Contacts of the helix formed by residues 256 - 261 (chain F) in PDB entry 4LQL
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 GLN 256 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F ASN 3.6 15.3 - - - +
253F VAL* 3.2 15.0 + - + +
255F TYR* 1.3 78.1 - - - +
257F LEU* 1.3 60.2 + - - +
258F ARG 3.6 0.2 - - - -
259F GLU* 4.2 8.5 - - - -
260F TYR* 3.7 3.9 + - - +
287F GLN* 3.6 16.8 - - + +
290F GLY 6.1 1.6 - - - +
291F LEU* 5.2 11.3 - - + +
292F ALA* 3.3 33.8 + - + +
377F ALA* 5.4 6.3 - - + +
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ILE* 3.6 20.9 - - + +
229F ALA* 4.7 11.7 - - + -
230F TYR* 5.8 2.5 - - + +
253F VAL 3.0 13.3 + - - +
254F ARG* 3.6 1.3 + - - -
256F GLN* 1.3 79.5 - - - +
258F ARG* 1.3 55.5 + - - +
259F GLU 2.8 9.3 + - - -
260F TYR* 4.0 9.0 - - + +
261F LEU* 3.1 37.8 + - + +
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Residues in contact with ARG 258 (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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218F VAL* 3.1 42.6 - - + +
221F ILE* 3.6 22.8 - - + +
226F ILE* 4.2 7.0 - - + -
254F ARG 3.1 17.6 + - - +
255F TYR* 4.1 14.4 - - + +
256F GLN 3.6 0.8 - - - +
257F LEU* 1.3 74.5 - - - +
259F GLU* 1.3 58.8 + - + +
261F LEU* 5.3 0.2 - - - -
262F GLY 4.6 0.4 + - - -
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Residues in contact with GLU 259 (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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218F VAL* 4.6 8.5 - - + -
255F TYR 4.0 14.8 - - - +
256F GLN* 4.4 4.9 - - - +
257F LEU 2.8 2.6 - - - -
258F ARG* 1.3 86.2 - - + +
260F TYR* 1.3 51.7 + - - +
261F LEU 2.8 9.3 + - - -
262F GLY* 2.8 2.9 + - - +
263F ILE* 2.7 45.2 + - + +
285F LEU* 3.9 31.2 - - + -
289F PRO* 5.5 12.3 - - + -
292F ALA* 4.4 11.9 - - + -
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Residues in contact with TYR 260 (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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256F GLN 3.7 8.8 + - - +
257F LEU* 3.8 7.3 + - + -
259F GLU* 1.3 77.0 - - - +
261F LEU* 1.3 62.4 + - + +
263F ILE* 4.5 4.9 - - - -
264F LYS* 3.6 21.2 + - + +
291F LEU* 6.1 1.1 - - + -
292F ALA* 3.4 41.3 - - + +
295F LEU* 3.8 33.0 - - + -
296F LEU* 5.0 2.9 - - + +
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Residues in contact with LEU 261 (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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221F ILE* 5.3 10.1 - - + -
225F GLU* 4.5 9.9 - - + +
226F ILE* 4.1 27.6 - - + +
229F ALA* 4.1 22.7 - - + -
257F LEU* 3.1 23.2 + - + +
258F ARG* 5.3 0.4 - - - -
259F GLU 2.9 0.6 - - - -
260F TYR* 1.3 81.5 - - + +
262F GLY* 1.3 56.0 + - - +
263F ILE 3.3 0.2 - - - -
264F LYS* 3.0 11.1 + - + +
265F LYS* 2.8 36.3 + - - +
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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