Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 1TF6
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 TRP 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.3 53.8 - + + +
176A THR* 1.3 75.7 - - + +
178A THR* 1.3 57.6 + - + +
180A TYR* 2.6 38.5 + + - -
181A LEU* 2.5 78.7 + - + +
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Residues in contact with THR 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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176A THR* 4.4 11.1 - - + -
177A TRP* 1.3 82.8 - - + +
179A LEU* 1.3 85.4 + - - +
181A LEU* 3.9 8.6 + - - +
182A LYS* 2.9 32.5 + - - +
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Residues in contact with LEU 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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172A PHE* 5.2 5.6 - - + -
175A LYS* 3.4 23.1 - - + +
176A THR* 2.8 40.1 + - - +
178A THR* 1.3 91.2 - - - +
180A TYR* 1.3 66.3 + - - +
182A LYS* 3.4 25.5 - - - +
183A HIS* 3.5 17.3 + - - +
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Residues in contact with TYR 180 (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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162A TYR* 3.3 41.5 - + + +
163A PRO 5.0 1.1 - - - -
164A CYS* 4.8 13.5 - - + -
172A PHE* 5.3 0.7 - - - -
174A GLY* 4.7 8.9 - - - -
176A THR 2.4 22.8 + - - +
177A TRP* 2.6 65.1 + + - +
179A LEU* 1.3 68.8 - - - +
181A LEU* 1.3 87.0 + - + +
183A HIS* 3.0 23.1 + - + +
184A VAL* 3.5 20.2 + - + +
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Residues in contact with LEU 181 (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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177A TRP* 2.5 53.2 + - + +
178A THR* 3.9 9.9 - - - +
180A TYR* 1.3 88.2 - - + +
182A LYS* 1.3 55.0 + - + +
184A VAL* 2.6 35.4 + - + +
185A ALA* 3.0 13.3 + - + +
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Residues in contact with LYS 182 (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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178A THR* 2.9 26.7 + - - +
179A LEU* 3.4 33.2 - - - +
181A LEU* 1.3 76.9 - - + +
183A HIS* 1.3 62.5 + - - +
184A VAL 2.9 0.5 + - - -
185A ALA* 4.3 4.5 - - - +
186A GLU* 2.5 55.3 + - + +
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Residues in contact with HIS 183 (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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164A CYS* 3.6 10.5 - - + +
170A CYS* 3.0 11.0 - - - -
172A PHE* 3.0 51.3 + + + +
179A LEU 3.5 7.2 + - - +
180A TYR* 3.0 17.3 + - + +
181A LEU 3.0 0.2 + - - -
182A LYS* 1.3 77.2 - - - +
184A VAL* 1.3 56.4 + - - +
186A GLU* 5.2 0.4 - - - -
187A CYS* 3.1 29.6 - - + +
188A HIS* 3.1 26.4 + + - -
206A ZN 2.0 39.7 - - - -
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Residues in contact with VAL 184 (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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164A CYS* 4.8 2.9 - - + -
180A TYR* 3.5 32.8 - - + +
181A LEU* 2.6 22.1 + - + +
183A HIS* 1.3 71.5 - - + +
185A ALA* 1.3 56.8 + - - +
187A CYS 2.7 25.8 - - - +
188A HIS* 2.9 43.2 - - + +
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Residues in contact with ALA 185 (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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181A LEU* 3.0 11.9 + - + +
182A LYS* 4.0 6.1 - - - +
184A VAL* 1.3 73.5 - - - +
186A GLU* 1.3 68.5 + - - +
187A CYS 2.7 13.8 + - - +
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Residues in contact with GLU 186 (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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182A LYS* 2.5 36.8 + - + +
183A HIS* 5.2 0.4 - - - -
185A ALA* 1.3 75.7 - - - +
187A CYS* 1.3 58.1 + - + +
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Residues in contact with CYS 187 (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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182A LYS 3.3 2.8 + - - -
183A HIS* 3.1 24.5 - - + +
184A VAL 2.7 15.9 - - - +
185A ALA 2.7 12.1 + - - +
186A GLU* 1.3 79.9 - - + +
188A HIS* 1.3 72.0 + - + +
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Residues in contact with HIS 188 (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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164A CYS* 2.8 22.1 - - + +
165A LYS 4.9 0.7 - - - -
166A LYS* 3.4 31.9 - - + +
170A CYS* 4.6 2.2 - - - -
183A HIS* 3.1 22.7 - + - -
184A VAL* 2.9 46.3 - - + +
187A CYS* 1.3 82.6 - - - +
206A ZN 2.2 36.0 - - - -
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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