Contacts of the strand formed by residues 266 - 274 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A TYR* 4.5 24.0 - - + +
262A LEU* 3.6 20.9 - - + -
264A ALA 3.1 3.3 + - - +
265A PRO* 1.3 71.3 - - - +
267A ARG* 1.3 58.8 + - - +
268A VAL* 2.9 27.6 + - + +
288A TYR* 3.2 40.1 + - + +
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Residues in contact with ARG 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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265A PRO* 3.6 16.1 + - - +
266A VAL* 1.3 72.4 - - - +
268A VAL* 1.3 63.6 + - - +
285A GLU* 4.9 11.9 - - + +
287A GLN* 3.7 55.5 + - + +
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Residues in contact with VAL 268 (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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228A PHE* 4.9 1.8 - - + -
229A THR 4.6 3.6 - - - +
230A GLY* 4.6 10.5 - - - -
231A PRO* 6.2 0.7 - - + -
233A TRP* 4.0 24.5 - - + -
257A TYR* 4.5 7.0 - - + -
266A VAL* 2.9 27.6 + - + +
267A ARG* 1.3 76.0 - - - +
269A SER* 1.3 70.0 + - - +
285A GLU* 3.4 8.5 - - - +
286A PHE* 3.2 39.8 + - + +
288A TYR* 3.4 29.8 - - + -
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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
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227A TYR 3.7 0.5 - - - +
228A PHE* 3.3 6.3 - - - +
229A THR* 2.9 48.3 + - - +
230A GLY* 4.7 1.8 - - - +
268A VAL* 1.3 85.0 + - - +
270A MET* 1.3 62.3 + - - +
271A GLN* 4.3 3.4 - - - -
283A PRO* 4.2 20.1 - - - +
284A MET 3.4 8.4 + - - -
285A GLU* 4.5 3.5 + - - +
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Residues in contact with MET 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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196A ILE* 5.4 2.6 - - + +
199A VAL* 4.2 30.7 - - + -
201A ARG 5.4 2.2 - - - +
202A ASN* 5.8 0.9 - - - +
212A ILE* 5.0 2.9 - - + -
214A LEU* 4.6 6.5 - - + -
226A VAL* 4.1 7.9 - - + -
227A TYR 3.4 3.1 - - - -
228A PHE* 3.1 41.3 - - + -
252A PHE* 3.6 21.1 - - - -
269A SER* 1.3 75.0 - - - +
271A GLN* 1.3 64.4 + - - +
282A GLU 4.0 0.3 - - - +
283A PRO* 3.7 0.4 - - - -
284A MET* 2.5 60.5 + - + +
285A GLU 4.7 2.7 - - - +
286A PHE* 4.4 25.1 - - + -
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Residues in contact with GLN 271 (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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196A ILE* 5.2 3.1 - - - -
226A VAL* 4.5 4.5 - - - -
227A TYR* 2.4 53.9 + - - +
229A THR* 2.8 38.2 + - - +
269A SER* 5.1 4.0 + - - -
270A MET* 1.3 75.0 - - - +
272A LEU* 1.3 56.9 + - - +
280A LEU* 3.7 31.3 - - + +
281A SER* 2.9 19.5 - - - +
282A GLU 3.1 24.0 - - - +
283A PRO* 4.1 11.4 - - + +
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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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194A LEU* 3.4 13.4 - - + +
195A LYS 2.8 39.9 - - - +
196A ILE* 3.7 12.5 - - + +
214A LEU* 3.9 26.7 - - + -
216A CYS* 3.7 13.0 - - + -
219A VAL* 4.6 3.4 - - + -
224A ILE* 4.0 14.8 - - + -
225A GLU 3.2 6.1 - - - +
226A VAL* 4.5 4.9 - - + +
250A ILE* 3.9 20.9 - - + -
271A GLN* 1.3 66.8 - - - +
273A ARG* 1.3 57.1 + - - +
280A LEU* 3.4 2.0 - - - +
281A SER* 2.4 57.2 + - - +
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Residues in contact with ARG 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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194A LEU* 3.7 4.5 - - - +
224A ILE* 3.3 3.1 - - - +
225A GLU* 2.4 83.4 + - + +
227A TYR* 4.0 13.6 - - + -
236A ARG* 4.5 7.5 - - - +
272A LEU* 1.3 72.7 - - - +
274A ARG* 1.3 66.0 + - - +
275A PRO* 3.6 20.9 + - - +
278A ARG* 5.1 7.7 - - - +
279A GLU 3.3 7.4 - - - +
280A LEU* 3.4 36.9 - - + +
80E ASP* 4.2 11.5 + - - +
81E PRO* 3.7 39.6 - - - +
82E PRO* 4.2 9.2 - - - +
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Residues in contact with ARG 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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30A ARG* 3.3 18.0 - - - +
189A PRO 4.1 4.6 + - - -
190A ASN* 3.2 37.0 + - - +
191A THR 3.5 0.4 - - - +
192A ALA* 3.3 21.3 + - - +
194A LEU* 3.6 30.1 - - + +
223A ASP* 2.6 36.3 - - - +
224A ILE* 5.3 0.2 - - - -
273A ARG* 1.3 76.0 - - - +
275A PRO* 1.3 57.6 - - - +
276A SER* 3.3 5.4 - - - +
277A ASP* 2.6 41.2 + - + +
278A ARG* 2.6 36.6 + - - -
279A GLU* 2.8 25.4 + - - +
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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