Contacts of the helix formed by residues 215 - 219 (chain L) in PDB entry 2BM8
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 215 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I LEU* 4.0 14.3 - - + +
32I ARG* 4.0 10.7 + - - +
33I PRO 3.6 22.2 - - - +
34I ARG 2.8 15.9 + - - +
36I TRP* 3.8 30.3 - - + -
44I ALA* 4.1 3.8 - - + -
45I PRO* 3.4 47.8 - - + +
48I LEU 4.3 13.0 - - - +
213L MET* 4.0 22.2 - - - +
214L ASP* 1.3 70.1 - - - +
216L LEU* 1.3 63.4 + - - +
217L TYR 3.2 0.8 + - - -
218L ALA* 4.0 9.1 + - - -
219L ASN* 3.4 23.2 + - - +
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Residues in contact with LEU 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PRO* 5.8 4.5 - - + -
27I PRO* 3.8 32.1 - - + +
28I VAL* 5.0 0.2 - - - -
29I LEU* 3.9 23.0 - - + +
34I ARG* 3.7 38.3 - - + +
48I LEU* 5.4 0.9 - - - +
50I TYR* 3.9 37.3 + - + +
79L GLU* 4.4 2.7 - - - +
214L ASP* 3.0 11.9 + - - +
215L MET* 1.3 79.3 - - - +
217L TYR* 1.3 84.7 + - + +
220L ALA* 4.3 4.0 - - - +
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Residues in contact with TYR 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ARG* 3.6 10.5 - - - -
50I TYR* 5.9 0.2 - - - -
72L VAL* 4.0 28.9 - - + +
75L ASP* 3.5 37.7 + - + +
76L MET* 3.8 32.3 - - + -
79L GLU* 2.5 30.5 + - - +
182L TYR* 3.7 8.5 - + - -
214L ASP* 3.3 20.6 + - - +
216L LEU* 1.3 101.2 - - + +
218L ALA* 1.3 64.3 + - - +
219L ASN 3.2 2.7 - - - -
220L ALA* 3.1 20.8 + - + +
221L SER 4.5 1.4 + - - -
224L LEU* 4.7 3.3 - - - +
228L VAL* 4.1 20.9 - - + +
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Residues in contact with ALA 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L MET* 3.7 31.9 - - + -
214L ASP 3.0 19.1 + - - +
215L MET* 4.0 10.2 + - - -
216L LEU 3.8 0.2 - - - -
217L TYR* 1.3 78.1 - - - +
219L ASN* 1.3 61.7 + - - +
220L ALA 3.4 0.9 + - - -
224L LEU 3.7 1.4 - - - +
225L ASP* 3.3 11.6 + - - -
226L ARG* 2.9 27.7 + - - +
228L VAL* 4.1 15.9 - - + +
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Residues in contact with ASN 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ARG* 3.6 2.0 - - - +
45I PRO 2.9 27.0 + - - +
46I ARG* 3.5 23.1 + - - +
47I ASP 3.0 26.1 + - - +
48I LEU* 3.5 20.7 + - - +
215L MET* 3.4 26.2 + - - +
217L TYR 3.2 0.6 - - - -
218L ALA* 1.3 81.6 - - - +
220L ALA* 1.3 58.1 + - - +
221L SER 3.6 4.8 - - - -
225L ASP* 4.5 5.5 - - - +
226L ARG* 4.4 13.7 - - - +
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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