Contacts of the helix formed by residues 253 - 268 (chain B) in PDB entry 3LP4
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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236B LEU* 3.9 2.6 - - - +
237B ASP* 5.5 0.4 - - - -
240B PHE* 3.8 16.6 - - + -
251B GLY 4.7 4.7 - - - +
252B LEU* 1.3 77.0 - - - +
254B TYR* 1.3 64.8 + - - +
255B ARG* 3.3 11.3 + - - +
256B GLU* 2.9 41.3 + - - +
257B GLY* 2.9 19.8 + - - -
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 4.8 6.2 - - - +
240B PHE* 3.5 39.3 - + + -
253B THR* 1.3 72.4 - - - +
255B ARG* 1.3 66.0 + - + +
257B GLY* 2.9 18.4 + - - -
258B LEU* 3.0 40.6 + - + +
294B ASN 4.8 1.4 + - - -
295B THR* 3.7 42.4 - - + -
298B ALA* 3.3 25.2 - - + +
299B ILE* 5.4 2.4 - - + +
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Residues in contact with ARG 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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253B THR* 3.2 8.7 + - - +
254B TYR* 1.3 88.2 - - + +
256B GLU* 1.3 58.1 + - + +
258B LEU* 3.4 3.3 + - + +
259B TYR* 2.9 28.9 + - - +
308B ARG* 3.6 28.2 + - - +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B MET* 4.5 2.4 - - - +
203B VAL* 3.7 19.4 - - - +
207B GLY* 5.9 0.2 - - - -
208B ILE* 3.0 49.7 + - + +
251B GLY 4.3 1.2 - - - +
252B LEU* 3.2 28.0 - - + +
253B THR* 2.9 47.8 + - + +
255B ARG* 1.3 73.8 - - + +
257B GLY* 1.3 66.5 + - - +
259B TYR* 4.4 0.2 - - - -
260B ILE* 3.2 15.8 + - - +
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 4.6 3.0 - - - -
236B LEU* 3.7 24.2 - - - +
253B THR 2.9 6.3 + - - -
254B TYR 2.9 8.6 + - - -
256B GLU* 1.3 80.1 - - - +
258B LEU* 1.3 57.8 + - - +
260B ILE* 3.8 6.4 + - - +
261B THR* 3.0 27.4 + - - +
299B ILE* 4.0 16.7 - - - +
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Residues in contact with LEU 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 TYR* 3.0 44.5 + - + +
255B ARG 3.7 7.2 - - - +
256B GLU 3.2 0.2 - - - -
257B GLY* 1.3 74.4 - - - +
259B TYR* 1.3 59.4 + - - +
261B THR* 2.9 3.9 + - - -
262B GLU* 2.8 38.2 + - - +
298B ALA* 3.8 35.4 - - + +
299B ILE* 4.3 6.5 - - + +
302B ALA* 4.2 11.9 - - + -
308B ARG* 3.7 38.6 - - + +
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Residues in contact with TYR 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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208B ILE* 3.5 34.1 - - + -
209B GLY* 3.7 29.7 + - - -
212B MET* 3.6 15.3 - - + +
255B ARG 2.9 17.6 + - - +
256B GLU* 4.4 0.2 - - - -
257B GLY 3.5 0.2 - - - -
258B LEU* 1.3 74.1 - - - +
260B ILE* 1.3 65.6 + - - +
262B GLU* 3.2 8.5 + - - +
263B GLU* 2.9 66.3 + - + +
308B ARG* 3.6 15.2 - - - +
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Residues in contact with ILE 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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121B ILE* 5.1 3.1 - - + -
123B VAL* 4.3 22.2 - - + -
177B ILE* 3.9 26.7 - - + -
208B ILE* 3.5 16.4 - - + -
212B MET* 3.6 35.7 - - + +
229B LEU* 5.2 0.2 - - + -
231B PHE* 5.6 1.8 - - + -
252B LEU* 4.1 18.8 - - + -
256B GLU 3.2 19.8 + - - +
257B GLY* 4.0 5.8 - - - +
259B TYR* 1.3 76.4 - - - +
261B THR* 1.3 62.6 + - + +
263B GLU 3.1 0.3 + - - -
264B ILE* 2.9 44.5 + - + +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 4.0 13.7 - - + -
231B PHE* 4.4 5.4 - - + -
257B GLY 3.0 11.3 + - - +
258B LEU* 2.9 18.2 + - - -
260B ILE* 1.3 80.1 - - + +
262B GLU* 1.3 60.1 + - - +
264B ILE* 3.8 7.9 - - - +
265B TYR* 3.0 24.3 + - - +
299B ILE* 3.3 29.1 + - + +
302B ALA* 3.4 16.3 - - - +
303B CYS* 3.3 33.8 - - - -
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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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258B LEU* 2.8 29.3 + - + +
259B TYR* 3.6 10.7 - - - +
261B THR* 1.3 73.0 - - - +
263B GLU* 1.3 62.2 + - - +
265B TYR* 3.6 4.7 - - - +
266B LYS* 2.9 40.9 + - - +
302B ALA* 4.0 20.4 - - + +
306B LEU 3.9 7.1 - - - +
307B ALA* 3.8 7.8 - - + -
308B ARG* 2.9 68.1 + - - +
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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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212B MET* 4.0 19.5 - - + -
216B LEU* 3.9 11.6 - - + +
259B TYR* 2.9 67.6 + - + +
260B ILE 3.6 3.6 - - - +
262B GLU* 1.3 75.6 - - - +
264B ILE* 1.3 64.1 + - - +
266B LYS* 2.9 38.1 + - - +
267B THR* 3.2 18.3 + - - +
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Residues in contact with ILE 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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121B ILE* 4.2 15.5 - - + -
212B MET* 3.8 11.9 - - + -
216B LEU* 4.7 7.2 - - + -
227B ILE* 4.0 13.2 - - + -
229B LEU* 3.3 38.6 - - + -
260B ILE* 2.9 33.4 + - + +
261B THR* 3.8 5.6 - - - +
263B GLU* 1.3 76.3 - - - +
265B TYR* 1.3 62.2 + - - +
267B THR* 2.8 32.3 + - + +
268B GLY 3.8 0.5 + - - -
269B LEU 4.6 1.2 + - - -
270B LEU* 3.8 35.6 + - + -
303B CYS* 5.9 0.9 - - - -
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Residues in contact with TYR 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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6B ARG* 5.8 8.5 - - + -
44B GLU* 3.8 22.8 + - + +
261B THR 3.0 9.7 + - - +
262B GLU* 3.6 5.6 - - - +
263B GLU 3.2 0.2 - - - -
264B ILE* 1.3 78.4 - - - +
266B LYS* 1.3 74.6 + - + +
268B GLY* 2.9 23.0 + - - -
270B LEU* 5.4 4.4 - - - +
302B ALA 3.4 17.0 - - - +
303B CYS* 3.3 16.6 - - - +
304B PHE* 3.7 5.4 - - - -
305B GLY* 3.2 40.6 - - - -
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Residues in contact with LYS 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 GLU* 2.9 35.5 + - - +
263B GLU* 2.9 40.9 + - - +
264B ILE 3.3 1.0 - - - -
265B TYR* 1.3 87.3 - - + +
267B THR* 1.3 64.5 + - - +
268B GLY* 3.3 0.9 + - - -
307B ALA* 6.0 6.7 - - - -
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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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216B LEU* 3.4 36.1 - - + -
220B LEU* 4.1 17.7 - - + -
224B LYS* 6.0 0.5 + - - +
227B ILE* 4.6 3.0 - - + +
263B GLU 3.2 17.9 - - - +
264B ILE* 2.8 17.5 + - + +
266B LYS* 1.3 77.3 - - - +
268B GLY* 1.3 62.1 + - - +
269B LEU* 3.0 25.9 + - - +
270B LEU 4.2 0.9 + - - -
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Residues in contact with GLY 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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6B ARG* 4.8 12.5 + - - -
265B TYR 2.9 15.8 + - - -
266B LYS 3.0 1.9 - - - -
267B THR* 1.3 81.0 + - - +
269B LEU* 1.3 63.9 + - - +
270B LEU* 3.6 4.1 - - - +
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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