Contacts of the helix formed by residues 192 - 201 (chain C) in PDB entry 3ULA
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 CYS 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191C TYR* 1.3 73.6 - - - +
193C THR* 1.3 59.5 + - + +
194C ASP 2.5 15.1 + - - -
195C LEU* 3.1 9.5 + - - +
196C ARG* 4.0 3.1 + - - -
219C GLN* 2.5 19.8 + - - +
220C PRO 3.4 26.5 - - - -
221C GLY* 3.5 19.5 - - - -
222C ALA* 4.0 12.9 - - - +
224C LYS* 5.8 0.7 - - - -
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Residues in contact with THR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS* 4.0 27.5 - - - +
167C LEU 5.2 1.7 - - - +
191C TYR* 4.4 7.4 - - - +
192C CYS* 1.3 78.3 - - + +
194C ASP* 1.3 64.0 + - - -
195C LEU 2.7 2.8 + - - -
196C ARG* 2.7 47.2 + - + +
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Residues in contact with ASP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C SER* 4.4 3.0 + - - -
165C PHE* 2.3 49.3 + - + +
166C LYS* 3.5 19.8 - - - +
167C LEU* 3.2 30.0 + - - +
189C SER 3.8 7.3 - - - +
190C ILE* 4.5 1.6 - - + -
191C TYR* 3.1 50.0 + - - +
192C CYS 2.5 4.6 + - - -
193C THR* 1.3 81.0 + - - +
195C LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C PHE* 3.6 30.1 - - + -
167C LEU* 3.6 25.6 - - + -
190C ILE* 5.3 4.3 - - + -
191C TYR 5.7 0.4 - - - +
192C CYS 3.1 4.2 + - - -
193C THR 2.7 1.6 + - - -
194C ASP* 1.3 76.2 - - + +
196C ARG* 1.3 68.0 + - - +
197C VAL* 3.5 5.3 - - - +
198C LEU* 2.9 36.4 + - + +
199C HIS 4.4 0.2 + - - -
208C LEU* 4.3 15.5 - - + -
222C ALA 4.4 6.1 - - - +
223C PHE* 4.0 27.4 - - + -
226C ILE* 3.7 35.8 - - + +
228C LEU* 4.8 2.7 - - + -
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C CYS 4.0 2.4 + - - -
193C THR* 2.7 29.9 + - - +
195C LEU* 1.3 75.5 - - - +
197C VAL* 1.3 63.3 + - + +
198C LEU 2.6 14.4 + - - -
199C HIS* 2.7 48.0 + - + +
200C GLN* 3.5 31.1 + - - +
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LEU* 4.0 35.4 - - + +
168C PRO 4.1 2.0 - - - +
169C GLU* 3.7 41.1 - - + +
171C PHE* 4.1 17.3 - - + -
172C SER* 5.0 7.2 + - - +
195C LEU 4.0 4.3 - - - +
196C ARG* 1.3 83.8 - - + +
198C LEU* 1.3 66.7 + - + +
200C GLN* 3.0 28.9 + - - +
201C MET* 3.9 7.4 - - - +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LEU* 4.4 12.8 - - + -
171C PHE* 6.3 2.0 - - + -
195C LEU* 2.9 39.4 + - + +
196C ARG 2.6 5.3 + - - -
197C VAL* 1.3 79.1 - - + +
199C HIS* 1.3 51.9 + - - +
201C MET* 2.6 47.5 + - - +
204C LEU* 3.2 40.6 - - + -
206C LEU* 5.0 5.6 - - + -
208C LEU* 6.1 0.2 - - + -
225C GLU 5.6 0.4 - - - -
226C ILE* 3.6 32.1 - - + -
227C ARG 6.0 1.3 - - - +
228C LEU* 5.0 10.1 - - + -
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Residues in contact with HIS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ARG* 2.7 53.2 + - + +
198C LEU* 1.3 71.8 - - - +
200C GLN* 1.3 73.1 + - - +
201C MET 3.0 8.0 + - - -
202C PRO* 4.5 4.5 - - - +
224C LYS* 3.3 33.6 - - + +
225C GLU* 3.2 33.5 + - + +
226C ILE* 4.2 10.7 - - + +
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Residues in contact with GLN 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C SER* 6.1 3.1 - - - -
196C ARG* 3.5 26.9 + - - +
197C VAL* 3.0 34.6 + - - +
198C LEU 3.0 1.0 - - - -
199C HIS* 1.3 96.7 - - - +
201C MET* 1.3 63.9 + - + +
202C PRO* 3.4 12.3 - - - +
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Residues in contact with MET 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PHE* 3.6 20.4 - - - +
172C SER* 2.9 35.7 - - - +
174C LEU* 3.9 5.8 - - - +
175C THR* 3.8 21.3 - - - +
197C VAL* 3.9 8.7 - - - +
198C LEU* 2.6 37.2 + - - +
199C HIS 3.0 4.4 + - - -
200C GLN* 1.3 78.5 - - + +
202C PRO* 1.3 65.0 - - - +
203C LEU 3.6 2.2 - - - -
204C LEU* 3.4 40.1 - - + +
227C ARG* 4.9 7.1 - - - +
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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