Contacts of the helix formed by residues 170 - 185 (chain C) in PDB entry 1ZUM
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 PHE 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 4.3 0.2 - - - -
112C LYS* 3.2 26.9 - - - +
121C ASP* 3.4 12.8 - - - +
124C MET* 5.6 3.1 - - + -
167C PRO 4.7 0.7 - - - -
169C ASN* 1.3 102.0 + - - +
171C PRO* 1.3 62.0 - - - +
172C LEU 3.5 2.0 - - - -
173C LEU* 4.0 26.2 - - + -
174C MET* 2.8 47.8 + - + +
296C PHE* 3.7 36.8 - + - -
297C ASN* 3.4 17.3 - - + -
300C GLN 3.7 8.5 - - - -
301C CYS* 4.3 15.9 - - + -
302C CYS* 6.5 0.4 - - - -
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Residues in contact with PRO 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 3.3 30.1 - - - +
110C ASN* 3.9 8.3 - - + +
112C LYS* 4.6 1.3 - - - +
166C ILE* 3.5 10.0 - - + +
167C PRO 4.2 9.6 - - - +
168C TRP 3.4 17.9 - - - +
169C ASN 3.6 3.4 - - - +
170C PHE* 1.3 86.7 - - - +
172C LEU* 1.3 61.5 + - - +
175C GLN* 3.2 23.0 + - - +
197C THR* 3.4 36.3 - - + +
200C THR* 3.8 9.0 - - - +
201C ALA* 5.3 5.3 - - + +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 6.2 1.1 - - + -
102C LEU* 4.2 15.9 - - + +
106C GLU* 3.0 28.0 + - - +
121C ASP* 5.6 2.5 - - + -
122C LEU* 3.9 28.7 - - + -
125C VAL* 3.5 23.1 - - + +
171C PRO* 1.3 71.1 - - - +
173C LEU* 1.3 67.3 + - - +
175C GLN* 3.2 15.1 + - - +
176C ALA* 3.0 18.5 + - - +
200C THR* 3.4 35.4 - - + +
201C ALA 4.4 0.2 - - - +
204C VAL* 3.6 30.5 - - + -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 4.7 0.6 + - - -
121C ASP* 4.7 10.1 + - - +
124C MET* 3.5 66.4 - - + +
125C VAL* 3.5 12.7 - - + +
128C CYS* 4.7 1.3 - - + -
170C PHE* 3.4 23.3 + - + +
172C LEU* 1.3 77.7 - - - +
174C MET* 1.3 63.3 + - + +
176C ALA* 3.1 2.5 + - + -
177C TRP* 2.8 68.9 + - + +
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Residues in contact with MET 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ILE* 4.0 22.2 - - + -
167C PRO* 3.8 27.4 - - + +
169C ASN* 4.2 4.3 - - - +
170C PHE* 2.8 46.4 + - + +
173C LEU* 1.3 80.1 - - + +
175C GLN* 1.3 63.8 + - - +
177C TRP* 3.4 48.2 + - + +
178C LYS* 3.2 32.9 + - - +
244C THR* 4.3 16.4 - - - -
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Residues in contact with GLN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ILE* 3.6 12.7 - - + +
171C PRO 3.2 12.8 + - - +
172C LEU* 3.2 16.0 + - - +
174C MET* 1.3 79.0 - - - +
176C ALA* 1.3 57.5 + - - +
178C LYS* 3.2 3.1 + - - +
179C LEU* 2.8 46.4 + - + +
191C MET* 3.7 18.9 - - - +
201C ALA* 3.3 36.8 - - + +
204C VAL* 3.3 42.7 - - - +
208C ILE* 5.1 0.2 - - - +
220C ILE* 3.6 13.9 - - - +
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Residues in contact with ALA 176 (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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125C VAL* 4.0 28.9 - - + +
128C CYS* 3.4 19.7 - - + -
129C LEU* 4.1 22.8 - - + +
172C LEU 3.0 13.3 + - - +
173C LEU* 3.6 7.2 - - + +
175C GLN* 1.3 78.7 - - - +
177C TRP* 1.3 55.6 + - - +
179C LEU* 4.4 1.8 - - - +
180C GLY* 2.9 27.0 + - - -
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Residues in contact with TRP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C MET* 6.2 0.4 - - - -
128C CYS* 3.8 18.7 - - - +
132C TYR* 5.2 0.9 - - - -
173C LEU* 2.8 57.4 + - + +
174C MET* 3.4 32.8 - - + +
175C GLN 3.3 0.4 - - - -
176C ALA* 1.3 73.1 - - - +
178C LYS* 1.3 60.8 + - + +
181C PRO* 3.1 23.2 - - - +
459C PHE* 4.3 23.1 - + + -
465C PHE* 3.9 30.3 - + - -
476C GLU* 3.5 41.3 - - + +
477C LEU* 3.6 39.7 + - + +
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Residues in contact with LYS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLN* 3.2 38.1 + - + +
165C ILE 5.1 0.2 - - - -
166C ILE* 3.7 18.4 - - + +
174C MET* 3.2 22.3 + - - +
175C GLN 3.7 2.9 - - - +
177C TRP* 1.3 81.1 - - - +
179C LEU* 1.3 63.9 + - - +
181C PRO* 3.7 4.0 - - - +
182C ALA* 3.2 14.2 + - - +
191C MET* 4.2 4.7 - - + -
242C ALA* 3.9 22.2 - - + -
244C THR* 2.9 30.8 + - - +
268C GLU* 3.8 7.0 - - - -
476C GLU* 2.9 35.3 + - - +
485C TYR* 3.9 15.9 + - + +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 5.0 6.7 - - + -
129C LEU* 4.7 6.7 - - + -
164C GLN* 3.9 7.0 - - - +
175C GLN* 2.8 44.1 + - + +
176C ALA* 4.3 4.0 - - - +
178C LYS* 1.3 71.3 - - - +
180C GLY* 1.3 66.2 + - - +
182C ALA* 4.5 1.1 - - - -
183C LEU* 2.9 40.4 + - + +
189C VAL* 4.2 18.6 - - + -
191C MET* 3.5 21.8 - - + -
204C VAL* 4.9 3.8 - - + -
208C ILE* 3.9 27.4 - - + -
218C VAL* 4.3 17.7 - - + -
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 4.0 6.5 - - - +
128C CYS* 5.1 0.7 - - - -
129C LEU* 4.2 13.3 - - - +
132C TYR* 3.5 22.4 - - - +
176C ALA 2.9 15.8 + - - -
179C LEU* 1.3 79.6 - - - +
181C PRO* 1.3 62.9 - - - +
184C ALA* 3.0 26.7 + - - +
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Residues in contact with PRO 181 (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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132C TYR* 3.6 43.0 - - + +
177C TRP 3.1 29.4 - - - +
178C LYS 3.7 4.5 - - - +
180C GLY* 1.3 82.9 - - - +
182C ALA* 1.3 63.2 + - - +
184C ALA* 3.5 0.5 + - - +
185C THR* 2.8 32.6 + - - +
476C GLU* 5.9 0.2 - - - +
477C LEU 5.9 1.6 - - - +
481C GLY* 4.0 10.3 - - - +
482C LEU* 4.1 4.7 - - + -
485C TYR* 3.9 25.5 - - + +
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Residues in contact with ALA 182 (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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162C CYS* 5.2 0.2 - - - -
164C GLN* 3.6 17.3 - - - +
178C LYS 3.2 17.3 - - - +
179C LEU 3.4 1.7 + - - +
180C GLY 3.4 0.6 - - - -
181C PRO* 1.3 82.1 - - - +
183C LEU* 1.3 59.2 + - - +
185C THR* 3.3 8.7 + - - -
187C ASN* 2.9 32.1 + - + +
189C VAL* 4.0 17.5 - - + -
485C TYR* 3.7 22.8 - - + -
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Residues in contact with LEU 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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76C TRP* 3.5 22.2 - - + -
84C ARG* 3.5 6.8 + - - +
88C LEU* 4.2 19.1 - - + -
91C LEU* 5.4 3.1 - - + -
179C LEU* 2.9 39.5 + - + +
182C ALA* 1.3 69.2 - - - +
184C ALA* 1.3 61.5 + - - +
185C THR 3.1 2.2 - - - -
186C GLY 2.9 16.6 + - - -
187C ASN 3.8 10.8 - - - +
189C VAL* 4.4 8.1 - - + -
208C ILE* 5.7 0.7 - - + -
213C PHE* 3.8 25.4 - - + -
217C VAL* 3.7 30.3 - - + +
218C VAL* 4.0 22.2 - - + -
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Residues in contact with ALA 184 (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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84C ARG* 3.0 23.3 + - - +
88C LEU* 3.8 9.8 - - + +
132C TYR* 3.4 32.8 - - + +
135C TRP* 4.7 3.8 - - + -
136C ALA* 3.4 23.2 - - - +
180C GLY 3.0 19.3 + - - +
181C PRO* 3.9 6.5 - - + +
182C ALA 3.5 0.2 - - - -
183C LEU* 1.3 76.0 - - - +
185C THR* 1.3 58.8 + - - +
482C LEU* 4.9 2.9 - - + -
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Residues in contact with THR 185 (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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500B SER* 5.4 0.2 - - - -
84C ARG* 3.9 9.5 + - - +
135C TRP 6.1 0.7 - - - +
139C TYR* 4.4 11.7 - - + -
156C HIS 5.7 0.3 - - - +
158C PRO* 3.1 24.9 - - - +
181C PRO 2.8 18.6 + - - +
182C ALA 3.3 0.2 + - - -
183C LEU 3.1 0.2 - - - -
184C ALA* 1.3 78.0 - - + +
186C GLY* 1.3 57.0 + - - +
187C ASN* 2.9 23.3 + - - -
482C LEU* 3.8 32.1 - - + +
485C TYR* 3.5 5.1 - - + +
486C THR* 3.9 22.9 - - - +
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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
------------------------------------------------------------
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