Contacts of the strand formed by residues 265 - 270 (chain F) 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 GLU 265 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ARG* 4.3 9.5 + - - -
199E VAL 5.6 0.5 - - - +
200E ASN* 4.9 10.0 - - - +
254F ASP* 5.2 2.3 - - - +
255F ARG* 5.6 3.6 - - - +
263F GLY 4.0 3.2 + - - -
264F GLU* 1.3 73.1 - - - +
266F ILE* 1.3 71.9 + - - +
267F TYR* 4.3 16.0 + - + -
310F VAL* 3.5 29.1 - - + +
311F PHE 3.4 8.1 - - - +
312F LYS* 4.3 20.9 - - + +
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Residues in contact with ILE 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F MET* 4.6 6.1 - - + -
254F ASP* 3.6 11.2 - - - +
255F ARG* 3.7 25.6 - - + +
257F ALA 5.0 2.2 - - - +
258F GLY* 6.0 0.2 - - - -
264F GLU* 3.7 8.7 - - + +
265F GLU* 1.3 85.3 - - - +
267F TYR* 1.3 76.2 + - - +
310F VAL* 3.3 5.0 - - - +
311F PHE* 2.7 65.4 + - + +
313F THR* 3.6 16.8 - - + -
345F PHE* 3.4 34.8 - - + -
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Residues in contact with TYR 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ARG* 3.0 33.1 - - - +
199E VAL 3.3 10.0 + - - -
200E ASN* 3.3 35.4 - - + -
213E PHE* 3.5 37.8 - + + -
215E LEU* 3.7 27.8 - - + -
252F ARG 3.6 0.3 - - - +
253F MET* 3.0 26.2 - - - +
254F ASP* 2.7 22.2 + - - +
265F GLU* 4.3 12.3 + - + -
266F ILE* 1.3 79.8 - - - +
268F LEU* 1.3 60.9 + - - +
269F LEU* 4.1 1.8 - - + -
308F ALA* 6.0 0.9 - - + -
309F ILE 3.7 2.9 - - - -
310F VAL* 3.6 31.3 - - + +
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ILE* 3.8 32.5 - - + -
252F ARG 3.1 8.5 - - - +
253F MET* 4.0 15.5 - - + -
266F ILE 4.1 0.2 + - - -
267F TYR* 1.3 74.1 - - - +
269F LEU* 1.3 63.4 + - - +
270F CYS* 3.4 33.2 - - + -
280F ILE* 4.6 19.5 - - + -
308F ALA* 3.4 1.8 - - - -
309F ILE* 2.8 50.4 + - + +
311F PHE* 4.2 10.1 - - + -
331F LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E PHE* 3.5 32.8 - - + -
215E LEU* 4.1 7.0 - - + -
245E HIS* 3.3 30.1 - - + -
249E ALA* 3.6 26.9 - - + -
251E VAL* 4.0 19.5 - - + -
251F VAL* 2.9 24.1 + - - +
252F ARG* 2.6 34.0 + - + +
267F TYR* 5.7 0.4 - - + -
268F LEU* 1.3 74.9 - - - +
270F CYS* 1.3 58.3 + - - +
307F PHE* 3.5 3.1 - - + +
308F ALA* 3.8 19.1 - - + -
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Residues in contact with CYS 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E HIS* 2.8 26.0 - - - -
249F LYS 3.5 13.9 - - - +
251F VAL* 4.0 1.6 - - - -
268F LEU* 3.4 21.5 - - + -
269F LEU* 1.3 75.0 - - - +
271F ASP* 1.3 71.9 + - - +
273F VAL* 3.8 20.4 - - - -
307F PHE* 2.5 46.6 + - - +
308F ALA* 3.8 3.4 - - - -
309F ILE* 4.4 5.2 - - - -
331F LEU* 3.8 9.0 - - + -
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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