Contacts of the helix formed by residues 199 - 207 (chain C) in PDB entry 5T0I
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 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.4 0.9 - - + -
151C ILE* 3.8 25.1 - - + +
154C LEU* 3.7 21.1 - - + -
157C GLN* 5.3 4.3 - - + +
158C ILE* 3.7 28.7 - - + +
161C ILE* 4.5 15.5 - - + -
188C LEU* 5.1 13.0 - - + -
195C GLY 2.9 18.4 + - - +
196C LYS 4.2 4.7 - - - +
197C THR 3.2 0.4 - - - -
198C LEU* 1.3 75.1 - - - +
200C ALA* 1.3 66.8 + - - +
201C ARG 3.5 0.2 - - - -
202C ALA* 3.2 11.4 + - + -
203C VAL* 3.3 31.6 + - + +
292C ILE* 5.1 2.4 - - + +
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Residues in contact with ALA 200 (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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196C LYS 3.8 3.0 + - - -
197C THR* 3.2 15.8 + - + +
199C LEU* 1.3 81.7 - - - +
201C ARG* 1.3 60.5 + - - +
203C VAL* 4.7 1.2 - - - +
204C ALA* 3.6 17.5 + - - +
211C PHE* 3.6 33.9 - - + -
245C ILE* 5.4 1.9 - - - +
247C PHE* 3.8 22.0 - - + -
292C ILE* 3.8 18.9 - - + +
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Residues in contact with ARG 201 (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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143C VAL* 5.3 3.8 - - + -
144C PRO 4.2 5.6 - - - +
145C ASP* 3.3 44.7 + - - +
146C SER* 3.5 6.6 - - - +
147C THR* 4.4 0.2 - - - -
197C THR 4.2 1.4 + - - +
198C LEU 4.0 2.6 + - - -
200C ALA* 1.3 76.7 - - - +
202C ALA* 1.3 57.1 + - - +
203C VAL 3.7 0.2 - - - -
204C ALA* 3.8 9.0 - - + -
205C HIS* 3.0 38.5 + - + +
209C CYS 6.0 0.2 - - - +
210C THR* 4.3 9.2 + - - +
211C PHE* 3.3 65.4 + - + +
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Residues in contact with ALA 202 (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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146C SER 3.1 13.4 + - - +
147C THR 3.5 19.1 - - - +
148C TYR* 3.9 13.8 + - + +
151C ILE* 3.7 15.5 - - + -
198C LEU 3.3 17.9 + - - +
199C LEU* 3.2 13.2 + - + +
200C ALA 3.2 1.0 - - - -
201C ARG* 1.3 73.9 - - - +
203C VAL* 1.3 68.8 + - - +
204C ALA 3.1 0.7 - - - -
205C HIS* 3.0 17.5 + - - +
206C HIS 3.7 3.6 + - - -
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Residues in contact with VAL 203 (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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148C TYR* 3.3 36.0 + - + +
158C ILE* 4.9 1.3 - - + -
161C ILE* 4.0 19.5 - - + -
162C LYS* 3.8 10.5 - - + -
165C ILE* 4.1 24.2 - - + -
166C GLU* 3.6 16.2 - - - +
199C LEU* 3.3 28.0 + - + +
200C ALA 4.8 1.1 - - - +
202C ALA* 1.3 75.4 - - - +
204C ALA* 1.3 54.8 + - - +
205C HIS 3.4 0.2 + - - -
206C HIS* 3.7 2.6 + - - +
207C THR* 2.2 34.5 + - - +
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Residues in contact with ALA 204 (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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165C ILE* 5.2 3.1 - - + +
200C ALA 3.6 18.7 + - - +
201C ARG* 4.1 9.0 - - + -
202C ALA 3.1 0.6 - - - -
203C VAL* 1.3 77.0 - - - +
205C HIS* 1.3 64.4 + - - +
207C THR* 3.4 5.8 + - - -
208C ASP 3.2 13.5 + - - -
209C CYS* 2.9 45.0 + - - +
211C PHE* 4.7 8.1 - - + -
245C ILE* 4.3 12.6 - - + -
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Residues in contact with HIS 205 (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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145C ASP* 6.3 1.5 - - + +
147C THR* 3.0 34.1 - - - +
201C ARG* 3.0 31.2 + - + +
202C ALA 3.0 7.3 + - - +
204C ALA* 1.3 76.8 - - - +
206C HIS* 1.3 68.1 + + - +
208C ASP* 3.2 22.0 + - - +
209C CYS 5.0 0.4 - - - -
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Residues in contact with HIS 206 (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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147C THR* 3.6 23.7 + - - -
148C TYR* 3.2 47.4 - + + +
149C GLU* 5.1 6.3 - - + +
166C GLU* 5.0 2.1 - - - +
170C LYS* 4.3 5.4 + - - -
202C ALA 3.7 2.6 + - - -
205C HIS* 1.3 82.9 - + - +
207C THR* 1.3 59.7 - - - +
208C ASP* 3.1 15.7 + - - +
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Residues in contact with THR 207 (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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165C ILE* 4.2 8.9 - - + +
166C GLU* 2.3 41.6 + - - +
169C VAL* 3.8 33.2 - - + +
170C LYS* 2.9 26.4 + - - +
203C VAL* 2.2 30.4 + - - +
204C ALA* 3.7 5.6 - - - -
205C HIS 3.2 0.6 - - - -
206C HIS* 1.3 74.7 - - - +
208C ASP* 1.3 62.0 + - - +
209C CYS* 3.1 19.1 + - - -
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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