Contacts of the helix formed by residues 160 - 165 (chain A) in PDB entry 1TDH
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 PRO 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ARG* 1.3 87.3 - - + +
161A ILE* 1.3 66.4 + - - +
163A GLU* 3.0 43.6 + - + +
164A ALA* 3.0 18.7 + - - +
190A PRO 3.6 3.1 - - - +
191A PHE* 3.6 44.0 - - + +
192A GLU 3.3 8.1 - - - +
288A LEU* 4.0 17.0 - - + +
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Residues in contact with ILE 161 (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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159A ARG 3.6 0.6 + - - -
160A PRO* 1.3 72.2 - - - +
162A CYS* 1.3 64.6 + - - +
164A ALA* 4.4 4.0 - - + +
165A LEU* 3.0 33.8 + - + +
171A PHE* 5.4 1.6 - - + -
183A LEU* 3.9 25.6 - - + -
188A ILE* 4.3 4.9 - - + -
189A PRO 3.3 19.7 - - - +
190A PRO* 3.2 15.7 - - + +
192A GLU* 2.8 16.1 + - + +
194A ALA* 3.8 29.1 - - + +
197A VAL* 4.4 8.5 - - + -
198A LEU* 4.7 7.9 - - + -
225A LEU* 3.6 26.5 - - + -
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Residues in contact with CYS 162 (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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160A PRO* 4.5 0.9 - - - -
161A ILE* 1.3 76.2 - - - +
163A GLU* 1.3 66.4 + - - +
165A LEU* 3.9 5.8 + - - +
166A LEU* 3.9 3.8 - - - +
179A ARG* 2.8 38.7 + - - +
183A LEU* 3.9 13.5 - - + -
190A PRO* 2.9 42.0 + - + +
191A PHE* 3.8 31.0 - - - -
273A ASP* 4.7 1.8 - - - -
279A ILE* 3.8 19.5 - - + -
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Residues in contact with GLU 163 (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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159A ARG* 4.0 9.8 - - + +
160A PRO* 3.0 38.7 + - + +
162A CYS* 1.3 77.0 - - - +
164A ALA* 1.3 66.0 + - - +
165A LEU 3.1 1.3 - - - -
166A LEU* 3.0 18.3 + - + +
167A ASP* 3.6 7.1 + - - +
179A ARG* 4.3 2.0 - - - +
191A PHE* 4.1 5.0 - - - -
273A ASP* 3.3 26.6 - - + +
274A ARG* 3.1 57.5 + - + +
275A HIS* 4.5 11.9 + - + +
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Residues in contact with ALA 164 (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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156A ALA* 3.9 16.8 - - + +
157A PHE* 4.5 9.6 - - + -
159A ARG* 4.7 2.6 - - - +
160A PRO 3.0 8.7 + - - +
161A ILE* 3.3 5.8 + - + +
163A GLU* 1.3 77.2 - - - +
165A LEU* 1.3 57.7 + - - +
166A LEU 3.1 0.2 - - - -
167A ASP* 3.0 26.7 + - + +
171A PHE* 3.1 20.8 - - + -
194A ALA* 3.8 29.4 - - + -
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Residues in contact with LEU 165 (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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161A ILE* 3.0 32.2 + - + +
162A CYS* 3.9 7.0 - - - +
163A GLU 3.1 0.4 - - - -
164A ALA* 1.3 75.6 - - - +
166A LEU* 1.3 57.8 + - - +
167A ASP 3.4 0.4 - - - -
171A PHE* 3.3 52.6 - - + +
174A ILE* 3.3 20.4 - - + +
179A ARG* 3.9 24.9 - - + +
182A ILE* 5.0 4.3 - - + -
183A LEU* 3.7 37.0 - - + -
225A LEU* 4.8 8.7 - - + -
229A CYS* 4.0 15.5 - - - -
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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