Contacts of the helix formed by residues 260 - 269 (chain B) in PDB entry 4IRX
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 ILE 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PRO* 5.1 13.5 - - + -
51B PHE* 5.0 15.9 - - + +
205B ARG* 4.8 6.7 - - - +
232B ASP* 2.8 34.5 + - + +
233B ASP* 4.4 9.6 - - + +
236B MSE 5.1 1.6 - - + -
258B ASP* 3.8 24.7 - - + +
259B ALA* 1.3 75.5 - - - +
261B PRO* 1.3 74.4 - - + +
262B GLU* 4.1 21.1 - - + +
263B ALA* 3.0 21.2 + - - +
264B LEU* 3.0 9.7 + - - +
321B ARG* 3.8 17.0 - - - +
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Residues in contact with PRO 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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259B ALA 3.7 1.8 - - - +
260B ILE* 1.3 86.1 - - + +
262B GLU* 1.3 61.6 + - - +
264B LEU* 3.3 13.6 + - + +
265B ALA* 3.0 23.2 + - - +
321B ARG* 3.3 31.9 - - - +
324B GLU* 3.5 56.1 - - + +
325B MSE 4.1 6.2 - - + +
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Residues in contact with GLU 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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205B ARG* 3.1 40.4 + - - -
236B MSE 3.9 16.2 - - - +
260B ILE* 3.2 14.1 - - + +
261B PRO* 1.3 78.8 - - - +
263B ALA* 1.3 62.2 + - - +
265B ALA* 3.4 7.7 + - - +
266B ARG* 3.2 28.2 + - + +
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Residues in contact with ALA 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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232B ASP* 3.4 37.0 - - + +
236B MSE 3.5 20.7 - - + +
260B ILE* 3.0 7.0 + - - +
262B GLU* 1.3 76.6 - - - +
264B LEU* 1.3 67.1 + - - +
266B ARG* 3.1 4.1 + - - +
267B ILE* 2.9 27.4 + - - +
272B MSE 3.7 11.8 - - + +
275B THR* 4.7 5.8 - - + -
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Residues in contact with LEU 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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259B ALA* 3.8 21.8 - - + +
260B ILE 3.0 13.8 + - - +
261B PRO* 3.3 12.5 + - + +
263B ALA* 1.3 77.0 - - - +
265B ALA* 1.3 57.0 + - - +
267B ILE* 3.1 4.6 + - - +
268B LYS* 2.9 28.9 + - - +
275B THR* 4.2 6.5 - - + -
311B ILE* 4.0 10.3 - - + -
316B LEU* 3.9 22.9 - - + +
319B ALA* 3.7 33.9 - - + -
321B ARG 4.1 5.6 - - - +
322B ILE* 3.9 27.4 - - + +
325B MSE 3.7 16.9 - - + +
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Residues in contact with ALA 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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261B PRO 3.0 13.1 + - - +
262B GLU* 3.6 11.0 - - - +
264B LEU* 1.3 77.1 - - - +
266B ARG* 1.3 69.0 + - - +
268B LYS* 3.4 5.3 + - + +
269B ALA* 3.0 27.5 + - - +
325B MSE 3.8 19.9 - - + -
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Residues in contact with ARG 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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236B MSE 4.0 20.0 - - - -
239B LEU* 4.0 7.2 - - + -
243B ARG* 5.6 1.1 - - - +
262B GLU* 3.2 17.6 + - + +
263B ALA* 3.1 9.2 + - - +
265B ALA* 1.3 85.0 + - - +
267B ILE* 1.3 57.6 + - - +
269B ALA* 3.4 23.4 + - - +
270B GLY 3.1 6.4 + - - -
271B GLU* 2.3 81.4 + - - +
272B MSE 3.2 20.4 + - + +
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Residues in contact with ILE 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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159A ALA* 4.9 0.2 - - - +
263B ALA 2.9 17.7 + - - +
264B LEU* 3.5 9.2 - - - +
266B ARG* 1.3 75.0 - - - +
268B LYS* 1.3 65.9 + - - +
270B GLY* 3.0 13.7 + - - -
272B MSE 3.3 32.2 - - + +
273B VAL 4.0 4.9 - - - +
274B ALA* 3.6 17.9 - - - +
275B THR* 3.6 33.7 - - + +
311B ILE* 3.9 8.7 - - + +
312B THR 3.8 4.9 - - - -
313B SER* 3.6 36.8 - - - +
316B LEU* 3.9 8.5 - - + -
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Residues in contact with LYS 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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158A PRO* 3.5 39.4 + - + +
159A ALA* 3.6 20.2 - - - +
264B LEU 2.9 15.8 + - - +
265B ALA* 3.6 5.8 - - - +
267B ILE* 1.3 78.4 - - - +
269B ALA* 1.3 59.9 + - - +
270B GLY* 3.4 0.3 + - - -
316B LEU* 4.2 8.9 - - + +
325B MSE 3.8 29.5 - - + +
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Residues in contact with ALA 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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265B ALA 3.0 16.7 + - - +
266B ARG* 3.6 34.1 - - - +
267B ILE 3.2 0.4 - - - -
268B LYS* 1.3 76.3 - - - +
270B GLY* 1.3 60.0 + - - +
271B GLU* 3.6 1.4 + - + +
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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