Contacts of the helix formed by residues 178 - 194 (chain C) in PDB entry 1Z83
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 SER 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C GLY* 1.3 73.9 - - - -
179C VAL* 1.3 66.6 + - - +
180C ASP* 3.8 4.9 + - - +
181C SER* 2.7 42.8 + - - -
182C VAL* 3.0 12.1 + - - +
633C AP5 3.8 3.6 - - - -
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 4.0 23.6 - - + -
24C GLN* 3.1 21.8 + - - +
27C LYS* 3.5 31.2 - - + +
178C SER* 1.3 73.5 - - - +
180C ASP* 1.3 64.2 + - - +
182C VAL 3.4 0.2 + - - -
183C PHE* 2.9 24.1 + - - +
633C AP5 3.7 27.0 + - + +
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Residues in contact with ASP 180 (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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27C LYS* 3.2 29.8 + - - -
178C SER* 3.2 4.9 + - - +
179C VAL* 1.3 78.5 - - - +
181C SER* 1.3 61.3 + - - +
183C PHE* 3.8 5.5 - - - +
184C SER* 2.9 28.8 + - - -
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU 4.3 2.1 + - - -
177C GLY* 3.6 6.6 - - - -
178C SER* 2.7 44.0 + - - -
180C ASP* 1.3 78.8 - - - +
182C VAL* 1.3 61.8 + - - +
184C SER* 3.5 16.2 - - - -
185C GLN* 3.6 16.5 + - - +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.6 32.1 - - + +
118C VAL* 5.3 0.7 - - + -
173C VAL* 4.4 14.4 - - + -
174C ASN 3.9 19.7 - - - +
175C ALA* 3.9 26.0 - - + +
176C GLU 3.9 9.9 - - - +
177C GLY 4.2 3.8 - - - +
178C SER 3.0 15.3 + - - +
179C VAL 3.7 1.1 - - - +
181C SER* 1.3 77.6 - - - +
183C PHE* 1.3 61.3 + - - +
185C GLN* 3.1 22.6 + - - +
186C VAL* 3.2 11.3 + - + +
633C AP5 4.3 4.9 - - - +
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Residues in contact with PHE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.2 22.6 + - - +
27C LYS* 3.5 58.1 - - + -
28C ILE* 3.7 21.3 - - + -
31C LYS* 3.9 19.5 - - + -
32C TYR* 4.3 3.1 - + - -
179C VAL 2.9 16.0 + - - +
180C ASP* 4.0 4.9 - - - +
182C VAL* 1.3 72.3 - - - +
184C SER* 1.3 66.8 + - - +
186C VAL* 3.2 11.7 + - + -
187C CYS* 2.8 53.4 + - - -
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Residues in contact with SER 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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180C ASP 2.9 15.2 + - - -
181C SER* 3.5 14.4 - - - -
182C VAL 3.3 0.2 - - - -
183C PHE* 1.3 77.1 - - - +
185C GLN* 1.3 61.6 + - - +
187C CYS* 3.3 7.2 + - - +
188C THR* 3.3 22.6 + - - -
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Residues in contact with GLN 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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172C LYS 4.8 1.3 - - - +
173C VAL* 3.7 16.5 - - + +
174C ASN* 2.9 53.1 + - - +
176C GLU 5.0 2.0 + - - -
181C SER* 3.6 18.9 + - - +
182C VAL* 3.1 12.0 + - - +
184C SER* 1.3 73.2 - - - +
186C VAL* 1.3 65.9 + - - +
188C THR* 3.2 17.9 + - - -
189C HIS* 3.4 19.6 + - + +
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Residues in contact with VAL 186 (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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24C GLN* 3.9 21.1 - - + +
28C ILE* 3.8 34.8 - - + -
116C LEU* 4.1 17.3 - - + -
118C VAL* 6.0 0.9 - - + -
173C VAL* 4.0 25.3 - - + +
182C VAL* 3.5 13.2 - - + +
183C PHE* 3.2 15.6 + - + +
185C GLN* 1.3 77.5 - - - +
187C CYS* 1.3 61.5 - - - +
189C HIS* 3.3 6.9 + - - +
190C LEU* 3.0 28.5 + - + +
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Residues in contact with CYS 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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31C LYS* 2.8 33.7 - - - +
32C TYR* 3.5 8.3 - - - -
183C PHE* 2.8 57.9 + - - +
184C SER* 3.7 7.9 - - - +
185C GLN 3.3 0.2 - - - -
186C VAL* 1.3 69.1 - - - +
188C THR* 1.3 67.7 + - - +
190C LEU* 4.6 0.4 - - - -
191C ASP* 2.8 33.9 + - - +
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Residues in contact with THR 188 (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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184C SER* 3.3 12.5 + - - -
185C GLN* 3.2 12.8 + - - -
187C CYS* 1.3 80.0 - - - +
189C HIS* 1.3 69.8 + - + +
191C ASP* 3.9 6.0 - - - +
192C ALA* 3.3 19.9 + - - +
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Residues in contact with HIS 189 (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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114C LEU* 4.8 7.8 - - + +
116C LEU* 4.5 7.0 - - + -
171C ARG* 3.6 48.3 + - + +
172C LYS 3.2 26.0 + - - -
173C VAL* 3.7 18.3 - - + +
185C GLN* 3.4 19.3 + - - +
186C VAL* 3.3 5.7 + - - +
187C CYS 3.2 0.6 - - - -
188C THR* 1.3 86.9 - - + +
190C LEU* 1.3 63.5 + - + +
192C ALA* 3.3 7.6 + - - +
193C LEU* 3.2 21.1 + - - +
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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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11C ILE* 3.8 31.0 - - + -
28C ILE* 3.7 31.4 - - + -
32C TYR* 3.4 45.5 - - + +
34C TYR* 6.0 0.4 - - + -
91C LEU* 5.6 0.2 - - + -
114C LEU* 4.4 13.0 - - + -
116C LEU* 5.5 5.6 - - + -
186C VAL* 3.0 25.3 + - + +
189C HIS* 1.3 76.8 - - + +
191C ASP* 1.3 66.6 + - - +
193C LEU* 3.3 4.9 + - + +
194C LEU* 3.2 36.6 + - + +
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Residues in contact with ASP 191 (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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31C LYS* 4.1 9.4 + - - -
32C TYR* 2.7 32.1 + - - -
187C CYS* 2.8 22.9 + - - +
188C THR* 3.9 5.1 - - - +
190C LEU* 1.3 75.8 - - - +
192C ALA* 1.3 61.6 + - - +
194C LEU* 3.3 20.6 - - - +
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Residues in contact with ALA 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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3B GLU* 4.8 27.4 - - + +
171C ARG* 6.1 2.7 - - - +
188C THR* 3.3 12.3 + - + +
189C HIS* 3.5 11.2 - - - +
190C LEU 3.2 0.6 - - - -
191C ASP* 1.3 80.8 - - - +
193C LEU* 1.3 60.9 + - - +
194C LEU 3.6 1.9 + - - +
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Residues in contact with LEU 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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7B LYS* 4.9 11.8 - - - +
9C ASN* 5.8 0.8 + - - +
11C ILE* 6.3 1.3 - - + -
113C THR* 6.1 4.3 - - + -
114C LEU* 4.7 23.3 - - + -
189C HIS 3.2 10.2 + - - +
190C LEU* 3.7 12.3 - - + +
191C ASP 3.3 0.4 - - - -
192C ALA* 1.3 82.4 - - - +
194C LEU* 1.3 68.8 + - + +
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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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9C ASN* 3.7 15.3 - - - +
32C TYR* 3.9 28.9 - - + -
34C TYR* 3.3 36.3 - - + +
190C LEU* 3.2 26.4 + - + +
191C ASP* 3.3 15.5 + - - +
192C ALA 3.4 2.5 - - - +
193C LEU* 1.3 89.8 - - + +
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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