Contacts of the helix formed by residues 190 - 195 (chain B) in PDB entry 1ULH
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A TYR* 4.7 0.4 - - - -
147B GLN* 2.7 39.8 + - - +
148B MET 3.1 6.2 + - - +
149B THR* 3.4 13.5 - - - +
150B ASP* 2.8 11.2 + - - +
151B ASP* 2.9 39.2 - - - +
188B PHE* 3.5 5.4 + - - -
189B SER* 1.3 69.7 - - - +
191B LEU* 1.3 64.7 + - - +
193B TYR* 4.8 0.7 - - - -
194B MET* 2.9 30.2 + - + +
200B PHE* 3.5 12.1 - - + -
236B ILE* 3.4 11.9 - - - +
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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
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201A TYR* 4.2 15.8 - - + +
202A LYS* 4.4 29.7 - - + +
205A VAL* 4.2 16.2 - - + -
150B ASP* 3.0 35.7 + - + +
151B ASP* 3.5 28.5 - - + -
161B LEU* 3.8 47.6 - - + +
164B ALA* 4.6 2.2 - - + -
165B TYR* 4.7 7.0 - - + +
189B SER* 3.5 0.4 - - - +
190B ASP* 1.3 76.1 - - - +
192B ASP* 1.3 61.3 + - - +
195B GLY* 4.1 9.7 + - - -
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Residues in contact with ASP 192 (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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198A SER* 5.8 4.2 - - - -
202A LYS* 4.7 13.0 + - - -
165B TYR* 3.4 31.1 + - - -
189B SER* 3.0 20.6 + - - +
191B LEU* 1.3 78.5 - - - +
193B TYR* 1.3 65.1 + - - +
194B MET 3.3 1.0 + - - -
195B GLY* 3.4 8.8 + - - -
196B MET* 3.2 42.7 + - + +
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Residues in contact with TYR 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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186B PHE* 3.6 26.5 - + - -
188B PHE* 3.5 31.0 - + + -
189B SER 2.9 18.4 + - - +
190B ASP* 4.4 0.9 - - - +
192B ASP* 1.3 75.6 - - - +
194B MET* 1.3 63.7 + - - +
196B MET* 3.8 14.8 - - + -
197B SER* 3.3 40.4 + - - -
200B PHE* 3.9 25.4 - + + +
245B SER 2.5 29.6 + - - -
246B PHE* 3.3 16.1 - + - -
248B GLN* 2.8 29.7 + - - -
416B PRO* 4.3 8.5 - - + -
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Residues in contact with MET 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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194A MET* 3.3 17.8 - - + +
195A GLY* 3.6 8.8 - - - -
201A TYR* 3.5 44.9 - - + -
151B ASP* 4.7 0.7 - - - +
190B ASP 2.9 19.3 + - - +
193B TYR* 1.3 77.7 - - - +
195B GLY* 1.3 58.6 + - - +
196B MET 3.3 3.9 + - - -
197B SER* 4.0 3.5 + - - +
200B PHE* 3.3 42.1 - - + -
201B TYR* 3.9 32.9 + - + +
204B VAL* 4.0 7.6 - - + -
236B ILE* 3.7 34.5 - - + -
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Residues in contact with GLY 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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194A MET 3.1 9.9 - - - -
195A GLY 3.2 7.0 - - - +
196A MET 3.7 1.4 - - - -
197A SER 2.6 43.2 + - - +
198A SER* 4.6 1.6 - - - -
201A TYR* 4.7 7.3 - - - +
191B LEU 4.1 6.0 + - - -
192B ASP 3.4 8.9 + - - -
193B TYR 3.3 0.2 - - - -
194B MET* 1.3 78.2 - - - +
196B MET* 1.3 58.3 + - - +
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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