Contacts of the strand formed by residues 266 - 274 (chain E) in PDB entry 1LE9
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 VAL 266 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231E PRO* 6.4 2.0 - - + -
257E TYR* 3.4 32.8 - - + +
262E LEU* 3.2 39.5 - - + -
263E GLN* 5.1 2.5 - - - +
264E ALA* 3.2 4.4 + - + +
265E PRO* 1.3 72.3 - - - +
267E ARG* 1.3 60.4 + - - +
268E VAL* 2.8 24.9 + - + +
288E TYR* 3.2 19.9 + - + +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E PRO* 3.6 5.6 - - + +
266E VAL* 1.3 72.1 - - - +
268E VAL* 1.3 63.2 + - - +
285E GLU* 3.4 31.5 + - + +
287E GLN* 4.0 38.1 + - + +
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E PHE* 5.3 2.0 - - + -
229E THR 4.6 3.4 - - - +
230E GLY* 4.2 22.7 - - - -
231E PRO* 5.4 3.4 - - + -
233E TRP* 4.4 8.1 - - + -
257E TYR* 3.7 24.0 - - + +
266E VAL* 2.8 17.0 + - + +
267E ARG* 1.3 76.5 - - - +
269E SER* 1.3 64.5 + - - +
285E GLU* 3.4 9.9 - - - +
286E PHE* 3.0 41.6 + - + +
288E TYR* 3.5 26.5 - - + -
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Residues in contact with SER 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E TYR 3.7 0.2 - - - +
228E PHE* 3.2 7.8 - - - +
229E THR* 2.8 49.6 + - - -
230E GLY* 4.6 2.0 - - - +
268E VAL* 1.3 81.8 - - - +
270E MET* 1.3 63.1 + - - +
271E GLN* 3.6 7.6 + - - -
283E PRO* 3.4 29.3 - - - +
284E MET 3.4 4.8 + - - -
285E GLU* 5.9 1.6 - - - -
286E PHE* 5.2 0.7 - - - -
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Residues in contact with MET 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ILE* 3.6 7.7 - - + +
199E VAL* 4.4 26.2 - - + -
201E ARG 5.2 0.2 - - - +
202E ASN* 5.7 0.4 - - - -
212E ILE* 4.7 2.9 - - + -
214E LEU* 4.8 7.2 - - + -
226E VAL* 4.5 9.9 - - + -
227E TYR 3.5 4.0 - - - -
228E PHE* 4.0 20.6 - - + +
252E PHE* 3.8 28.5 - - - -
269E SER* 1.3 75.8 + - - +
271E GLN* 1.3 63.6 + - - +
284E MET* 2.5 51.4 + - + +
285E GLU 4.3 9.0 - - - +
286E PHE* 3.8 31.2 - - + +
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Residues in contact with GLN 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ILE* 3.7 4.7 - - - -
214E LEU* 6.2 0.4 - - - -
226E VAL* 4.5 2.5 - - - -
227E TYR* 2.5 63.6 + - + +
229E THR* 2.7 42.2 + - - +
269E SER* 3.6 11.3 + - - -
270E MET* 1.3 76.1 - - - +
272E LEU* 1.3 63.2 + - - +
280E LEU* 3.8 21.0 - - + +
281E SER* 3.2 25.6 - - - +
282E GLU 3.3 12.2 - - - +
283E PRO* 4.3 6.9 - - + +
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Residues in contact with LEU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E LEU* 3.5 6.3 - - + +
195E LYS 3.4 36.1 - - - +
196E ILE* 3.8 10.8 - - + +
214E LEU* 4.3 10.1 - - + -
216E CYS* 3.6 20.0 - - + -
219E VAL* 4.6 8.7 - - + -
224E ILE* 3.8 22.2 - - + -
225E GLU 3.2 14.1 - - - +
226E VAL* 4.2 10.3 - - + +
250E ILE* 4.1 17.9 - - + -
271E GLN* 1.3 73.3 - - - +
273E ARG* 1.3 57.2 + - - +
280E LEU* 3.5 1.9 - - - -
281E SER* 2.4 51.3 + - - +
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Residues in contact with ARG 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 4.6 9.3 + - - +
81A PRO* 3.0 52.6 - - - +
82A PRO* 4.1 8.3 - - - +
194E LEU* 4.2 0.4 - - - -
224E ILE* 3.0 5.5 - - - +
225E GLU* 2.5 77.9 + - + +
227E TYR* 3.9 24.3 - - + -
271E GLN 3.6 0.4 + - - -
272E LEU* 1.3 75.6 - - - +
274E ARG* 1.3 63.4 + - - +
275E PRO* 3.9 23.9 + - - +
278E ARG* 4.0 17.0 - - - +
279E GLU 3.3 13.0 - - - +
280E LEU* 4.3 15.9 - - + -
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Residues in contact with ARG 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ARG* 3.4 28.3 - - - +
189E PRO 3.3 12.5 + - - -
190E ASN* 3.2 13.6 + - - +
191E THR* 3.1 17.8 - - - +
192E ALA 2.8 29.0 + - - -
193E GLU* 5.2 0.4 - - - +
194E LEU* 4.0 24.2 - - + +
220E GLN* 6.6 0.2 - - - -
223E ASP* 2.8 33.4 - - - +
224E ILE* 4.7 0.9 - - + -
273E ARG* 1.3 76.2 - - - +
275E PRO* 1.3 56.2 - - - +
276E SER* 3.3 7.1 + - - +
277E ASP* 2.9 18.3 + - - +
278E ARG* 2.6 36.4 + - - -
279E GLU* 2.8 27.1 + - + +
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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