Contacts of the helix formed by residues 243 - 255 (chain B) in PDB entry 1UMD
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 ASP 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B GLY 3.7 15.1 + - - +
195B LYS* 3.3 22.6 + - - +
196B ALA* 2.8 43.4 + - + +
236B LEU* 5.2 5.1 + - + +
238B THR 4.5 2.6 + - - -
242B TRP* 1.3 72.1 - - - +
244B TYR* 1.3 63.7 + - - +
245B GLU* 3.7 8.0 + - - +
246B ALA* 3.0 30.0 + - + +
247B VAL* 3.1 23.0 + - - +
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Residues in contact with TYR 244 (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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354A TRP* 3.6 47.9 - + + +
358A ARG* 3.0 24.6 + - - -
242B TRP* 2.8 21.5 + + - -
243B ASP* 1.3 70.5 + - - +
245B GLU* 1.3 86.8 + - + +
247B VAL* 3.2 2.9 + - - +
248B MET* 2.9 66.8 + - + +
276B THR* 3.8 6.1 - - + -
280B ASP* 2.6 39.7 + - - +
281B LEU* 6.0 0.3 - - - +
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Residues in contact with GLU 245 (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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195B LYS* 5.9 4.5 - - - +
243B ASP* 3.3 6.0 + - - +
244B TYR* 1.3 102.7 - - + +
246B ALA* 1.3 62.9 + - - +
248B MET* 4.9 3.0 - - - +
249B ASN* 2.9 47.0 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA* 4.1 6.1 - - + -
234B LEU* 3.7 21.8 - - + +
243B ASP* 3.0 36.3 + - + +
245B GLU* 1.3 76.1 - - - +
247B VAL* 1.3 62.4 + - - +
249B ASN* 4.0 6.6 - - - +
250B SER* 3.3 23.6 + - - -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 3.7 26.7 - - + -
234B LEU* 4.0 11.9 - - + -
236B LEU* 3.6 27.8 - - + -
242B TRP* 3.8 17.3 - - + -
243B ASP 3.1 14.6 + - - +
244B TYR 3.6 7.4 - - - +
245B GLU 3.2 0.2 - - - -
246B ALA* 1.3 77.4 - - - +
248B MET* 1.3 74.7 - - + +
250B SER* 3.3 3.2 + - - -
251B VAL* 3.1 28.1 + - - +
273B VAL* 4.2 2.5 - - + -
277B ILE* 3.9 18.2 - - + -
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Residues in contact with MET 248 (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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242B TRP* 3.9 10.3 - - + -
244B TYR* 2.9 66.1 + - + +
245B GLU* 4.2 4.5 - - - +
247B VAL* 1.3 81.8 - - + +
249B ASN* 1.3 60.2 + - - +
252B ALA* 3.0 32.2 + - - +
276B THR* 3.8 18.2 - - + +
277B ILE* 3.8 30.7 - - + -
280B ASP* 5.0 1.6 - - - -
281B LEU* 3.5 36.0 - - + +
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Residues in contact with ASN 249 (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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245B GLU* 2.9 41.2 + - - +
246B ALA* 4.0 5.6 - - - +
248B MET* 1.3 79.2 - - - +
250B SER* 1.3 63.9 + - - +
252B ALA* 3.7 5.0 - - - +
253B LYS* 3.2 23.8 + - - +
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Residues in contact with SER 250 (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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198B LEU* 6.1 0.4 - - - -
206B THR* 2.8 34.7 + - - +
232B GLU* 2.6 32.3 + - - +
234B LEU* 4.8 9.1 - - - +
246B ALA 3.3 16.0 + - - -
247B VAL 3.7 3.4 - - - -
249B ASN* 1.3 79.3 - - - +
251B VAL* 1.3 57.9 + - - +
253B LYS* 3.0 7.5 + - - +
254B THR* 2.9 29.1 + - - +
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Residues in contact with VAL 251 (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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206B THR* 3.9 7.2 - - + -
208B ILE* 4.4 0.2 - - + -
247B VAL* 3.1 20.3 + - + +
250B SER* 1.3 75.6 - - - +
252B ALA* 1.3 55.9 + - - +
254B THR* 3.8 7.0 - - - -
255B GLY* 2.7 34.1 + - - -
256B ARG 4.9 0.2 - - - +
257B VAL* 4.1 23.8 - - + -
277B ILE* 4.0 32.8 - - + -
281B LEU* 4.0 13.9 - - + -
284B MET* 4.2 2.9 - - + +
285B LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 252 (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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248B MET 3.0 20.8 + - - +
249B ASN* 3.7 7.2 - - - +
251B VAL* 1.3 78.3 - - - +
253B LYS* 1.3 61.8 + - - +
255B GLY* 4.1 3.6 + - - -
281B LEU* 4.1 8.7 - - + +
284B MET* 3.5 44.9 - - + +
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Residues in contact with LYS 253 (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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201B GLU* 4.0 13.5 + - - +
202B GLY 3.0 19.6 + - - +
203B LYS* 4.1 19.7 - - + +
232B GLU* 2.6 38.0 + - - -
249B ASN 3.2 11.7 + - - +
250B SER* 3.0 7.7 + - - +
252B ALA* 1.3 82.6 - - - +
254B THR* 1.3 60.9 + - + +
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Residues in contact with THR 254 (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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202B GLY 4.0 7.6 - - - +
203B LYS* 3.6 32.0 - - - +
204B ASP* 4.1 1.7 - - - +
205B LEU* 3.8 27.1 - - - +
206B THR* 2.6 30.4 + - - +
232B GLU* 4.7 1.1 - - + -
250B SER* 2.9 12.0 + - - +
251B VAL* 3.7 2.4 + - - -
253B LYS* 1.3 78.3 - - + +
255B GLY* 1.3 61.0 + - - +
256B ARG* 3.0 28.9 + - - -
286B LEU* 3.9 8.3 - - - +
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Residues in contact with GLY 255 (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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251B VAL 2.7 24.7 + - - -
252B ALA 4.1 2.2 + - - -
253B LYS 3.6 1.4 - - - -
254B THR* 1.3 71.6 + - - +
256B ARG* 1.3 57.3 + - - +
284B MET 3.3 18.2 - - - -
285B LEU* 3.5 9.3 - - - +
286B LEU* 2.6 40.9 + - - +
287B ALA 3.5 2.6 + - - -
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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