Contacts of the helix formed by residues 178 - 189 (chain H) in PDB entry 4GTU
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 PRO 178 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138H SER* 5.6 0.2 - - - +
175H ASP 4.2 4.4 - - - +
176H ALA 3.3 12.3 - - - +
177H PHE* 1.3 84.6 - - - +
179H ASN* 1.3 61.9 + - + +
181H LYS* 2.9 33.2 + - + +
182H ASP* 3.0 14.2 + - - +
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Residues in contact with ASN 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H SER* 2.5 37.0 + - - +
141H LEU* 3.5 18.2 - - + +
142H GLY* 2.9 44.4 + - - +
177H PHE* 3.7 6.7 + - - +
178H PRO* 1.3 81.0 - - + +
180H LEU* 1.3 65.9 + - - +
182H ASP* 3.3 9.3 + - - +
183H PHE 3.1 22.2 + - - -
186H ARG* 3.7 7.2 + - - +
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Residues in contact with LEU 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H MET* 3.8 45.1 - - + +
137H PHE* 4.1 14.4 - - + +
138H SER* 3.9 18.2 - - - +
141H LEU* 3.6 24.2 - - + -
147H PHE* 4.5 8.1 - - + -
163H LEU* 4.2 13.1 - - + +
174H LEU* 3.7 13.4 - - + +
177H PHE* 2.9 21.7 + - + +
179H ASN* 1.3 87.3 - - - +
181H LYS* 1.3 66.0 + - - +
183H PHE* 3.6 3.2 + - - +
184H ILE* 3.5 26.0 + - - +
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Residues in contact with LYS 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H LEU* 3.4 46.0 - - + +
175H ASP* 3.9 24.4 + - - +
177H PHE 3.6 12.8 - - - +
178H PRO* 2.9 19.0 + - + +
180H LEU* 1.3 78.4 - - - +
182H ASP* 1.3 61.9 + - - +
184H ILE* 3.1 17.2 + - - +
185H SER* 3.2 10.1 + - - -
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Residues in contact with ASP 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H PRO* 3.0 17.6 + - - +
179H ASN* 3.3 8.2 + - - +
181H LYS* 1.3 77.7 - - - +
183H PHE* 1.3 56.6 + - - +
185H SER* 2.9 13.8 + - - -
186H ARG* 2.8 56.6 + - + +
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Residues in contact with PHE 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H LEU* 3.8 21.3 - - + -
145H PRO 3.5 18.4 - - - -
146H TRP* 3.5 13.0 - + - -
147H PHE* 4.1 17.0 - + - -
156H ASP* 3.1 55.2 - - + -
159H ALA* 4.5 5.8 - - + -
160H TYR* 4.2 20.4 - - + -
163H LEU* 4.1 17.5 - - + -
179H ASN 3.1 16.7 + - - +
180H LEU* 3.7 5.6 - - - +
181H LYS 3.3 0.4 - - - -
182H ASP* 1.3 76.5 - - - +
184H ILE* 1.3 59.3 + - + +
186H ARG* 3.3 10.2 - - - +
187H PHE* 2.9 33.6 + - + +
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Residues in contact with ILE 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H TYR* 3.5 26.2 - - + -
163H LEU* 3.8 30.3 - - + -
167H ARG* 3.4 32.8 - - - +
174H LEU* 3.3 34.5 - - + -
180H LEU 3.5 11.4 + - - +
181H LYS* 3.1 8.8 + - - +
183H PHE* 1.3 75.2 - - + +
185H SER* 1.3 64.5 + - - +
187H PHE 3.6 3.3 - - - +
188H GLU* 3.3 27.0 - - - +
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Residues in contact with SER 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H LYS 3.2 8.4 + - - -
182H ASP* 2.9 20.8 + - - -
184H ILE* 1.3 77.1 - - - +
186H ARG* 1.3 66.6 + - - +
188H GLU* 3.8 3.3 - - - +
189H GLY* 3.3 18.7 + - - -
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Residues in contact with ARG 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H LEU* 4.8 3.6 - - - +
142H GLY 5.9 0.8 + - - -
143H LYS 5.6 2.4 + - - -
144H ARG 4.7 4.6 + - - -
145H PRO* 3.7 40.7 + - - +
146H TRP* 4.3 17.8 - - + -
179H ASN* 3.7 10.3 + - - +
182H ASP* 2.8 34.0 + - + +
183H PHE* 3.3 27.4 - - - +
185H SER* 1.3 80.6 - - - +
187H PHE* 1.3 57.0 + - - +
188H GLU 2.9 7.1 + - - -
189H GLY* 3.4 7.7 + - - -
190H LEU* 3.7 15.2 + - - +
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Residues in contact with PHE 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.3 26.2 - - + -
146H TRP* 3.6 27.1 - + + -
152H ILE* 4.2 3.1 - - + -
156H ASP* 4.5 9.9 - - + -
157H PHE* 3.4 55.0 - + - -
160H TYR* 3.6 38.5 - + + -
183H PHE* 2.9 25.4 + + + +
184H ILE 3.6 4.3 - - - +
186H ARG* 1.3 73.8 - - - +
188H GLU* 1.3 62.4 + - - +
190H LEU* 4.0 18.2 - - + -
193H ILE* 4.5 13.6 - - + +
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Residues in contact with GLU 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H TYR* 2.9 24.6 + - - +
167H ARG* 4.2 4.3 + - - -
184H ILE* 3.3 22.9 - - - +
185H SER* 3.8 4.3 - - - +
186H ARG 2.9 2.4 + - - -
187H PHE* 1.3 75.3 - - - +
189H GLY* 1.3 62.7 + - - +
190H LEU* 2.9 8.6 + - - +
193H ILE* 4.1 9.3 - - - +
194H SER* 3.0 27.0 + - - -
197H MET* 3.8 33.2 - - + +
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Residues in contact with GLY 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H SER 3.3 13.1 + - - -
186H ARG 3.4 3.3 + - - -
188H GLU* 1.3 78.8 - - - +
190H LEU* 1.4 56.4 + - - +
191H GLU* 2.8 11.4 + - - -
194H SER* 3.4 9.3 + - - -
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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