Contacts of the helix formed by residues 167 - 179 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A CYS* 3.6 10.9 - - - -
165A VAL* 3.5 7.6 - - - +
166A THR* 1.3 83.9 + - - +
168A LYS* 1.3 65.5 + - - +
169A GLU* 3.2 17.1 + - - +
170A ASP* 2.8 33.0 + - - +
171A ALA* 3.2 15.8 + - - +
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR 5.2 0.9 - - - +
116A GLU* 2.8 59.9 + - + +
117A CYS* 3.9 3.8 - - - -
167A SER* 1.3 75.3 - - - +
169A GLU* 1.3 69.1 + - - +
171A ALA* 3.2 4.7 + - + +
172A ARG* 3.1 54.1 + - - +
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER* 3.1 12.6 - - - +
168A LYS* 1.3 94.4 + - - +
170A ASP* 1.3 66.0 + - - +
172A ARG* 3.3 35.6 + - - +
173A TYR* 3.0 23.3 + - - +
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN 5.0 2.5 - - - +
142A VAL* 3.8 37.8 - - + +
143A VAL* 4.4 3.5 + - - +
165A VAL* 4.0 9.4 - - + -
166A THR* 3.5 17.9 + - - -
167A SER* 2.8 28.3 + - - +
169A GLU* 1.3 72.3 - - - +
171A ALA* 1.3 60.0 + - - +
173A TYR* 3.3 8.7 + - - +
174A CYS* 2.8 32.9 + - - -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU 4.1 14.4 - - - +
117A CYS* 4.6 4.7 - - - -
118A THR 5.0 1.6 - - - +
119A LEU* 3.6 18.5 - - + +
165A VAL* 3.8 15.2 - - + +
167A SER 3.2 11.4 + - - +
168A LYS 3.4 9.9 - - - +
169A GLU 3.2 0.2 - - - -
170A ASP* 1.3 76.4 - - - +
172A ARG* 1.3 64.0 + - + +
174A CYS* 3.2 12.7 + - - +
175A VAL* 3.3 17.5 + - - +
192A VAL* 4.8 11.2 - - + -
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LYS* 3.1 51.6 + - - +
169A GLU* 3.7 38.5 + - - +
171A ALA* 1.3 78.3 - - - +
173A TYR* 1.3 61.5 + - - +
175A VAL* 3.2 8.8 + - - +
176A GLU* 3.1 27.6 + - - +
192A VAL* 5.1 10.5 - - + -
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.5 29.7 + - + +
142A VAL* 4.0 17.5 - - + -
169A GLU 3.0 16.4 + - - +
170A ASP* 3.6 9.6 - - - +
172A ARG* 1.3 73.7 - - - +
174A CYS* 1.3 64.3 + - - +
175A VAL 3.3 0.2 + - - -
176A GLU* 3.3 24.4 + - - +
177A LYS* 3.0 62.6 + - + +
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Residues in contact with CYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.6 29.4 - - + -
137A LEU* 4.2 13.5 - - - -
140A ILE* 4.2 11.9 - - - -
142A VAL* 3.8 31.4 - - - -
165A VAL* 4.6 0.7 - - - -
170A ASP 2.8 22.1 + - - -
171A ALA 3.2 8.0 + - - +
173A TYR* 1.3 72.0 - - - +
175A VAL* 1.3 54.5 + - - +
178A LEU* 2.7 45.5 + - + +
190A THR* 4.4 2.7 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.9 7.6 - - + -
171A ALA 3.3 12.1 + - - +
172A ARG* 3.2 9.5 + - - +
174A CYS* 1.3 76.0 - - - +
176A GLU* 1.3 62.7 + - + +
179A ASN* 2.9 38.4 + - + +
190A THR* 3.9 18.4 - - + +
191A LYS* 3.9 11.0 - - + -
192A VAL* 3.8 32.5 - - + +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 3.1 16.1 + - - +
173A TYR* 3.7 28.1 - - - +
174A CYS 3.3 0.2 - - - -
175A VAL* 1.3 84.5 - - + +
177A LYS* 1.3 65.6 + - + +
179A ASN 4.7 4.3 - - - +
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.9 32.5 - - + -
173A TYR* 3.0 61.9 + - + +
176A GLU* 1.3 83.9 - - + +
178A LEU* 1.3 68.4 + - + +
179A ASN 3.6 2.5 - - - +
181A LEU* 4.4 14.4 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 4.3 10.8 - - + -
136A LEU* 4.0 18.2 - - + +
137A LEU* 3.8 28.9 - - + -
140A ILE* 4.0 33.2 - - + -
174A CYS* 2.7 31.5 + - + +
177A LYS* 1.3 79.7 - - + +
179A ASN* 1.3 63.7 + - - +
180A GLY 3.2 0.5 + - - -
181A LEU* 3.1 39.8 + - + +
188A LEU* 3.4 15.6 - - + +
190A THR* 3.6 12.8 - - - +
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A CYS 3.9 0.8 + - - -
175A VAL* 2.9 26.7 + - + +
176A GLU 4.7 4.0 - - - +
177A LYS 4.6 2.9 - - - +
178A LEU* 1.3 78.2 - - - +
180A GLY* 1.3 62.8 + - - +
181A LEU 3.5 0.2 + - - -
188A LEU 3.8 0.5 - - - +
189A VAL* 3.4 13.9 - - - +
190A THR* 3.0 45.1 + - - +
191A LYS* 5.2 1.3 - - - +
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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