Contacts of the helix formed by residues 220 - 224 (chain A) in PDB entry 3M2K
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 LEU 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR 4.4 1.6 - - - +
217A GLY* 3.3 13.5 + - - +
218A ASP 3.3 0.2 - - - -
219A ALA* 1.4 100.8 - - + +
221A ILE* 1.3 70.1 + - - +
222A ARG 3.1 3.1 + - - -
223A ALA* 3.1 16.6 - - - +
235A THR* 3.8 31.2 - - + -
244A ARG* 3.8 28.5 - - - +
245A ASN 4.1 10.5 - - - +
246A ASP* 3.4 10.5 - - + +
276A ASP* 3.9 14.4 - - + +
279A ILE* 3.8 32.1 - - + -
280A ALA* 3.7 8.9 - - - +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLY 4.2 0.4 + - - -
220A LEU* 1.3 80.0 - - - +
222A ARG* 1.3 55.5 + - - +
224A GLY* 2.8 22.6 + - - -
225A VAL* 3.5 10.4 + - + +
231A VAL* 4.0 17.0 - - + -
233A ASP* 5.3 0.7 - - + +
246A ASP* 2.9 56.5 + - + +
247A ILE 4.2 0.4 - - - -
248A ALA* 3.6 18.6 - - + -
250A ILE* 3.7 28.3 - - + -
261A LEU* 4.2 15.9 - - + +
263A VAL* 4.4 2.9 - - + -
279A ILE* 4.2 4.7 - - + -
283A THR* 3.7 26.2 - - + +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A MET 2.7 28.9 + - - -
212A LYS* 3.1 16.7 + - - +
214A ASN* 3.0 16.5 + - - +
217A GLY* 3.6 13.7 + - - +
218A ASP* 3.4 29.8 + - + -
220A LEU 3.2 0.6 - - - -
221A ILE* 1.3 78.4 - - - +
223A ALA* 1.3 55.8 + - - +
225A VAL* 3.5 22.2 - - - +
231A VAL* 2.7 47.6 + - + +
233A ASP* 2.7 34.9 + - - +
246A ASP* 4.7 0.2 + - - -
128B ARG* 5.9 3.0 - - - +
213B ARG* 5.8 1.2 - - - +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP 3.6 19.6 + - - +
219A ALA* 3.7 13.2 - - - +
220A LEU 3.1 13.9 + - - +
222A ARG* 1.3 73.2 - - - +
224A GLY* 1.3 54.6 + - - -
225A VAL 3.3 6.4 - - - +
280A ALA* 3.8 9.7 - - + +
284A LYS* 4.0 14.0 - - - -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU 3.8 1.0 + - - -
221A ILE 2.8 12.3 + - - -
223A ALA* 1.3 71.5 - - - +
225A VAL* 1.3 64.5 + - - +
226A PRO* 4.4 2.1 - - - +
280A ALA 3.6 21.8 - - - -
283A THR* 3.6 15.8 - - - +
284A LYS* 3.5 29.6 - - - +
287A MET* 4.1 8.3 - - - +
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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