Contacts of the helix formed by residues 247 - 251 (chain X) in PDB entry 1M6E
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 MET 247 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242X ILE* 3.0 28.0 - - + +
243X GLU* 4.1 8.3 - - - -
244X GLU* 4.2 11.7 - - + +
245X GLU 3.7 1.4 - - - +
246X LYS* 1.3 75.5 - - + +
248X ASP* 1.3 61.0 + - - +
249X LYS 3.1 1.1 - - - -
250X PHE* 2.8 21.6 + - - +
319X HIS* 3.1 35.0 + - - +
320X PHE* 3.6 40.2 - - + +
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Residues in contact with ASP 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162X ASN 4.5 2.4 - - - +
163X LYS 4.2 3.1 - - - +
165X ASN* 3.3 17.2 + - - +
166X ILE* 4.0 13.0 - - - +
230X ALA* 5.6 0.3 - - - +
233X LEU* 3.2 41.7 - - - +
234X ASN* 3.9 16.6 + - - +
237X VAL* 3.8 26.6 - - + +
243X GLU* 4.6 1.8 - - + +
245X GLU* 4.2 7.1 - - - +
247X MET* 1.3 78.1 - - - +
249X LYS* 1.3 60.1 + - + +
250X PHE 2.8 6.4 + - - -
251X ASN* 3.2 10.7 + - - +
320X PHE* 3.7 15.3 - - + -
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Residues in contact with LYS 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X ILE* 5.5 3.5 - - - +
162X ASN* 3.8 49.1 - - - +
165X ASN* 2.7 21.3 + - - +
245X GLU* 2.6 74.5 + - + +
246X LYS* 4.1 5.2 - - - +
247X MET 3.1 1.6 - - - -
248X ASP* 1.3 74.8 - - + +
250X PHE* 1.3 71.7 + - + +
252X ILE* 5.5 0.9 - - - +
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Residues in contact with PHE 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ASP* 5.2 2.3 - - - +
155X VAL* 6.1 0.7 - - - +
246X LYS* 3.3 22.0 - - + -
247X MET* 2.8 9.9 + - - +
249X LYS* 1.3 92.6 - - + +
251X ASN* 1.3 64.9 + - - +
252X ILE* 3.5 13.1 + - - +
319X HIS* 3.6 18.1 - + + -
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Residues in contact with ASN 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ARG* 5.9 1.0 + - - -
165X ASN* 2.6 34.8 - - - +
166X ILE* 3.5 25.4 - - + +
229X LEU* 5.3 1.2 - - - +
233X LEU* 4.6 1.2 - - - +
248X ASP 3.2 6.6 + - - +
250X PHE* 1.3 72.0 - - - +
252X ILE* 1.3 63.4 + - - +
253X PRO* 4.2 10.3 - - - +
315X LEU* 4.4 10.6 - - - +
316X LEU* 3.9 20.3 - - - +
319X HIS* 3.3 28.7 + - + +
320X PHE* 3.6 30.3 - - + -
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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