Contacts of the helix formed by residues 291 - 297 (chain B) in PDB entry 1MDU
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 ILE 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.3 50.7 - - + +
173B LEU* 3.8 29.6 - - + -
287B CYS* 4.1 7.9 - - + -
288B ASP* 2.9 30.8 + - + +
290B ASP* 1.3 76.4 - - + +
292B ARG* 1.3 65.9 + - - +
293B LYS 3.2 3.4 - - - -
294B ASP* 3.1 25.6 + - + +
295B LEU* 3.3 26.7 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ILE* 3.1 35.4 - - + +
285B MET* 3.3 47.3 + - - +
287B CYS* 2.7 29.0 + - + +
288B ASP 3.4 14.8 - - - +
289B ILE* 3.3 46.7 + - - +
290B ASP 3.6 0.2 - - - -
291B ILE* 1.3 78.0 - - - +
293B LYS* 1.3 57.5 + - + +
295B LEU* 3.1 12.3 + - - +
296B TYR* 2.9 40.1 + - + -
327B MET* 5.6 2.0 - - + -
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ILE 5.0 1.3 + - - +
290B ASP 5.1 2.6 + - - +
291B ILE 3.2 1.4 - - - -
292B ARG* 1.3 77.1 - - + +
294B ASP* 1.3 65.9 + - - +
296B TYR* 3.5 1.8 + - - +
297B ALA* 3.2 26.0 + - - +
326B THR* 5.7 6.1 - - - -
327B MET* 3.4 43.4 - - + +
328B LYS 4.8 0.5 - - - +
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Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B THR* 3.4 27.8 - - + +
168B TYR* 3.9 16.5 - - - -
290B ASP 5.2 2.0 - - - +
291B ILE* 3.1 18.0 - - + +
293B LYS* 1.3 78.5 - - - +
295B LEU* 1.3 64.3 + - + +
297B ALA* 4.9 0.9 - - - -
298B ASN* 2.6 37.6 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B THR* 4.3 6.1 - - + -
152B GLY* 3.6 38.4 - - - +
153B ILE* 3.5 15.0 - - + +
166B PRO* 4.3 7.4 - - + -
167B ILE 3.9 12.1 - - - +
284B ILE* 4.4 18.2 - - + -
287B CYS* 3.8 33.0 - - + -
291B ILE* 3.4 28.3 - - + +
292B ARG* 3.1 10.9 + - - +
294B ASP* 1.3 74.6 - - - +
296B TYR* 1.3 66.5 + - - +
297B ALA 3.1 1.3 - - - -
298B ASN 3.0 15.2 + - - -
299B ASN* 3.3 11.4 + - - -
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 3.4 28.8 - + - -
284B ILE* 3.6 39.4 - - + +
285B MET* 4.2 7.4 - - - -
292B ARG* 2.9 30.4 + - + +
293B LYS 4.1 2.9 - - - +
295B LEU* 1.3 75.9 - - - +
297B ALA* 1.3 58.4 + - - +
299B ASN* 3.2 15.2 + - - +
319B ILE* 3.8 20.6 - - + -
323B ALA* 3.6 23.2 - - + +
324B PRO* 4.0 6.1 - - + +
327B MET* 3.2 39.3 - - + -
328B LYS 3.6 13.5 - - - +
329B ILE* 3.4 7.3 - - + +
330B LYS 2.9 21.5 + - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LYS 3.2 15.8 + - - +
294B ASP* 4.6 0.7 - - - -
295B LEU 3.1 1.0 - - - -
296B TYR* 1.3 80.4 - - - +
298B ASN* 1.3 74.0 + - - +
328B LYS* 3.7 18.6 - - + +
330B LYS* 3.4 38.6 + - + +
332B ILE* 5.0 2.3 - - - +
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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