Contacts of the helix formed by residues 167 - 179 (chain C) in PDB entry 5TF6
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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C CYS* 3.5 15.2 - - - -
165C VAL* 3.5 9.2 - - - +
166C THR* 1.3 81.5 + - - +
168C LYS* 1.3 59.2 + - - +
169C GLU* 3.4 18.6 + - - +
170C ASP* 2.9 29.2 + - - +
171C ALA* 3.1 20.1 + - - +
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Residues in contact with LYS 168 (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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115C THR 5.1 1.6 - - - +
116C GLU* 2.7 64.7 + - + +
117C CYS* 3.8 4.0 - - - -
167C SER* 1.3 75.1 - - - +
169C GLU* 1.3 68.3 + - - +
171C ALA* 3.2 3.2 + - - +
172C ARG* 3.1 25.9 + - + +
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Residues in contact with GLU 169 (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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167C SER* 3.5 20.0 - - - +
168C LYS* 1.3 86.0 + - + +
170C ASP* 1.3 67.6 + - - +
172C ARG* 3.2 8.7 + - - +
173C TYR* 2.9 24.0 + - - +
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Residues in contact with ASP 170 (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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77C LYS* 5.1 9.7 + - - -
141C ASN 4.7 3.0 - - - +
142C VAL* 3.8 36.8 - - + +
143C VAL* 4.5 3.1 + - - +
165C VAL* 4.1 8.7 - - + -
166C THR* 3.6 16.4 + - - -
167C SER* 2.9 23.5 + - - +
169C GLU* 1.3 79.0 - - - +
171C ALA* 1.3 61.2 + - - +
173C TYR* 3.4 7.8 + - - +
174C CYS* 3.0 27.9 + - - -
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Residues in contact with ALA 171 (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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116C GLU 4.1 13.5 - - - +
117C CYS* 4.7 4.0 - - - -
118C THR 5.2 1.6 - - - +
119C LEU* 3.6 18.7 - - + +
165C VAL* 3.8 13.9 - - + +
167C SER 3.1 13.7 + - - +
168C LYS 3.4 10.3 - - - +
169C GLU 3.1 0.4 - - - -
170C ASP* 1.3 77.7 - - - +
172C ARG* 1.3 61.8 + - - +
174C CYS* 3.2 6.7 + - - +
175C VAL* 3.1 25.9 + - - +
192C VAL* 5.0 10.1 - - + -
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Residues in contact with ARG 172 (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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168C LYS* 3.1 11.0 + - + +
169C GLU* 3.2 11.0 + - - +
171C ALA* 1.3 77.0 - - - +
173C TYR* 1.3 66.5 + - - +
175C VAL* 3.1 23.0 + - - +
176C GLU* 1.6 54.3 + - + +
192C VAL* 5.4 4.0 - - - +
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Residues in contact with TYR 173 (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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140C ILE* 3.5 34.3 - - + +
141C ASN* 6.1 0.2 - - - -
142C VAL* 4.2 12.8 - - + -
169C GLU 2.9 15.8 + - - +
170C ASP* 3.8 8.1 - - - +
172C ARG* 1.3 77.7 - - - +
174C CYS* 1.3 64.5 + - - +
176C GLU* 3.0 10.9 + - + +
177C LYS* 2.8 66.6 + - + +
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Residues in contact with CYS 174 (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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119C LEU* 3.7 29.2 - - + -
137C LEU* 4.1 13.7 - - - -
140C ILE* 4.3 11.0 - - - -
142C VAL* 3.8 31.9 - - - -
165C VAL* 4.4 0.9 - - - -
170C ASP 3.0 21.0 + - - -
171C ALA 3.5 7.4 - - - +
172C ARG 3.2 0.2 - - - -
173C TYR* 1.3 75.6 - - - +
175C VAL* 1.3 57.9 + - - +
178C LEU* 2.8 41.5 + - + +
179C ASN 3.9 0.2 + - - -
190C THR* 4.1 3.0 - - + +
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 4.1 7.6 - - + -
171C ALA 3.1 14.5 + - - +
172C ARG* 3.1 24.4 + - - +
174C CYS* 1.3 71.4 - - - +
176C GLU* 1.3 67.3 + - - +
179C ASN* 3.2 29.9 + - + +
190C THR* 3.6 23.8 - - - +
191C LYS* 5.3 0.7 - - - -
192C VAL* 3.9 35.7 - - + +
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Residues in contact with GLU 176 (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 ARG* 1.6 64.8 + - + +
173C TYR* 3.0 18.8 + - + +
175C VAL* 1.3 78.5 - - - +
177C LYS* 1.3 62.7 + - + +
179C ASN 4.6 5.2 - - - +
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Residues in contact with LYS 177 (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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140C ILE* 4.0 24.9 - - + -
173C TYR* 2.8 67.0 + - + +
176C GLU* 1.3 78.1 - - + +
178C LEU* 1.3 64.8 + - + +
179C ASN 3.7 2.5 - - - +
181C LEU* 4.3 13.0 + - - +
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Residues in contact with LEU 178 (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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121C MET* 4.1 12.8 - - + -
136C LEU* 4.1 20.4 - - + +
137C LEU* 3.7 30.5 - - + -
140C ILE* 4.0 29.4 - - + -
174C CYS* 2.8 30.1 + - + +
177C LYS* 1.3 80.3 - - + +
179C ASN* 1.3 65.3 + - - +
180C GLY 3.4 0.5 + - - -
181C LEU* 3.2 32.9 + - + +
188C LEU* 3.3 21.6 - - + +
190C THR* 3.6 11.2 - - + +
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Residues in contact with ASN 179 (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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174C CYS 3.9 1.4 + - - -
175C VAL* 3.2 25.8 + - + +
176C GLU 4.6 4.9 - - - +
177C LYS 4.6 1.7 - - - +
178C LEU* 1.3 78.4 + - - +
180C GLY* 1.3 64.1 + - - +
181C LEU 3.5 0.3 + - - -
188C LEU 3.5 1.6 - - - +
189C VAL* 3.4 14.2 - - - +
190C THR* 3.0 41.5 + - - +
191C LYS* 5.6 3.2 - - - +
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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