Contacts of the helix formed by residues 264 - 278 (chain A) in PDB entry 1L4E
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 GLY 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 1.3 87.9 + - - +
265A PHE* 1.3 65.1 + - - -
266A LEU 3.4 2.9 - - - -
267A SER* 2.7 23.8 + - - +
268A TYR* 3.0 15.8 + - - -
289A HIS* 3.9 11.0 - - - -
291A SER* 3.9 11.7 - - - -
316A GLY* 6.1 1.6 - - - -
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Residues in contact with PHE 265 (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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180A THR* 4.4 2.9 - - + -
183A ALA* 3.9 11.2 - - + -
184A ALA* 3.8 24.2 - - + -
187A VAL* 3.8 21.1 - - + -
198A VAL* 3.3 35.4 - - + -
264A GLY* 1.3 68.0 - - - -
266A LEU* 1.3 74.6 + - + +
268A TYR* 3.1 13.8 + + - +
269A SER* 3.1 21.0 + - - -
291A SER* 3.7 9.0 + - - +
293A GLU* 3.5 41.5 - - + -
295A GLY* 3.5 36.1 - - - -
296A ALA* 3.9 6.7 - - - -
299A ALA* 4.5 1.6 - - + -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.6 31.6 - - + +
179A ASN* 3.5 50.3 - - - +
180A THR* 3.8 17.0 - - + -
183A ALA* 3.6 20.0 - - + -
242A ASP* 5.0 0.9 - - - +
243A LEU* 3.6 36.5 - - + +
246A MET* 4.5 2.2 - - + -
264A GLY 3.3 0.8 + - - -
265A PHE* 1.3 82.0 - - + +
267A SER* 1.3 63.1 + - - +
269A SER* 3.1 7.3 + - - -
270A ALA* 3.1 16.8 + - - +
990A RBZ 6.2 0.2 - - - -
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Residues in contact with SER 267 (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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172A VAL* 4.1 9.6 - - - -
246A MET* 3.7 26.2 - - - +
250A MET* 3.7 5.4 - - - +
262A LEU* 3.6 9.8 - - - +
263A ASP* 2.9 35.2 + - - -
264A GLY 2.7 19.6 + - - +
266A LEU* 1.3 77.9 - - - +
268A TYR* 1.3 59.3 + - - +
270A ALA* 3.3 2.1 + - - +
271A ALA* 2.9 28.9 + - - +
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.5 14.4 - - + -
263A ASP 3.4 13.7 + - - -
264A GLY 3.0 29.9 + - - -
265A PHE* 3.1 17.6 + + - +
267A SER* 1.3 81.0 + - - +
269A SER* 1.3 56.9 + - - +
271A ALA* 3.3 6.9 + - - +
272A LEU* 2.9 34.7 + - - +
287A PRO* 6.3 1.8 - - + -
288A SER 6.2 0.9 - - - -
289A HIS 2.8 25.5 + - - -
290A PHE* 3.8 2.6 - - - -
291A SER* 3.1 17.1 + - - -
296A ALA* 3.7 27.6 - - + -
299A ALA* 3.7 30.1 - - + -
300A LEU* 3.7 31.1 - - + +
303A LEU* 3.8 7.4 - - + +
307A PRO* 5.6 0.2 - - + -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA* 2.9 36.8 + - - -
186A MET* 3.2 37.7 - - - +
187A VAL* 3.5 15.1 - - - +
190A PHE* 4.4 0.2 - - - -
243A LEU* 4.3 2.7 - - - -
265A PHE 3.1 10.9 + - - -
266A LEU 3.2 10.5 - - - -
268A TYR* 1.3 77.3 - - - +
270A ALA* 1.3 61.5 + - - +
272A LEU* 3.3 7.3 + - - +
273A ALA 3.2 13.2 + - - -
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Residues in contact with ALA 270 (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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186A MET* 4.2 5.8 - - - +
243A LEU* 3.9 8.9 - - + +
246A MET* 3.7 28.3 - - + -
247A THR* 3.3 24.6 + - - +
250A MET* 3.9 8.5 - - + +
266A LEU 3.1 8.9 + - - +
267A SER* 3.3 7.4 + - - +
269A SER* 1.3 83.0 - - - +
271A ALA* 1.3 56.6 + - - +
273A ALA 3.4 0.9 + - - -
274A ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A MET* 3.5 19.7 - - - -
262A LEU* 4.1 16.2 - - + -
267A SER 2.9 17.1 + - - +
268A TYR* 3.8 5.6 - - - +
270A ALA* 1.3 75.0 - - - +
272A LEU* 1.3 65.4 + - - +
274A ALA* 4.3 1.3 - - - -
275A CYS* 2.9 29.1 + - - -
285A LEU* 4.0 18.4 - - + -
303A LEU* 4.1 10.8 - - + -
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Residues in contact with LEU 272 (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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187A VAL* 4.1 25.6 - - + -
190A PHE* 3.8 27.7 - - + -
191A THR* 4.2 18.8 - - + -
268A TYR 2.9 19.1 + - - +
269A SER* 3.3 7.6 + - - +
271A ALA* 1.3 76.3 - - - +
273A ALA* 1.3 62.6 + - - +
275A CYS* 3.5 2.4 + - - +
276A GLN* 3.0 24.3 + - - +
299A ALA* 4.3 10.8 - - + -
302A HIS* 4.1 21.3 - - + +
303A LEU* 3.4 30.7 - - + -
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Residues in contact with ALA 273 (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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186A MET* 4.0 2.9 - - + -
190A PHE* 3.6 26.4 - - + -
231A GLY* 4.5 1.8 - - - +
235A LEU* 3.9 33.2 - - + -
247A THR* 4.0 2.7 - - - +
269A SER 3.2 7.7 + - - +
270A ALA 3.5 8.3 - - - +
271A ALA 3.2 0.2 - - - -
272A LEU* 1.3 79.1 - - - +
274A ALA* 1.3 63.9 + - - +
276A GLN* 2.9 3.5 + - - +
277A ILE* 2.9 28.6 + - - +
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Residues in contact with ALA 274 (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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247A THR* 3.8 19.9 - - + +
250A MET* 4.1 26.5 - - + -
251A LEU* 4.2 11.8 - - + +
270A ALA 2.9 17.2 + - - +
271A ALA* 3.4 4.2 + - - +
273A ALA* 1.3 75.7 - - - +
275A CYS* 1.3 59.0 + - - +
277A ILE* 3.3 5.8 + - - +
278A ALA* 2.9 31.4 + - - +
281A VAL* 4.5 8.5 - - + -
285A LEU* 5.8 0.2 - - + -
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Residues in contact with CYS 275 (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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271A ALA 2.9 20.5 + - - +
272A LEU* 4.0 3.1 - - - +
274A ALA* 1.3 76.3 - - - +
276A GLN* 1.3 65.4 + - - +
278A ALA 3.8 6.7 - - - -
279A PRO* 3.3 28.2 - - + +
281A VAL* 4.9 1.3 - - - -
282A ARG* 4.0 31.2 - - + -
285A LEU* 3.8 25.1 - - - -
303A LEU* 4.3 13.9 - - + -
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Residues in contact with GLN 276 (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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190A PHE* 3.9 14.9 - - + -
228A PRO 3.6 17.5 + - - +
229A ARG* 3.1 27.5 - - - +
231A GLY* 3.7 22.2 + - - +
272A LEU 3.0 13.1 + - - +
273A ALA 2.9 9.5 + - - +
275A CYS* 1.3 78.3 - - - +
277A ILE* 1.3 62.7 + - - +
279A PRO* 4.5 5.2 - - - +
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Residues in contact with ILE 277 (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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4A LEU* 5.8 0.2 - - + -
8A LEU* 3.8 37.1 - - + +
152A LEU* 4.5 6.5 - - + -
231A GLY* 3.9 18.8 - - - +
232A ILE* 3.6 35.9 - - + +
235A LEU* 4.2 15.3 - - + -
247A THR* 4.2 13.9 - - + -
251A LEU* 4.6 7.4 - - + -
273A ALA 2.9 16.9 + - - +
274A ALA* 3.6 6.3 - - - +
276A GLN* 1.3 79.7 - - - +
278A ALA* 1.3 57.9 + - + +
279A PRO* 4.2 2.8 - - - +
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Residues in contact with ALA 278 (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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8A LEU* 3.9 30.1 - - + +
11A ILE* 4.1 9.2 - - + -
251A LEU* 4.3 1.1 - - + -
274A ALA 2.9 14.5 + - - +
275A CYS* 3.5 4.5 - - - -
277A ILE* 1.3 80.2 - - - +
279A PRO* 1.3 70.9 - - - +
280A ALA* 3.0 4.3 - - + +
281A VAL* 2.9 28.6 + - + +
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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