* 3.4 54.1 - - - +
228B ILE* 4.0 14.6 - - + -
250B GLY* 1.3 73.2 - - - +
252B LYS* 1.3 66.5 + - - +
253B GLU* 4.6 4.5 - - + +
254B ILE* 3.1 11.4 + - + +
255B ILE* 3.0 19.4 + - - +
318B PRO 5.8 0.2 - - - +
319B PHE* 3.3 61.9 - - + +
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Residues in contact with LYS 252 (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 GLY 3.5 2.1 + - - -
251B MSE 1.3 71.6 - - - +
253B GLU* 1.3 70.2 + - + +
255B ILE* 3.3 7.5 + - - +
256B ARG* 2.8 31.5 + - - +
312B PHE 5.6 0.7 - - - -
313B TYR* 3.5 20.0 - - + +
314B PHE* 3.8 18.2 - - + +
315B PRO* 3.2 28.1 + - + +
316B ASP 4.8 0.8 - - - -
317B SER* 3.0 27.5 + - - +
318B PRO* 4.9 3.9 - - - +
319B PHE* 3.0 28.5 + - - +
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Residues in contact with GLU 253 (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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199B ARG* 5.6 1.7 + - - -
228B ILE* 4.2 18.4 - - + +
251B MSE 3.3 4.7 - - + +
252B LYS* 1.3 90.7 - - + +
254B ILE* 1.3 67.3 + - + +
256B ARG* 3.6 7.1 - - - +
257B ARG* 3.3 32.2 + - - +
319B PHE* 5.8 2.2 - - - +
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Residues in contact with ILE 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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224B ASP* 3.8 28.9 - - + +
227B ALA* 5.2 2.0 - - + -
228B ILE* 4.1 19.1 - - + -
231B MSE 3.8 28.7 - - + -
247B GLY* 6.0 0.4 - - - -
251B MSE 3.1 13.4 + - + +
253B GLU* 1.3 78.0 - - + +
255B ILE* 1.3 65.8 + - - +
257B ARG* 3.2 10.7 + - - +
258B ILE* 3.0 31.3 + - + +
265B LEU* 4.3 21.5 - - + -
268B ASN* 3.6 26.5 - - - +
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Residues in contact with ILE 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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250B GLY* 3.9 24.7 - - - +
251B MSE 3.0 17.2 + - - +
252B LYS* 3.6 9.0 - - - +
254B ILE* 1.3 77.5 - - - +
256B ARG* 1.3 56.1 + - - +
258B ILE* 3.2 11.0 + - + +
259B ALA* 2.9 29.4 + - + +
268B ASN* 4.8 3.6 - - - +
304B VAL* 4.0 28.0 - - + -
309B ALA* 3.3 27.3 - - + +
312B PHE* 3.7 22.4 - - + +
313B TYR* 3.7 24.0 - - + +
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Residues in contact with ARG 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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252B LYS 2.8 21.2 + - - +
253B GLU* 3.6 9.4 - - - +
254B ILE 3.2 0.2 - - - -
255B ILE* 1.3 75.0 - - - +
257B ARG* 1.3 59.8 + - + +
259B ALA* 3.4 10.1 + - - +
260B ASP* 2.9 70.1 + - - +
310B GLU* 2.6 41.4 + - - -
313B TYR* 3.3 47.1 - - + +
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Residues in contact with ARG 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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228B ILE* 6.0 0.4 - - - +
231B MSE 3.6 24.2 - - - +
253B GLU* 3.3 17.4 + - - +
254B ILE* 3.2 11.5 + - - +
256B ARG* 1.3 76.3 - - + +
258B ILE* 1.3 64.9 + - - +
260B ASP* 3.2 6.9 + - - +
261B GLY 3.0 4.9 + - - -
262B ASP* 2.9 61.2 + - + +
264B GLN* 3.0 25.1 + - - -
265B LEU* 3.5 24.6 - - + +
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Residues in contact with ILE 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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254B ILE* 3.0 31.1 + - + +
255B ILE* 3.7 9.0 - - + +
257B ARG* 1.3 73.7 - - - +
259B ALA* 1.3 67.7 + - - +
261B GLY* 3.0 11.4 + - - -
262B ASP 4.9 0.4 - - - +
265B LEU* 3.3 33.0 - - + +
266B PRO 4.4 2.7 - - - +
267B ALA 4.0 7.9 - - - +
268B ASN* 3.5 32.5 - - + +
304B VAL* 4.4 9.2 - - + +
305B THR* 3.7 31.2 - - - +
306B PRO* 3.4 19.2 - - + +
309B ALA* 4.1 5.2 - - + -
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Residues in contact with ALA 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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255B ILE* 2.9 18.2 + - + +
256B ARG* 3.5 25.6 - - - +
258B ILE* 1.3 78.0 - - - +
260B ASP* 1.3 60.1 + - - +
261B GLY 3.3 2.8 + - - -
306B PRO* 4.2 14.7 - - - +
309B ALA* 3.7 19.0 - - + +
310B GLU* 3.7 18.6 - - + +
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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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256B ARG* 2.9 58.5 + - - +
257B ARG* 3.2 7.1 + - - +
258B ILE 3.0 0.6 - - - -
259B ALA* 1.3 76.0 - - - +
261B GLY* 1.3 61.4 + - - +
262B ASP* 3.4 2.8 + - + +
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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