Contacts of the helix formed by residues 234 - 240 (chain A) in PDB entry 1MDF
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 HIS 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.2 18.8 - - + +
188A GLN* 4.6 4.1 + - - +
189A LEU 5.6 5.5 + - - -
191A GLY* 5.5 9.6 - - - -
231A PRO 3.4 5.7 + - - +
232A MET 3.3 0.4 - - - -
233A ALA* 1.3 79.3 - - - +
235A ASN* 1.3 72.4 + - + +
236A TYR* 3.1 39.6 + + + +
237A PRO* 3.0 18.5 - - + +
238A LEU* 2.9 15.8 + - - +
307A GLY* 5.6 4.0 - - - -
333A ALA* 5.8 4.5 + - + -
517A VAL* 3.4 44.6 - - + +
519A LYS* 4.8 13.2 + - - -
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Residues in contact with ASN 235 (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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188A GLN* 3.7 15.2 + - - +
202A ARG* 4.2 4.7 + - - +
207A TYR* 2.7 39.9 + - - -
233A ALA 3.6 2.8 + - - -
234A HIS* 1.3 79.4 + - + +
236A TYR* 1.3 57.1 + - - +
238A LEU* 3.8 1.3 - - - -
239A SER* 2.6 39.5 + - - -
240A SER* 3.8 8.7 + - - -
332A MET 3.1 27.7 + - - +
333A ALA* 3.5 28.8 - - + +
335A GLY 4.9 0.6 + - - -
337A VAL* 4.7 6.7 - - - +
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Residues in contact with TYR 236 (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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226A TYR* 4.5 0.7 + - - -
230A LEU* 3.6 20.4 - - + -
234A HIS* 3.0 17.7 + + + +
235A ASN* 1.3 73.4 - - - +
237A PRO* 1.3 62.9 - - + +
238A LEU 2.9 8.5 + - - -
240A SER* 3.0 44.0 + - - -
242A GLY 3.9 2.6 + - - -
277A ALA* 3.6 17.3 - - + -
278A LEU 2.7 30.6 + - - -
279A VAL* 4.1 4.9 - - + -
304A GLN* 3.2 29.2 + - - +
305A VAL 3.5 0.2 - - - -
306A GLY* 3.1 33.4 + - - -
307A GLY* 4.2 6.3 - - - -
329A VAL* 4.1 16.4 - - + -
517A VAL* 5.0 0.9 - - + -
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Residues in contact with PRO 237 (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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226A TYR* 3.5 19.7 + - + +
228A ALA* 6.0 0.9 - - - -
229A ALA 5.9 0.9 - - - +
230A LEU* 3.8 31.2 - - + +
231A PRO 2.9 29.2 - - - +
232A MET* 3.7 9.6 - - + +
234A HIS* 3.0 26.2 - - + +
236A TYR* 1.3 95.0 - - + +
238A LEU* 1.3 54.3 + - - -
242A GLY* 3.1 5.1 - - - -
243A VAL* 3.1 27.0 + - - +
277A ALA* 5.2 0.2 - - + -
517A VAL* 4.5 0.4 - - + -
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Residues in contact with LEU 238 (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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88A PHE* 4.0 16.6 - - + -
92A ILE* 5.2 0.9 - - + -
104A PHE* 4.6 17.9 - - + -
186A PHE* 5.4 0.7 - - + -
188A GLN* 3.8 10.1 - - - +
207A TYR* 3.7 19.1 - - + +
232A MET 3.0 14.8 - - - +
233A ALA* 3.4 19.3 - - - +
234A HIS 2.9 15.2 + - - +
235A ASN 3.8 1.6 - - - +
236A TYR 2.9 0.6 - - - -
237A PRO* 1.3 79.7 - - - +
239A SER* 1.3 58.2 + - - +
242A GLY* 3.5 5.4 - - - -
243A VAL* 3.8 12.1 - - + +
244A LEU* 3.4 52.5 + - + +
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Residues in contact with SER 239 (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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207A TYR* 3.0 29.4 + - - -
210A SER* 4.5 6.7 + - - +
211A LEU* 3.4 23.6 - - - +
214A SER* 3.3 13.3 + - - -
235A ASN* 2.6 26.4 + - - -
238A LEU* 1.3 80.6 - - - +
240A SER* 1.3 62.4 + - - +
241A PRO* 2.9 21.6 - - - +
242A GLY* 3.4 0.8 - - - -
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Residues in contact with SER 240 (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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214A SER* 4.9 0.2 + - - -
235A ASN* 4.0 5.9 + - - -
236A TYR* 3.0 32.0 + - - -
239A SER* 1.3 86.2 + - - +
241A PRO* 1.3 57.6 - - - +
242A GLY 3.3 2.7 - - - -
304A GLN* 2.8 21.5 + - - +
329A VAL* 4.1 4.5 - - - -
331A GLY* 5.6 0.9 - - - -
337A VAL* 3.7 27.8 - - - +
339A TYR* 3.0 22.7 + - - -
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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