Contacts of the helix formed by residues 183 - 194 (chain C) in PDB entry 1T4P
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 ASP 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C ASN* 3.1 19.4 + - - +
136C SER* 4.8 12.2 + - - +
181C ASP* 4.9 6.6 - - - +
182C VAL* 1.3 76.1 - - - +
184C PRO* 1.3 77.5 - - + +
185C GLY 4.4 2.9 - - - +
186C GLU* 3.1 22.6 + - + +
187C HIS* 2.8 20.8 + - - +
1002C 2BH 3.0 29.3 + - - -
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Residues in contact with PRO 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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311B ASN 3.2 22.6 - - - +
312B HIS* 3.6 5.4 - - - +
313B LYS* 6.6 0.2 - - - -
318B TYR* 3.9 23.8 - - + +
182C VAL 3.8 1.8 - - - +
183C ASP* 1.3 87.7 - - + +
185C GLY* 1.3 63.4 + - - +
187C HIS* 3.2 2.9 + - - +
188C TYR* 2.9 21.8 + - - +
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Residues in contact with GLY 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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318B TYR* 3.5 24.0 - - - -
130C ASN* 5.1 0.9 - - - -
134C THR* 4.9 15.0 - - - -
183C ASP* 3.2 3.0 - - - +
184C PRO* 1.3 78.8 - - - +
186C GLU* 1.3 63.1 + - - +
188C TYR* 2.9 15.1 + - - +
189C ILE* 2.9 20.2 + - - +
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Residues in contact with GLU 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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126C HIS* 5.4 1.4 - - - +
127C THR* 2.9 29.0 + - - +
128C ASP* 3.1 9.9 + - - -
129C ILE* 2.9 33.3 + - + -
130C ASN* 3.5 34.8 + - - +
142C GLY 4.0 0.2 - - - +
181C ASP 4.7 1.2 - - - +
182C VAL* 3.5 9.9 - - + -
183C ASP* 3.1 34.3 + - + +
185C GLY* 1.3 73.3 - - - +
187C HIS* 1.3 64.6 + - - +
189C ILE* 3.1 8.8 + - - +
190C ILE* 3.0 26.9 + - - +
1002C 2BH 3.9 8.0 + - - +
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Residues in contact with HIS 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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307B LYS* 6.2 0.4 - - + -
309B GLU* 3.0 49.5 + - - -
310B GLY 3.2 19.8 + - - -
311B ASN* 3.5 18.9 - - - +
312B HIS* 3.1 27.6 + + - -
182C VAL* 3.6 8.7 - - + +
183C ASP 2.8 16.5 + - - +
184C PRO 3.6 7.4 - - - +
186C GLU* 1.3 72.9 - - - +
188C TYR* 1.3 61.5 + - - +
190C ILE* 3.3 10.6 - - + +
191C LYS* 2.9 58.7 + - + +
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Residues in contact with TYR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 3.7 33.0 - + + -
316B THR 3.5 12.6 - - - -
317B ASP* 2.5 29.2 + - - +
318B TYR* 3.4 45.3 - + + -
319B LEU* 4.0 22.2 - - + -
184C PRO 2.9 11.9 + - - +
185C GLY 2.9 10.4 + - - +
187C HIS* 1.3 78.7 + - - +
189C ILE* 1.3 58.2 + - + +
191C LYS* 3.6 1.7 - - + +
192C THR* 2.8 62.9 + - - +
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Residues in contact with ILE 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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318B TYR* 5.9 0.7 - - + -
319B LEU* 4.5 20.4 - - + -
129C ILE* 3.4 48.9 - - + +
131C THR* 3.9 23.3 - - + +
134C THR* 4.9 7.6 - - + +
152C LEU* 4.2 9.6 - - + -
185C GLY 2.9 19.5 + - - +
186C GLU* 3.4 11.0 - - - +
188C TYR* 1.3 82.5 - - + +
190C ILE* 1.3 58.6 + - - +
192C THR* 3.3 3.9 + - - -
193C LEU* 2.9 47.9 + - + +
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Residues in contact with ILE 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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309B GLU 4.2 15.7 - - - +
127C THR* 4.4 23.6 - - + -
129C ILE* 4.3 15.5 - - + -
176C TYR* 4.5 8.1 - - + -
179C LEU* 5.0 1.3 - - + -
182C VAL* 4.9 0.4 - - + -
186C GLU 3.0 16.3 + - - +
187C HIS* 3.3 23.8 - - + +
189C ILE* 1.3 71.7 - - - +
191C LYS* 1.3 69.6 + - + +
194C GLY* 3.2 17.3 + - - -
195C ILE* 3.2 44.0 + - + +
197C TYR* 4.7 28.4 - - + -
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Residues in contact with LYS 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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309B GLU* 3.6 9.4 + - - -
312B HIS* 4.3 13.9 - - + +
187C HIS* 2.9 55.0 + - + +
188C TYR 3.6 2.9 - - - +
190C ILE* 1.3 82.4 - - + +
192C THR* 1.3 64.1 + - - +
194C GLY* 3.4 9.4 + - - -
197C TYR* 3.4 27.8 + - + +
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Residues in contact with THR 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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319B LEU* 5.1 6.7 - - + -
188C TYR* 2.8 57.1 + - + +
189C ILE* 3.7 4.0 - - - -
191C LYS* 1.3 78.0 - - - +
193C LEU* 1.3 72.3 + - + +
194C GLY 3.5 0.9 + - - -
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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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319B LEU* 5.1 8.1 - - + -
149C LEU* 3.9 19.3 - - + -
151C GLU* 3.7 31.2 - - + +
152C LEU* 3.4 33.0 - - + -
171C ALA* 3.5 16.8 - - + +
172C LYS* 4.0 6.6 + - - -
189C ILE* 2.9 25.7 + - + +
192C THR* 1.3 91.1 - - + +
194C GLY* 1.3 62.5 + - - +
195C ILE* 3.4 11.7 + - + -
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Residues in contact with GLY 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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171C ALA* 4.9 0.4 - - - +
172C LYS* 3.5 19.5 + - - -
190C ILE 3.2 7.1 + - - -
191C LYS 3.4 6.1 + - - -
192C THR 3.3 4.9 + - - -
193C LEU* 1.3 78.5 - - - +
195C ILE* 1.3 64.7 + - - +
196C LYS* 3.6 2.1 + - - -
218C TYR* 4.3 5.0 + - - -
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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