Contacts of the helix formed by residues 285 - 294 (chain B) in PDB entry 3L6D
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 ASP 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLU* 5.6 1.6 - - - +
226B ALA* 5.4 1.0 - - - +
229B ARG* 3.2 38.6 + - - +
235B PHE* 2.9 25.8 + - + +
236B LYS 3.8 10.7 - - - +
237B GLY* 3.9 2.8 - - - -
239B GLN* 5.2 0.9 - - - +
240B ALA* 3.4 25.1 + - - +
242B LEU* 4.3 1.7 - - - +
284B GLN* 1.3 75.3 - - - +
286B ILE* 1.3 64.4 + - - +
287B ALA* 2.8 33.2 + - - +
288B ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 286 (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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130A TYR* 4.7 1.1 - - + +
187A MSE 3.9 22.4 - - + -
188A VAL* 5.5 0.9 - - + -
191A PHE* 3.7 17.5 - - + -
226B ALA* 6.2 0.7 - - + -
240B ALA* 3.0 28.8 + - + +
242B LEU* 4.1 17.0 - - + -
245B HIS* 3.7 40.8 - - + +
249B PHE* 4.7 4.3 - - + -
273B VAL* 4.4 13.0 - - + -
284B GLN 3.6 0.2 + - - -
285B ASP* 1.3 77.9 - - - +
287B ALA* 1.3 59.8 + - + +
288B ALA 3.0 0.2 - - - -
289B THR* 2.7 44.5 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 3.9 12.6 - - + -
226B ALA* 4.0 35.7 - - + +
229B ARG* 4.6 4.5 - - + -
230B LEU* 4.1 3.5 - - + +
235B PHE* 3.8 17.4 - - + -
285B ASP* 2.8 18.2 + - - +
286B ILE* 1.3 79.4 - - + +
288B ALA* 1.3 54.5 + - - +
289B THR 3.0 1.3 - - - -
290B THR* 3.0 30.7 + - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.7 15.9 - - + -
242B LEU* 4.4 2.7 - - + -
281B TYR* 4.1 20.1 - - + -
284B GLN* 3.4 33.7 - - + +
285B ASP 2.8 17.4 + - - +
287B ALA* 1.3 71.9 - - - +
289B THR* 1.3 66.7 + - - +
290B THR 3.0 2.2 - - - -
291B LYS* 2.9 22.5 + - + +
292B SER* 3.5 3.8 + - - -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.8 2.7 - - + -
191A PHE* 3.7 23.7 - - + -
242B LEU* 3.3 20.8 - - - +
272B VAL* 3.6 30.5 - - + -
273B VAL* 4.3 11.1 - - + +
276B ALA* 4.5 5.3 - - + +
286B ILE* 2.7 29.8 + - - +
288B ALA* 1.3 78.1 - - - +
290B THR* 1.3 62.4 + - - +
292B SER* 2.7 28.3 + - - +
293B PHE* 3.4 6.0 - - + -
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Residues in contact with THR 290 (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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191A PHE* 3.4 33.5 - - - +
194A VAL* 3.6 29.3 - - + +
195A GLY* 4.1 13.2 - - - +
204A VAL* 4.5 8.3 - - + -
230B LEU* 3.8 21.6 - - + +
287B ALA 3.0 16.3 + - - -
289B THR* 1.3 78.2 - - - +
291B LYS* 1.3 64.0 + - + +
293B PHE* 3.2 20.8 + - - +
294B ALA* 4.3 1.6 + - - +
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Residues in contact with LYS 291 (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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230B LEU* 6.0 0.4 - - + -
233B GLN* 5.1 6.1 - - - +
235B PHE* 3.6 45.9 - - + -
279B MSE 5.3 1.4 - - - +
281B TYR* 3.7 28.1 + - + +
284B GLN* 2.7 34.4 + - - +
288B ALA* 2.9 14.7 + - - +
290B THR* 1.3 72.0 - - + +
292B SER* 1.3 56.2 + - - +
293B PHE 3.1 5.8 - - - -
294B ALA* 3.0 31.4 + - + +
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Residues in contact with SER 292 (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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272B VAL* 4.5 5.4 + - - +
275B ARG* 2.7 34.0 + - - -
276B ALA* 3.9 30.3 - - - +
279B MSE 4.0 14.2 - - - +
281B TYR* 4.0 17.7 - - - -
288B ALA 3.5 2.2 + - - -
289B THR* 2.7 23.5 + - - +
291B LYS* 1.3 78.2 - - - +
293B PHE* 1.3 65.4 + - - +
294B ALA 3.3 2.7 + - - +
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Residues in contact with PHE 293 (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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191A PHE 3.9 11.4 - - - -
192A GLU* 3.6 43.3 - - + -
195A GLY* 4.0 20.2 - - - -
196A ALA 5.6 0.2 - - - -
199A ARG* 2.9 37.3 + - - +
262A TRP* 3.4 54.1 - + + -
264A PRO* 4.3 0.4 - - + -
272B VAL* 3.5 31.6 - - + -
275B ARG* 4.7 0.9 - - - +
289B THR* 3.4 21.8 - - + -
290B THR 3.2 11.2 + - - +
291B LYS 3.1 1.0 - - - -
292B SER* 1.3 82.2 - - - +
294B ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 294 (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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195A GLY 5.8 0.2 - - - -
198A ASP* 4.4 14.8 - - - +
199A ARG* 4.2 3.5 + - - +
279B MSE 5.7 3.1 - - - +
290B THR 4.3 1.4 + - - -
291B LYS* 3.0 23.4 + - + +
292B SER 3.3 3.7 - - - +
293B PHE* 1.3 82.2 - - - +
295B ARG* 1.3 65.2 + - - +
296B GLU* 3.8 33.0 - - - +
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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