Contacts of the helix formed by residues 249 - 255 (chain E) 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 TYR 249 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242E GLY* 3.1 29.4 + - - +
243E ASP* 4.3 0.8 - - - +
247E GLU 3.1 1.4 + - - -
248E LYS* 1.3 81.2 - - + +
250E VAL* 1.3 61.1 + - - +
251E HIS 3.5 1.3 - - - -
252E ASN* 4.2 7.8 + - + +
253E VAL* 3.1 27.4 + - + +
364E GLU* 5.3 8.1 - - + -
375E ASP* 4.6 17.7 - - - +
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Residues in contact with VAL 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E ASP* 5.4 1.1 - - - +
244E ASN 4.0 15.0 - - - +
245E ASP 3.8 21.1 - - - +
246E HIS* 4.6 6.7 - - - +
247E GLU 3.1 17.0 + - - +
248E LYS 3.2 3.2 + - - +
249E TYR* 1.3 76.3 - - - +
251E HIS* 1.3 67.1 + - - +
253E VAL* 3.2 7.7 + - - +
254E ARG* 3.1 37.8 + - + +
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Residues in contact with HIS 251 (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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248E LYS 4.7 3.2 + - - +
249E TYR 3.5 0.2 - - - -
250E VAL* 1.3 79.6 - - - +
252E ASN* 1.3 58.1 + - - +
254E ARG* 3.0 11.2 + - + +
255E TYR* 2.9 36.5 + + - +
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Residues in contact with ASN 252 (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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249E TYR* 4.2 8.1 + - + +
250E VAL 3.4 0.4 - - - -
251E HIS* 1.3 76.6 - - - +
253E VAL* 1.3 57.2 + - + +
254E ARG 3.1 5.4 - - - -
255E TYR* 3.5 9.6 - - - +
256E GLN* 3.1 15.1 + - - +
286E GLU* 4.9 4.0 - - - +
287E GLN* 2.7 34.9 - - - +
374E ASP* 3.5 27.8 + - - +
375E ASP* 3.5 27.6 + - - +
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Residues in contact with VAL 253 (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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234E GLU* 5.8 3.6 - - - +
243E ASP* 3.6 31.4 - - + +
249E TYR* 3.1 19.0 + - + +
250E VAL* 3.2 10.6 + - - +
252E ASN* 1.3 78.5 - - + +
254E ARG* 1.3 60.4 + - + +
256E GLN* 3.5 15.1 + - - +
257E LEU* 4.2 7.1 + - - +
291E LEU* 5.7 4.9 - - + +
362E ARG* 5.2 6.3 - - + -
364E GLU* 4.6 8.7 - - + -
375E ASP 5.7 1.6 - - - +
377E ALA* 3.5 31.4 - - + +
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Residues in contact with ARG 254 (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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226E ILE* 5.2 18.9 - - + +
230E TYR* 5.3 15.3 - - + -
250E VAL* 3.1 31.5 + - + +
251E HIS* 3.0 12.5 + - + +
253E VAL* 1.3 78.6 - - + +
255E TYR* 1.3 58.0 + - + +
256E GLN 3.1 7.2 + - - -
257E LEU* 3.7 5.0 + - - +
258E ARG* 3.6 15.9 + - - +
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Residues in contact with TYR 255 (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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251E HIS* 2.9 25.7 + + - +
252E ASN* 3.5 15.4 + - - +
254E ARG* 1.3 75.2 - - + +
256E GLN* 1.3 56.3 + - - +
257E LEU 3.5 1.3 - - - -
258E ARG* 3.8 43.5 - - + +
259E GLU* 4.1 8.8 - - - +
286E GLU* 5.7 6.9 - - + +
287E GLN* 4.1 10.3 - - + +
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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