Contacts of the helix formed by residues 157 - 166 (chain C) in PDB entry 3F22
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 THR 157 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C THR* 1.3 80.2 + - - +
158C ALA* 1.3 64.4 + - - +
159C HIS* 3.5 11.4 + - - +
160C ASP* 3.0 24.3 + - - +
161C LEU* 3.0 24.3 + - - +
192C PRO* 4.2 21.1 - - + -
193C PRO 4.0 11.9 - - - +
194C LEU* 3.6 22.7 - - + -
195C TRP* 4.3 1.6 - - - -
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Residues in contact with ALA 158 (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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157C THR* 1.3 72.9 - - - +
159C HIS* 1.3 58.4 + - - +
161C LEU* 3.2 2.0 + - - +
162C SER* 2.8 32.7 + - - -
169C LYS* 4.1 8.5 - - + -
172C ILE* 3.8 15.8 - - + +
173C ASN* 3.3 35.0 - - - +
176C LEU* 3.8 15.3 - - + -
192C PRO* 6.2 0.4 - - - +
193C PRO 4.7 1.0 + - - -
195C TRP* 4.0 9.6 - - - +
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Residues in contact with HIS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C THR* 3.6 10.2 + - - +
158C ALA* 1.3 80.3 - - - +
160C ASP* 1.3 64.4 + - - +
162C SER* 3.4 4.8 + - - -
163C GLY* 3.0 19.6 + - - -
169C LYS* 3.8 26.6 - - + +
192C PRO* 6.2 2.5 - - + -
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Residues in contact with ASP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C PHE* 4.0 14.9 - - - -
156C THR* 2.5 29.4 + - - +
157C THR* 3.0 15.8 + - - +
159C HIS* 1.3 77.9 + - - +
161C LEU* 1.3 58.3 + - - +
163C GLY* 3.1 3.1 + - - -
164C LYS* 2.9 58.6 + - - +
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Residues in contact with LEU 161 (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 ILE* 4.5 7.0 - - + -
146C PHE* 3.3 40.6 - - + -
147C LEU* 3.9 10.8 - - + -
156C THR* 3.5 22.4 - - + -
157C THR 3.0 15.1 + - - +
158C ALA 3.4 7.6 - - - +
160C ASP* 1.3 76.8 - - - +
162C SER* 1.3 57.9 + - - +
164C LYS* 3.8 2.4 - - - -
165C LEU* 2.9 49.2 + - + +
172C ILE* 3.8 11.7 - - + -
176C LEU* 3.8 37.7 - - + -
195C TRP* 5.0 2.5 - - + -
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Residues in contact with SER 162 (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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158C ALA 2.8 20.0 + - - -
159C HIS* 3.5 7.1 - - - -
161C LEU* 1.3 72.4 - - - +
163C GLY* 1.3 59.4 + - - +
166C GLY* 2.8 26.3 + - - -
167C THR 2.5 33.0 + - - -
168C PRO* 4.1 0.9 - - - +
169C LYS* 3.3 21.9 + - - +
172C ILE* 3.6 14.5 - - - +
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Residues in contact with GLY 163 (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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159C HIS 3.0 14.4 + - - -
160C ASP* 3.6 2.7 - - - -
162C SER* 1.3 79.5 + - - +
164C LYS* 1.3 62.0 + - - +
166C GLY* 3.4 10.8 + - - -
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Residues in contact with LYS 164 (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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142C ARG* 5.0 1.2 + - - -
146C PHE* 3.6 35.4 - - + -
160C ASP* 2.9 42.6 + - - +
161C LEU 4.1 2.2 - - - +
163C GLY* 1.3 76.4 - - - +
165C LEU* 1.3 63.0 + - + +
166C GLY 3.7 0.2 + - - -
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Residues in contact with LEU 165 (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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139C GLN* 5.1 1.6 - - - +
142C ARG* 2.2 71.3 + - + +
143C ILE* 3.9 38.1 - - + +
146C PHE* 4.0 24.2 - - + -
161C LEU* 2.9 27.4 + - + +
164C LYS* 1.3 79.6 - - - +
166C GLY* 1.3 62.5 + - - +
167C THR* 4.0 7.6 - - - +
172C ILE* 4.0 9.2 - - + -
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Residues in contact with GLY 166 (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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142C ARG* 4.7 0.5 + - - -
162C SER 2.8 12.7 + - - -
163C GLY* 3.4 9.5 + - - -
164C LYS 3.4 0.2 - - - -
165C LEU* 1.3 79.1 - - - +
167C THR* 1.3 57.9 + - - -
168C PRO* 4.5 1.7 - - - +
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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