Contacts of the helix formed by residues 187 - 196 (chain B) in PDB entry 3UMO
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 ASN 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A MG 3.9 0.6 - - - -
315A ATP 3.0 38.0 + - - -
185B LYS* 3.7 1.8 + - - +
186B PRO* 1.3 74.9 - - - +
188B GLN* 1.3 59.5 + - - +
189B LYS* 3.2 7.5 + - - +
190B GLU* 2.7 58.3 + - - +
191B LEU* 2.8 27.2 + - - +
223B VAL* 4.3 2.0 - - - -
224B SER* 3.4 21.3 - - - +
313B ATP 3.1 22.0 + - - +
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Residues in contact with GLN 188 (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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187B ASN* 1.3 76.0 - - - +
189B LYS* 1.3 63.8 + - + +
191B LEU* 3.3 7.3 + - - +
192B SER* 3.0 23.9 + - - -
199B LEU* 4.4 4.5 - - + +
205B VAL* 4.7 15.9 - - + +
223B VAL* 4.5 4.5 - - + -
224B SER 3.5 2.7 + - - +
225B LEU* 3.4 51.2 - - + +
228B GLN* 4.7 9.6 + - - +
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Residues in contact with LYS 189 (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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315A ATP 2.6 52.7 + - - +
187B ASN* 3.2 9.5 + - - +
188B GLN* 1.3 78.9 - - + +
190B GLU* 1.3 57.5 + - + +
192B SER* 3.4 7.3 + - - -
193B ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.5 0.3 + - - -
315A ATP 4.3 11.3 + - - +
166B ASP* 4.2 5.2 - - - +
167B SER 3.6 24.6 - - - +
168B SER* 3.9 20.3 - - - +
172B LEU* 4.3 7.5 - - + +
185B LYS* 3.9 6.9 + - - +
186B PRO* 3.5 13.7 - - + +
187B ASN* 2.7 53.5 + - - +
189B LYS* 1.3 70.6 - - + +
191B LEU* 1.3 60.0 + - - +
193B ALA* 3.5 6.1 + - - +
194B LEU* 3.0 29.8 + - - +
311B MG 4.1 9.0 - - - -
313B ATP 4.5 0.7 + - - -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.6 20.5 - - + +
187B ASN 2.8 20.5 + - - +
188B GLN* 3.6 5.4 - - - +
190B GLU* 1.3 72.7 - - - +
192B SER* 1.3 62.6 + - - +
194B LEU* 3.2 5.6 + - + +
195B VAL* 3.0 23.7 + - + +
199B LEU* 3.7 21.5 - - + -
205B VAL* 3.8 29.6 - - + +
208B ALA* 3.9 12.8 - - + -
209B ALA* 4.4 3.4 - - - +
212B ILE* 3.5 31.4 - - + -
221B VAL* 5.0 0.2 - - + -
223B VAL* 3.8 22.7 - - + -
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN 3.0 16.8 + - - -
189B LYS* 3.6 7.6 - - - -
190B GLU 3.4 0.2 - - - -
191B LEU* 1.3 76.5 - - - +
193B ALA* 1.3 57.5 + - - +
195B VAL* 3.6 1.6 + - - -
196B ASN* 2.9 23.2 + - - -
197B ARG 2.7 37.6 + - - -
198B GLU* 4.0 11.4 + - - -
199B LEU* 3.9 16.1 - - - +
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Residues in contact with ALA 193 (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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169B GLY* 5.5 13.0 - - - +
189B LYS 3.0 16.8 + - - +
190B GLU* 3.8 6.3 - - - +
192B SER* 1.3 76.5 + - - +
194B LEU* 1.3 63.4 + - - +
196B ASN* 3.2 17.2 + - - +
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Residues in contact with LEU 194 (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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172B LEU* 4.1 20.0 - - + -
173B SER* 3.9 34.2 + - - +
176B LEU* 3.5 33.2 - - + -
184B VAL* 5.5 2.0 - - + -
186B PRO* 5.3 5.2 - - + -
190B GLU 3.0 18.7 + - - +
191B LEU* 3.5 8.1 - - + +
193B ALA* 1.3 79.1 - - - +
195B VAL* 1.3 60.4 + - + +
196B ASN* 3.2 2.3 + - - +
212B ILE* 3.6 28.7 - - + -
217B LYS* 5.7 7.0 - - + +
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Residues in contact with VAL 195 (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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191B LEU* 3.0 21.8 + - + +
192B SER 3.8 4.0 - - - +
194B LEU* 1.3 76.2 - - - +
196B ASN* 1.3 71.8 + - - +
197B ARG* 3.4 39.9 + - + +
199B LEU* 4.3 7.2 - - + -
208B ALA* 4.0 37.5 - - + +
211B GLU* 4.2 15.6 - - - +
212B ILE* 4.1 20.6 - - + -
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Residues in contact with ASN 196 (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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192B SER 2.9 8.6 + - - -
193B ALA* 3.2 14.4 + - - +
194B LEU 3.2 2.4 - - - +
195B VAL* 1.3 81.3 - - - +
197B ARG* 1.3 61.3 + - - +
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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