Contacts of the helix formed by residues 283 - 295 (chain A) in PDB entry 3L6B
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 GLU 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASN* 3.0 24.7 + - - -
114A LYS* 2.7 25.1 + - - -
238A ASP* 4.3 2.9 - - - +
239A GLY* 4.9 0.3 + - - -
271A THR* 4.5 0.7 - - - -
282A ILE* 1.3 77.7 - - - +
284A PRO* 1.3 78.4 - - + +
285A THR* 3.9 11.4 + - - +
286A ALA* 2.9 23.4 + - - +
287A GLY 3.3 6.8 + - - -
314A GLY* 3.0 25.4 + - - +
315A GLY* 3.6 3.1 + - - -
316A ASN* 3.0 42.5 + - - +
317A VAL* 3.9 4.0 - - + -
350A PLP 3.7 9.1 - - + +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.6 54.5 - - + +
237A ALA* 4.5 0.9 - - - -
238A ASP* 4.9 6.3 - - - +
267A ILE* 3.3 20.7 - - + +
271A THR* 3.5 18.1 - - + +
282A ILE 4.4 1.1 - - - +
283A GLU* 1.3 87.0 - - + +
285A THR* 1.3 57.5 + - - +
287A GLY* 2.9 15.8 + - - -
288A VAL 3.4 0.7 + - - -
317A VAL* 3.9 18.2 - - + -
322A SER* 5.4 0.2 - - - +
325A TRP* 4.1 14.8 - - + +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 3.9 6.8 - - + +
237A ALA* 3.1 18.6 - - - +
238A ASP* 3.2 2.3 + - - -
239A GLY* 2.9 26.8 + - - -
240A VAL* 3.5 30.7 - - + -
283A GLU* 3.1 18.5 + - - +
284A PRO* 1.3 77.2 - - - +
286A ALA* 1.3 61.6 + - - +
288A VAL* 3.2 20.1 + - - +
313A SER* 4.4 0.2 - - - -
350A PLP 3.2 29.4 - - + +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 5.1 1.1 - - - +
282A ILE* 3.9 13.5 - - + -
283A GLU* 2.9 11.9 + - - +
285A THR* 1.3 76.8 - - - +
287A GLY* 1.3 61.3 + - - +
288A VAL 3.1 1.9 + - - -
289A GLY* 3.8 7.3 + - - -
290A VAL* 4.0 3.1 + - - +
310A ILE* 5.2 0.2 - - - +
311A VAL 4.5 4.7 - - - +
312A LEU* 4.0 18.5 - - - +
313A SER* 3.5 31.8 + - - +
314A GLY 3.5 22.4 - - - +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 4.6 3.8 - - - -
270A ALA* 3.7 3.3 - - - +
271A THR* 3.5 20.0 - - - -
282A ILE* 3.7 11.8 - - - +
283A GLU 3.3 5.5 + - - -
284A PRO 2.9 11.9 + - - -
286A ALA* 1.3 75.9 - - - +
288A VAL* 1.3 57.9 + - - +
289A GLY 3.3 0.4 - - - -
290A VAL* 3.2 7.7 + - - +
291A ALA* 2.8 31.2 + - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 4.4 6.5 - - + -
184A VAL 5.5 0.2 - - - +
209A ALA* 3.5 33.0 - - + +
210A GLU* 3.6 10.1 - - - +
211A PRO* 4.1 5.8 - - + -
237A ALA* 3.7 28.5 - - + -
240A VAL* 4.8 3.6 - - + -
262A VAL* 3.8 13.8 - - + +
267A ILE* 3.9 15.7 - - + -
284A PRO 3.4 4.2 + - - +
285A THR* 3.2 17.3 - - - +
286A ALA 3.1 0.6 - - - -
287A GLY* 1.3 77.5 - - - +
289A GLY* 1.3 56.9 + - - +
291A ALA* 3.4 5.1 + - - +
292A ALA* 3.0 26.3 + - - +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 3.7 11.5 - - - +
183A PRO* 4.7 11.2 - - - +
209A ALA* 3.7 15.8 - - - +
285A THR 4.5 0.8 + - - -
286A ALA 3.8 4.9 + - - -
287A GLY 3.3 0.6 - - - -
288A VAL* 1.3 76.0 - - - +
290A VAL* 1.3 63.8 + - - +
292A ALA* 3.3 3.6 + - - +
293A VAL* 3.3 25.6 + - - +
310A ILE* 3.8 14.7 - - - +
311A VAL 5.6 0.2 - - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.3 14.6 - - + -
42A LEU* 6.4 0.4 - - + -
44A PHE* 4.0 13.5 - - + -
270A ALA* 4.0 15.0 - - + +
273A LEU* 5.4 0.9 - - + -
274A VAL* 3.9 26.7 - - + -
286A ALA 4.0 6.1 - - - +
287A GLY* 3.2 8.6 + - - +
289A GLY* 1.3 73.0 - - - +
291A ALA* 1.3 66.3 + - - +
293A VAL* 3.2 4.3 + - - +
294A LEU* 3.1 32.8 + - + +
310A ILE* 4.2 9.9 - - + -
312A LEU* 3.7 30.5 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A VAL* 3.6 20.2 - - + +
266A GLU* 3.6 34.4 - - + +
267A ILE* 4.1 2.5 - - - +
270A ALA* 3.5 8.4 - - + +
287A GLY 2.8 17.6 + - - +
288A VAL 3.6 5.8 - - - +
290A VAL* 1.3 76.6 - - - +
292A ALA* 1.3 61.7 + - - +
294A LEU* 3.2 7.1 + - - +
295A SER* 3.0 23.2 + - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 4.4 6.5 - - + -
209A ALA* 3.6 26.9 - - + -
260A PHE* 4.0 21.2 - - + +
262A VAL* 3.5 12.7 - - + +
288A VAL 3.0 8.1 + - - +
289A GLY 3.5 9.2 - - - +
290A VAL 3.2 0.4 - - - -
291A ALA* 1.3 76.5 - - - +
293A VAL* 1.3 62.1 + - - +
295A SER* 2.7 22.8 + - - -
298A PHE* 3.2 12.2 - - + +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 3.7 28.9 - - + +
40A ARG* 4.6 1.6 - - + -
42A LEU* 3.8 20.9 - - + -
181A VAL* 3.8 25.8 - - + -
289A GLY 3.3 12.1 + - - +
290A VAL 3.2 7.3 + - - +
292A ALA* 1.3 76.1 - - - +
294A LEU* 1.3 59.3 + - - +
295A SER 3.6 1.0 + - - +
298A PHE* 3.8 37.4 - - + +
299A GLN* 6.1 0.9 - - - +
308A ILE* 4.3 2.9 - - + -
310A ILE* 3.7 19.7 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.2 4.3 - - + +
37A LEU* 3.9 30.3 - - + +
38A THR* 3.7 23.1 - - + -
266A GLU* 5.3 0.2 - - - -
270A ALA* 4.1 14.6 - - + +
273A LEU* 3.9 22.9 - - + -
290A VAL* 3.1 33.7 + - + +
291A ALA* 3.2 5.6 + - - +
293A VAL* 1.3 76.5 - - + +
295A SER* 1.3 63.3 + - - +
296A GLN 3.9 0.2 + - - -
299A GLN* 4.9 5.8 + - - -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PHE* 4.7 6.1 - - - +
261A THR 4.9 4.7 + - - -
262A VAL* 4.3 6.4 - - - +
266A GLU* 3.5 20.9 - - - -
291A ALA 3.0 11.9 + - - -
292A ALA* 2.7 24.0 + - - -
293A VAL 3.3 0.7 - - - +
294A LEU* 1.3 81.2 - - - +
296A GLN* 1.3 66.6 + - - +
297A HIS* 3.8 6.5 + - - +
298A PHE* 3.2 25.8 + - - +
299A GLN* 3.7 8.4 + - - +
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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