Contacts of the helix formed by residues 201 - 205 (chain A) in PDB entry 3MVJ
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 THR 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 2.5 29.0 + - - +
167A LEU 5.6 0.2 - - - -
168A LYS* 3.2 34.1 + - + +
200A GLY* 1.3 74.8 + - - -
202A PRO* 1.3 79.8 - - + +
203A GLU* 3.3 4.3 - - - +
204A TYR* 2.8 29.7 + - + +
205A LEU* 3.3 12.0 + - - +
19J ARG* 3.9 19.3 - - + +
20J ASN 3.7 7.9 - - - +
21J ALA* 3.9 3.1 - - - -
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Residues in contact with PRO 202 (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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201A THR* 1.3 90.0 - - + +
203A GLU* 1.3 67.7 + - - +
204A TYR 3.1 0.7 + - - -
205A LEU* 3.2 17.5 + - + +
243A PRO* 4.0 17.7 - - + -
246A ILE* 3.8 10.4 - - + +
247A TYR* 3.7 25.3 - - + +
250A ILE* 3.4 14.4 - - - +
15J ARG* 3.9 18.8 - - - +
20J ASN 3.7 8.7 - - - +
22J ILE* 3.5 30.0 - - + -
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 3.3 2.0 - - - +
202A PRO* 1.3 76.8 - - - +
204A TYR* 1.3 74.2 + - + +
205A LEU 3.4 0.7 + - - -
226A VAL* 3.9 16.0 - - + +
236A PRO* 4.2 14.9 - - + +
238A PHE* 3.8 26.0 + - - +
239A PHE* 5.2 3.1 - - - +
246A ILE* 3.5 15.9 - - + +
250A ILE* 4.0 9.5 - - - +
10J PHE* 6.1 0.3 - - - -
15J ARG* 2.7 53.2 + - - +
19J ARG* 3.3 35.1 + - - +
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Residues in contact with TYR 204 (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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166A ASP* 6.0 0.9 - - - -
167A LEU 3.0 28.9 - - - +
168A LYS* 4.0 9.9 - - + -
169A PRO* 3.0 22.1 - - + +
201A THR* 2.8 20.3 + - + +
203A GLU* 1.3 84.8 - - + +
205A LEU* 1.3 64.7 + - - +
206A ALA 3.5 1.9 + - - -
219A VAL 5.1 0.5 - - - +
222A TRP* 3.7 13.2 - - - -
223A ALA* 3.7 26.6 - - + +
226A VAL* 3.5 26.0 - - + -
227A LEU* 3.5 23.4 - - + -
230A GLU* 2.7 40.1 + - - +
19J ARG* 4.0 16.4 - - - -
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Residues in contact with LEU 205 (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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198A LEU* 4.5 16.6 - - + -
199A CYS 3.5 24.7 - - - +
200A GLY* 3.6 2.7 - - - -
201A THR 3.4 31.0 - - - +
202A PRO* 3.2 11.3 + - + +
203A GLU 3.4 0.4 - - - -
204A TYR* 1.3 78.5 - - - +
206A ALA* 1.3 68.7 + - - +
209A ILE* 4.4 13.2 - - + -
210A ILE* 4.0 15.3 - - + -
222A TRP* 3.4 10.4 + - - -
247A TYR* 3.5 34.1 - - + +
250A ILE* 3.4 17.5 - - - +
22J ILE* 4.8 3.6 - - + -
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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