Contacts of the helix formed by residues 182 - 194 (chain C) in PDB entry 5KZ5
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 LEU 182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 6.6 0.2 - - + -
145C ILE* 4.1 16.4 - - + -
154C ILE* 4.0 17.9 - - + -
155C TRP 4.6 0.7 - - - +
156C LEU* 4.0 33.2 - - + -
166C TYR* 3.6 34.1 - - + +
173C TRP* 3.2 24.5 - - + +
181C SER* 1.4 71.4 - - - +
183C HIS* 1.4 68.7 + - + +
185C LEU* 3.4 3.5 + - - +
186C LEU* 3.2 41.6 + - + +
93Q HIS* 5.3 1.8 - - + -
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Residues in contact with HIS 183 (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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106C LEU* 5.7 4.9 - - + -
110C PHE* 5.6 2.0 - - + -
173C TRP* 4.4 6.5 - + + +
181C SER* 3.2 30.4 - - - -
182C LEU* 1.4 82.3 - - + +
184C GLU* 1.3 72.3 + - + +
186C LEU 3.6 0.5 + - - -
187C ALA* 3.0 25.1 + - - +
200C LEU* 3.9 4.9 - - + +
201C SER* 3.3 41.3 - - - -
202C SER 3.5 13.1 + - - +
203C LEU* 3.6 27.9 - - + +
206C SER* 3.4 20.2 + - - -
93Q HIS* 3.2 32.0 + - + +
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Residues in contact with GLU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 3.4 24.4 - - + +
181C SER* 3.5 11.4 + - - +
182C LEU 3.4 0.4 - - - -
183C HIS* 1.3 88.8 + - + +
185C LEU* 1.3 59.1 + - - +
187C ALA* 3.4 2.3 + - - +
188C ALA* 3.0 27.5 + - - +
200C LEU 3.8 11.7 - - - +
201C SER* 3.2 27.4 + - - +
208C LYS* 5.6 2.9 - - - +
108c TRP* 4.5 12.0 - - - -
124c ASP* 3.4 23.5 - - - +
127c LYS* 4.5 9.8 + - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 3.6 31.0 - - + -
161C SER* 4.7 5.6 - - - +
164C LYS* 4.0 6.5 - - - -
166C TYR* 4.0 3.1 - - - +
175C TYR* 3.8 39.3 - - + +
180C VAL* 5.2 3.7 - - + +
181C SER 3.2 14.1 + - - +
182C LEU* 3.7 9.0 - - - +
183C HIS 3.4 0.2 - - - -
184C GLU* 1.3 73.1 - - - +
186C LEU* 1.4 62.0 + - - +
188C ALA* 3.3 7.5 + - + +
189C GLU* 3.3 37.8 + - + +
121c LYS* 4.6 7.4 - - - +
123c THR* 4.4 26.0 - - + +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 6.0 1.1 - - + -
134C VAL* 6.0 1.3 - - + -
143C TYR* 4.9 13.0 - - + -
145C ILE* 4.3 22.9 - - + -
156C LEU* 4.1 23.6 - - + -
158C SER* 5.7 0.2 - - - +
182C LEU* 3.2 40.9 + - + +
183C HIS 3.9 4.0 - - - +
185C LEU* 1.4 70.1 - - - +
187C ALA* 1.4 65.9 + - - +
189C GLU* 3.4 14.7 + - - +
190C LEU* 3.2 36.0 + - + +
92Q THR* 5.3 7.9 - - + -
93Q HIS* 3.9 25.4 - - + +
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Residues in contact with ALA 187 (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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183C HIS 3.0 12.9 + - - +
184C GLU 3.5 6.5 - - - +
185C LEU 3.3 0.2 - - - -
186C LEU* 1.4 76.5 - - - +
188C ALA* 1.4 55.4 + - - +
190C LEU* 3.4 5.7 + - - +
191C THR* 2.9 33.1 + - - -
198C LEU* 3.8 19.7 - - + +
200C LEU* 3.4 34.8 - - + +
93Q HIS* 4.6 8.2 + - + -
127c LYS* 4.4 4.0 - - - +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C GLU 3.0 14.1 + - - +
185C LEU* 3.5 12.8 - - + +
186C LEU 3.3 0.2 - - - -
187C ALA* 1.4 73.7 - - - +
189C GLU* 1.4 64.2 + - + +
191C THR* 3.4 3.1 + - - -
192C LYS* 3.3 35.1 + - - +
123c THR* 4.5 16.4 - - - +
124c ASP* 5.0 5.4 - - - +
127c LYS* 3.8 31.2 - - + +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 3.8 24.3 + - + +
156C LEU* 5.1 1.0 - - - +
158C SER* 4.7 4.7 + - - -
160C SER* 3.2 25.6 + - - -
161C SER* 4.7 8.0 + - - -
185C LEU* 3.3 37.6 + - + +
186C LEU* 3.9 16.1 - - + +
187C ALA 3.4 0.2 - - - -
188C ALA* 1.4 76.5 - - + +
190C LEU* 1.4 68.5 + - + +
192C LYS* 3.6 18.1 + - - +
193C ALA* 3.3 21.3 + - - +
123c THR* 6.5 0.2 - - + -
134j VAL* 5.3 9.6 - - + +
137j HIS* 5.6 1.0 - - - -
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Residues in contact with LEU 190 (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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122C ASP* 6.3 1.1 - - + -
134C VAL* 6.1 1.1 - - + -
136C LEU* 5.6 12.1 - - + -
143C TYR* 5.2 12.1 - - + -
186C LEU* 3.2 29.8 + - + +
187C ALA* 3.9 4.9 - - - +
189C GLU* 1.4 83.7 - - + +
191C THR* 1.3 60.1 + - - +
193C ALA* 3.4 6.8 + - + +
194C LEU* 3.1 44.9 + - + +
198C LEU* 4.4 16.2 - - + -
92Q THR* 6.5 0.7 - - + -
93Q HIS* 5.8 3.8 - - + -
94Q ALA* 3.6 31.0 - - + +
95Q TYR* 5.8 9.2 - - + +
98Q GLU* 4.9 4.7 - - - +
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ALA 2.9 21.4 + - - -
188C ALA 3.4 5.6 + - - -
190C LEU* 1.3 74.1 - - - +
192C LYS* 1.4 57.0 + - - +
194C LEU* 3.6 0.6 + - - -
195C LYS* 3.0 26.2 + - - -
196C THR 3.3 25.0 - - - +
197C LYS* 4.0 10.8 - - + -
198C LEU* 3.2 33.3 + - - +
127c LYS* 3.4 36.8 - - + +
130c CYS* 5.1 1.3 - - - -
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Residues in contact with LYS 192 (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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188C ALA* 3.3 20.6 + - - +
189C GLU* 3.7 15.4 - - - +
190C LEU 3.4 0.2 - - - -
191C THR* 1.4 75.8 - - - +
193C ALA* 1.3 63.9 + - - +
195C LYS* 3.4 11.4 + - - +
123c THR* 3.2 47.0 + - - +
126c ALA* 3.9 8.5 - - - +
127c LYS* 3.6 22.9 - - - +
130c CYS* 3.5 23.0 - - - +
131c LEU 4.3 2.5 - - - -
132c PRO* 3.9 37.0 - - + +
133c PRO* 3.6 14.3 - - - +
134j VAL* 5.0 7.6 - - + +
137j HIS* 4.9 7.1 + - + -
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Residues in contact with ALA 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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136C LEU* 5.5 9.6 - - + -
140C LEU* 5.9 0.2 - - + -
189C GLU 3.3 11.1 + - - +
190C LEU* 3.7 14.1 - - + +
191C THR 3.3 0.2 - - - -
192C LYS* 1.3 81.4 - - - +
194C LEU* 1.4 66.2 + - + +
195C LYS* 3.9 6.2 - - - +
68j ALA 4.3 11.4 - - - +
137j HIS* 3.6 30.2 - - + +
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Residues in contact with LEU 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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119C THR* 3.8 24.5 - - + +
120C PHE* 5.7 4.7 - - + -
190C LEU* 3.1 40.3 + - + +
191C THR 3.8 4.0 - - - +
193C ALA* 1.4 78.4 - - + +
195C LYS* 1.3 69.0 + - - +
196C THR* 3.3 23.9 + - - +
197C LYS 5.5 1.1 - - - +
198C LEU* 4.5 12.1 - - + -
94Q ALA* 5.8 0.4 - - + -
97Q TRP* 3.6 37.2 - - + -
98Q GLU* 4.6 11.7 - - - +
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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