Contacts of the helix formed by residues 259 - 270 (chain B) in PDB entry 4J4L
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 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LYS 5.7 0.4 - - - +
230B SER* 6.5 0.7 - - - -
252B TRP* 4.4 7.9 - - + -
253B ASP 3.2 25.1 - - - +
254B CYS* 3.6 23.6 - - - -
255B THR 3.8 8.6 + - - +
257B PRO 3.4 0.4 - - - -
258B GLY* 1.3 75.9 - - - +
260B ARG* 1.3 67.1 + - - +
261B TYR 3.2 2.9 - - - -
262B LEU* 3.1 18.0 + - + +
263B SER* 2.8 27.9 + - - -
294B VAL* 3.5 35.0 - - + -
297B ILE* 3.6 32.5 - - + -
299B CYS* 4.7 7.2 - - - -
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Residues in contact with ARG 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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257B PRO* 3.2 26.8 + - + +
258B GLY 3.4 0.2 - - - -
259B ILE* 1.3 76.8 - - - +
261B TYR* 1.3 66.2 + - - +
263B SER* 4.0 2.3 - - - -
264B GLU* 2.9 54.8 + - - +
298B ILE* 5.1 4.6 - - - +
299B CYS* 3.6 55.7 + - - +
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Residues in contact with TYR 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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231B VAL* 4.1 15.7 - - + +
233B ASP* 3.8 27.5 + - - +
234B GLY* 3.2 34.2 - - - -
235B VAL* 3.8 10.5 - - + -
236B PHE* 3.3 33.2 + + - -
237B ASP* 3.2 22.5 + - - -
257B PRO 4.9 0.2 + - - -
258B GLY 4.9 3.6 + - - +
259B ILE 3.2 1.0 - - - -
260B ARG* 1.3 81.3 - - - +
262B LEU* 1.3 60.5 + - - +
264B GLU* 3.1 4.0 + - + +
265B TRP* 2.9 54.6 + + + +
268B LYS* 6.4 1.6 - - - -
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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
----------------------------------------------------------
230B SER* 5.7 0.2 - - - -
231B VAL* 3.9 19.3 - - + +
236B PHE* 4.3 24.5 - - + -
247B LEU* 4.3 9.0 - - + -
252B TRP* 3.8 45.3 - - + +
258B GLY 5.5 0.6 + - - +
259B ILE* 3.1 18.5 + - + +
261B TYR* 1.3 80.2 - - - +
263B SER* 1.3 65.2 + - - +
265B TRP* 3.5 3.7 + - + +
266B ILE* 3.1 45.1 + - + +
294B VAL* 4.2 11.9 - - + -
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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
----------------------------------------------------------
259B ILE* 2.8 28.2 + - - +
260B ARG* 4.1 3.4 - - - -
262B LEU* 1.3 74.5 - - - +
264B GLU* 1.3 62.3 + - - -
266B ILE* 3.4 1.7 + - - +
267B ASN* 2.9 29.7 + - - +
294B VAL* 2.7 32.2 + - - -
295B ARG* 3.5 9.3 + - - +
297B ILE 2.8 24.3 + - - -
299B CYS* 6.1 0.9 - - - -
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Residues in contact with GLU 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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260B ARG* 2.9 59.9 + - - +
261B TYR* 3.7 4.5 - - + +
263B SER* 1.3 76.8 - - - +
265B TRP* 1.3 58.1 + - - +
267B ASN* 3.4 6.0 + - + +
268B LYS* 2.8 49.3 + - - +
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Residues in contact with TRP 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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236B PHE* 3.3 53.2 + + + +
237B ASP* 5.2 2.2 + - - +
239B LEU* 6.0 0.4 - - + -
242B LEU* 4.0 14.6 - - + -
245B ILE* 3.7 34.8 - - + -
247B LEU* 4.8 1.3 - - + -
261B TYR* 2.9 44.0 + + + +
262B LEU* 3.5 9.9 - - + +
264B GLU* 1.3 72.3 - - - +
266B ILE* 1.3 69.2 + - + +
268B LYS* 2.9 16.1 + - - +
269B HIS* 2.4 74.8 + + + -
272B VAL* 3.9 13.2 - - + -
273B VAL* 4.2 10.1 - - + -
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Residues in contact with ILE 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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247B LEU* 4.1 11.2 - - + -
262B LEU* 3.1 39.6 + - + +
263B SER* 4.0 3.8 - - - +
265B TRP* 1.3 96.9 - - + +
267B ASN* 1.3 54.1 + - - +
269B HIS 4.1 1.6 - - - +
270B SER* 2.3 41.0 + - - +
273B VAL* 4.1 15.5 - - + -
282B PRO* 3.6 26.0 - - + +
285B ALA* 4.4 13.0 - - + -
294B VAL* 4.3 14.4 - - + -
295B ARG* 3.4 24.9 - - + -
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Residues in contact with ASN 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* 2.9 23.1 + - - +
264B GLU* 3.8 6.3 - - + +
266B ILE* 1.3 76.3 - - - +
268B LYS* 1.3 60.4 + - - +
269B HIS 3.6 0.2 + - - -
270B SER* 3.9 10.4 + - - -
295B ARG* 2.6 68.0 + - - +
297B ILE 5.1 0.3 - - - +
298B ILE* 6.0 1.0 - - - +
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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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261B TYR* 6.4 1.3 - - - -
264B GLU* 2.8 41.6 + - - +
265B TRP* 3.2 21.3 - - - +
267B ASN* 1.3 78.7 - - - +
269B HIS* 1.3 79.6 + - + +
270B SER 3.6 0.4 + - - -
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Residues in contact with HIS 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 TRP* 2.4 86.5 + + + +
266B ILE* 3.0 4.5 - - - -
268B LYS* 1.3 95.7 + - + +
270B SER* 1.3 49.9 + - - +
271B GLY 2.6 18.7 + - - -
272B VAL* 2.7 37.5 + - + +
273B VAL* 3.8 5.6 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ILE* 2.3 24.8 + - - -
267B ASN 4.0 8.7 + - - -
268B LYS 3.6 1.4 - - - -
269B HIS* 1.3 67.3 - - - +
271B GLY* 1.3 59.3 + - - +
272B VAL 3.5 0.4 + - - -
273B VAL 4.2 4.9 + - - +
280B VAL* 3.8 5.1 - - - +
282B PRO* 3.4 45.4 - - - +
295B ARG* 3.9 15.3 - - - -
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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