Contacts of the helix formed by residues 275 - 285 (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 GLY 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.6 0.9 - - - -
263B LEU 3.4 12.8 - - - -
264B PHE 3.6 17.4 + - - -
266B PRO* 3.9 9.2 - - - +
274B ALA* 1.3 75.9 - - - +
276B ILE* 1.3 65.5 + - - -
277B HIS* 3.2 5.6 - - - -
278B GLU* 2.9 25.3 + - - +
279B THR* 3.0 12.7 + - - -
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Residues in contact with ILE 276 (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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155B LEU* 4.1 14.4 - - + -
162B THR* 3.9 23.1 - - + -
164B ASN* 4.5 0.2 + - - -
180B LEU* 3.9 18.8 - - + +
263B LEU* 3.0 39.1 + - + +
264B PHE* 3.6 26.0 - - + -
275B GLY* 1.3 71.2 - - - -
277B HIS* 1.3 62.6 + - - +
279B THR* 3.4 9.6 + - - +
280B THR* 2.8 30.3 + - - -
311B ILE* 4.5 6.3 - - + -
315B MET* 2.9 31.6 - - + +
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Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.4 39.8 + + + +
275B GLY 3.8 9.6 - - - -
276B ILE* 1.3 79.9 - - - +
278B GLU* 1.3 95.3 + - + +
280B THR 3.5 0.7 + - - -
281B TYR* 3.1 25.1 + - - +
315B MET* 3.8 18.6 - - - -
318B GLU* 3.6 46.1 + - + +
319B ILE* 3.4 15.2 - - + +
322B LEU* 4.3 9.0 - - + +
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Residues in contact with GLU 278 (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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264B PHE 4.7 1.6 - - - +
274B ALA* 3.5 19.2 - - + +
275B GLY 2.9 31.4 + - - +
277B HIS* 1.3 106.5 + - + +
279B THR* 1.3 59.6 + - - +
281B TYR* 3.3 6.1 + - - +
282B ASN* 2.9 40.3 + - - +
322B LEU* 4.4 11.0 - - + -
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR* 6.1 0.3 - - - +
164B ASN* 2.5 27.7 + - - +
178B MET* 3.4 17.6 - - + +
179B ARG 5.5 4.3 - - - +
180B LEU* 5.0 14.6 - - + +
273B SER* 6.3 0.2 - - - -
274B ALA* 4.0 22.7 - - + +
275B GLY 3.0 10.6 + - - +
276B ILE* 3.4 19.1 + - - +
278B GLU* 1.3 73.5 - - - +
280B THR* 1.3 61.2 + - - +
282B ASN* 4.2 8.7 - - - +
283B SER* 3.1 25.6 + - - -
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Residues in contact with THR 280 (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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153B ILE* 3.8 9.8 - - + +
155B LEU* 4.2 8.9 - - + +
164B ASN* 3.1 22.0 + - - +
276B ILE 2.8 22.3 + - - -
277B HIS* 3.6 5.2 - - - -
279B THR* 1.3 78.2 + - - +
281B TYR* 1.3 62.5 + - - +
283B SER* 3.3 4.5 + - - -
284B ILE* 3.1 32.6 + - + +
299B ASN* 3.4 25.8 - - - +
315B MET* 4.4 7.3 - - - -
319B ILE* 4.0 15.7 - - + -
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Residues in contact with TYR 281 (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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277B HIS 3.1 17.4 + - - +
278B GLU* 3.6 4.3 - - - +
280B THR* 1.3 77.4 - - - +
282B ASN* 1.3 70.7 + - - +
284B ILE* 3.1 11.2 + - + +
285B MET* 2.9 62.7 + - + +
296B TYR* 3.4 30.7 - + - -
319B ILE* 4.4 6.7 - - + +
322B LEU* 3.6 59.6 + - + -
323B ALA* 4.4 0.4 - - - -
324B PRO* 5.7 0.8 - - + +
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Residues in contact with ASN 282 (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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178B MET* 3.8 19.9 - - + +
274B ALA* 5.1 4.9 - - - +
278B GLU* 2.9 30.6 + - - +
279B THR* 4.1 9.8 - - - +
281B TYR* 1.3 89.4 - - - +
283B SER* 1.3 61.9 + - - +
285B MET* 3.4 7.2 + - - +
286B LYS* 3.2 24.3 + - - +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.4 11.6 - - - +
164B ASN* 4.0 6.2 + - - -
166B PRO* 2.9 27.0 - - - +
176B ALA* 2.9 26.8 + - - +
178B MET* 3.7 10.0 - - - +
279B THR 3.1 19.5 + - - -
280B THR 3.4 6.1 - - - -
281B TYR 3.2 0.2 - - - -
282B ASN* 1.3 77.4 - - - +
284B ILE* 1.3 63.0 + - - +
286B LYS* 3.1 15.8 + - - +
287B CYS* 3.4 12.6 - - - -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 4.1 20.6 - - + -
280B THR* 3.1 29.3 + - + +
281B TYR* 3.1 9.7 + - - +
283B SER* 1.3 78.3 - - - +
285B MET* 1.3 57.1 + - - +
287B CYS* 3.0 24.4 + - - +
292B ARG* 3.1 37.5 - - + +
295B LEU* 4.4 16.8 - - + -
296B TYR* 3.6 57.7 - - + +
299B ASN* 4.8 2.0 - - - +
319B ILE* 5.1 2.5 - - + -
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 2.9 61.8 + - + +
282B ASN* 3.8 8.3 - - - +
283B SER 3.3 0.4 - - - -
284B ILE* 1.3 74.6 - - - +
286B LYS* 1.3 57.1 + - - +
287B CYS 3.3 0.7 - - - -
292B ARG* 3.3 45.3 + - - +
296B TYR* 4.2 10.1 - - - -
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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