Contacts of the helix formed by residues 213 - 227 (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 VAL 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B ARG* 4.6 0.2 - - - +
209B CYS* 4.0 4.3 - - + -
210B TYR 3.7 12.7 + - - +
212B THR* 1.3 74.2 - - - +
214B MET* 1.3 67.1 + - - +
215B PRO* 3.1 4.5 - - - -
216B GLU* 3.1 14.7 + - + +
217B VAL* 3.1 25.5 + - + +
260B VAL* 3.6 37.7 - - + +
261B SER* 3.7 5.8 - - - -
262B ASP* 3.6 34.8 - - + +
308B LEU* 4.6 3.4 - - + -
309B PRO* 4.1 20.0 - - + +
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER* 3.4 27.6 - - - +
176B LEU* 5.1 0.7 - - + -
199B ARG* 4.1 11.2 - - + +
209B CYS* 3.2 35.7 - - - -
210B TYR* 3.7 15.5 - - - -
211B GLY 3.1 20.7 + - - +
213B VAL* 1.3 76.2 - - - +
215B PRO* 1.3 71.1 - - + +
217B VAL* 3.2 2.5 + - + +
218B LEU* 2.9 47.4 + - + +
233B VAL* 4.0 17.0 - - + -
235B ASP* 4.1 18.2 - - + +
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Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 4.0 10.1 - - - +
176B LEU* 3.5 28.3 - - + -
179B SER* 6.2 0.4 - - - -
211B GLY 4.4 0.2 - - - +
212B THR 3.3 14.8 - - - +
213B VAL 3.3 1.6 - - - -
214B MET* 1.3 92.9 - - + +
216B GLU* 1.3 73.2 + - - +
218B LEU* 3.9 7.2 - - + +
219B GLN* 3.1 26.1 + - - +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 2.8 45.2 + - - -
213B VAL* 3.1 13.6 + - + +
215B PRO* 1.3 75.1 - - - +
217B VAL* 1.3 62.0 + - - +
219B GLN* 3.3 3.9 + - - +
220B ALA* 2.9 29.5 + - - +
308B LEU* 4.4 5.5 - - - +
309B PRO 3.4 21.8 - - - +
310B THR* 4.4 1.1 - - - -
311B VAL* 3.8 29.1 - - + +
314B ILE* 3.8 17.8 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.0 22.4 - - + +
209B CYS* 3.6 34.3 - - + -
213B VAL* 3.1 16.6 + - + +
214B MET* 3.7 6.7 - - - +
216B GLU* 1.3 76.4 - - - +
218B LEU* 1.3 57.6 + - - +
220B ALA* 3.2 5.4 + - - +
221B ALA* 2.9 26.9 + - - +
233B VAL* 4.0 14.4 - - + -
260B VAL* 3.9 24.0 - - + -
314B ILE* 3.8 20.2 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 3.9 32.5 - - + +
200B ARG* 5.8 3.1 - - + -
214B MET* 2.9 39.7 + - + +
215B PRO* 3.9 6.1 - - + +
217B VAL* 1.3 76.0 - - - +
219B GLN* 1.3 57.7 + - - +
221B ALA* 3.3 6.9 + - + +
222B ALA* 3.0 27.5 + - - +
233B VAL* 4.0 16.8 - - + -
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Residues in contact with GLN 219 (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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215B PRO 3.1 19.4 + - - +
216B GLU* 3.6 7.0 - - - +
218B LEU* 1.3 77.1 - - - +
220B ALA* 1.3 63.2 - - - +
222B ALA* 3.2 9.5 + - + +
223B GLU* 3.0 42.1 + - + +
311B VAL* 3.3 26.8 - - + +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 5.1 2.9 - - + -
216B GLU 2.9 17.5 + - - +
217B VAL 3.2 5.8 + - - +
219B GLN* 1.3 74.9 - - - +
221B ALA* 1.3 58.7 + - - +
223B GLU* 3.3 1.3 + - - -
224B LEU* 2.9 36.8 + - + +
311B VAL* 4.0 15.4 - - + +
314B ILE* 3.8 27.4 - - + -
315B LEU* 3.7 17.5 - - + +
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Residues in contact with ALA 221 (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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200B ARG* 3.8 20.1 + - - -
207B LEU* 4.3 4.9 - - + +
217B VAL 2.9 13.8 + - - +
218B LEU* 3.5 10.8 - - + +
219B GLN 3.2 0.2 - - - -
220B ALA* 1.3 77.5 - - - +
222B ALA* 1.3 61.8 + - - +
224B LEU* 3.2 14.1 + - - +
225B ALA* 3.0 22.0 + - - +
229B VAL 4.7 0.2 - - - +
231B ALA* 4.6 6.3 - - + +
233B VAL* 3.6 27.6 - - + -
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Residues in contact with ALA 222 (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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200B ARG* 5.0 3.1 - - - +
218B LEU 3.0 13.0 + - - +
219B GLN* 3.5 12.1 - - + +
221B ALA* 1.3 77.8 - - - +
223B GLU* 1.3 62.1 + - + +
225B ALA* 3.2 17.6 + - - +
226B LYS* 3.2 24.4 + - - +
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Residues in contact with GLU 223 (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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219B GLN* 3.0 42.3 + - + +
220B ALA 3.3 4.5 + - - +
222B ALA* 1.3 73.4 - - + +
224B LEU* 1.3 66.1 + - - +
226B LYS* 3.3 36.2 + - + +
227B ALA* 3.3 13.0 + - - +
311B VAL* 3.5 15.4 - - - +
315B LEU* 3.3 25.4 - - + +
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Residues in contact with LEU 224 (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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205B LEU* 4.2 18.2 - - + -
207B LEU* 4.6 5.8 - - + -
220B ALA* 2.9 20.6 + - + +
221B ALA* 3.2 9.8 + - - +
223B GLU* 1.3 74.0 - - - +
225B ALA* 1.3 60.2 + - - +
227B ALA* 3.0 14.0 + - + +
228B GLY 3.2 0.2 + - - -
229B VAL* 2.8 58.8 + - + +
231B ALA* 3.9 23.8 - - + -
314B ILE* 6.6 0.4 - - + -
315B LEU* 3.9 19.1 - - + +
318B ALA* 4.2 15.9 - - + -
322B LEU* 4.5 5.2 - - + -
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 3.4 27.8 - - - +
221B ALA 3.0 5.6 + - - +
222B ALA* 3.3 11.9 - - - +
224B LEU* 1.3 76.9 - - - +
226B LYS* 1.3 57.7 + - + +
228B GLY* 2.8 20.6 + - - -
229B VAL 3.3 11.6 + - - +
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ALA* 3.2 20.1 + - - +
223B GLU* 3.5 30.0 - - + +
225B ALA* 1.3 77.6 - - + +
227B ALA* 1.3 56.4 + - - +
228B GLY 3.2 3.0 + - - -
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Residues in contact with ALA 227 (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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223B GLU 3.3 8.4 + - - +
224B LEU* 3.0 13.4 + - + +
226B LYS* 1.3 77.5 - - - +
228B GLY* 1.3 61.9 + - - +
229B VAL* 3.3 12.1 + - + +
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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