Contacts of the helix formed by residues 164 - 173 (chain A) in PDB entry 1T8U
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 GLY 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLY* 1.3 79.8 - - - +
165A THR* 1.3 65.4 + - - +
166A ARG 3.4 2.5 - - - -
167A ALA* 3.5 2.3 + - - -
168A LEU* 3.1 20.4 + - - +
241A VAL* 4.1 5.6 - - - +
315A LEU* 3.5 16.0 - - - +
602B A3P 3.1 34.3 + - - -
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Residues in contact with THR 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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157A ILE* 3.8 17.4 - - + +
159A GLY* 3.5 27.6 - - - +
160A VAL 3.5 19.1 - - - +
164A GLY* 1.3 76.3 - - - +
166A ARG* 1.3 61.6 + - - -
168A LEU* 3.5 1.6 + - - +
169A LEU* 3.1 24.6 + - - +
215A LYS* 3.0 33.9 + - - +
217A PRO* 3.4 12.9 - - + +
241A VAL* 4.4 10.1 - - + -
602B A3P 2.7 20.5 + - - -
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Residues in contact with ARG 166 (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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165A THR* 1.3 81.2 + - - +
167A ALA* 1.3 65.0 + - - +
169A LEU* 3.3 17.3 + - - +
170A GLU* 2.9 60.9 + - + +
173A ARG* 4.6 1.8 - - - +
182A GLY 3.2 26.8 + - - -
183A ALA* 4.7 3.2 - - - +
184A GLU* 4.3 11.1 + - - +
215A LYS* 3.5 29.3 - - - +
364A LEU* 4.3 11.9 - - + -
368A LYS* 3.5 26.1 - - + +
602B A3P 3.1 15.5 + - - +
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Residues in contact with ALA 167 (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 GLY* 3.5 9.9 + - - +
165A THR 3.3 0.2 - - - -
166A ARG* 1.3 79.2 - - - +
168A LEU* 1.3 63.2 + - - +
170A GLU* 3.3 2.1 + - - +
171A PHE* 2.9 43.1 + - + -
315A LEU* 4.1 5.8 - - + -
364A LEU* 3.8 20.5 - - + +
602B A3P 3.5 34.7 + - + +
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Residues in contact with LEU 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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157A ILE* 3.9 16.2 - - + -
164A GLY 3.1 14.8 + - - +
165A THR 3.9 3.6 - - - +
166A ARG 3.3 0.2 - - - -
167A ALA* 1.3 79.6 - - - +
169A LEU* 1.3 57.9 + - - +
171A PHE* 3.3 4.5 + - - +
172A LEU* 2.9 30.5 + - + +
239A ILE* 3.8 25.1 - - + -
241A VAL* 3.5 25.4 - - + -
310A VAL* 4.3 9.4 - - + -
315A LEU* 4.0 13.6 - - + +
323A LEU* 4.1 30.1 - - + -
326A VAL* 4.2 18.2 - - + -
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Residues in contact with LEU 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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157A ILE* 4.1 20.2 - - + +
165A THR 3.1 16.7 + - - +
166A ARG* 3.7 21.8 - - - +
168A LEU* 1.3 78.2 - - - +
170A GLU* 1.3 65.0 + - - +
172A LEU* 3.2 7.3 + - + +
173A ARG* 2.9 38.4 + - + +
178A VAL* 5.8 0.9 - - + -
180A ALA* 3.7 23.6 - - + -
181A VAL 4.0 18.8 - - - +
182A GLY 4.9 0.2 - - - +
213A MET* 4.8 13.5 - - + -
214A GLU 5.2 2.0 - - - -
215A LYS* 3.7 28.0 - - + +
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Residues in contact with GLU 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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166A ARG* 2.9 62.3 + - + +
167A ALA* 3.8 4.7 - - - +
169A LEU* 1.3 76.2 - - - +
171A PHE* 1.3 70.3 + - + +
173A ARG* 3.3 42.9 + - - +
174A VAL* 3.9 2.9 + - - +
352A LEU* 3.7 18.4 - - + +
356A GLU* 5.5 1.2 + - - +
362A HIS* 4.8 15.9 + - + +
364A LEU* 5.0 12.1 - - + -
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Residues in contact with PHE 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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167A ALA* 2.9 29.0 + - + +
168A LEU* 3.7 3.8 - - - +
170A GLU* 1.3 77.9 - - + +
172A LEU* 1.3 63.2 + - - +
174A VAL* 3.2 17.0 + - - +
315A LEU* 3.9 33.4 - - + -
319A PRO* 4.2 7.6 - - + -
323A LEU* 4.0 18.8 - - + -
336A ILE* 3.2 15.9 - - - +
341A PHE* 3.6 30.3 - + + -
350A PRO* 4.8 6.1 - - + -
351A CYS 5.1 0.4 - - - -
352A LEU* 3.6 34.0 - - + +
364A LEU* 4.5 15.9 - - + -
602B A3P 3.8 23.8 - - - -
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Residues in contact with LEU 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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157A ILE* 5.0 2.7 - - + -
168A LEU* 2.9 24.2 + - + +
169A LEU* 3.6 7.2 - - + +
171A PHE* 1.3 77.0 - - - +
173A ARG* 1.3 59.1 + - - +
174A VAL 2.9 6.1 + - - -
175A HIS* 3.0 22.5 + - - +
178A VAL* 3.7 17.2 - - + +
213A MET* 3.5 40.8 - - + -
239A ILE* 4.8 1.8 - - + -
323A LEU* 3.6 22.0 - - + +
326A VAL* 3.7 20.9 - - + -
327A GLN* 4.6 9.6 - - + -
330A LEU* 3.8 12.6 - - + -
332A LEU* 5.0 4.3 - - + -
336A ILE* 3.7 8.5 - - + -
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 4.6 2.8 - - - +
169A LEU* 2.9 39.2 + - + +
170A GLU* 3.3 41.9 + - - +
171A PHE 3.2 0.6 - - - -
172A LEU* 1.3 75.5 - - - +
174A VAL* 1.3 55.8 + - - +
175A HIS 3.2 0.4 - - - -
178A VAL* 4.5 7.6 - - + +
179A ARG* 5.8 2.0 - - - +
180A ALA* 4.0 35.1 + - + +
181A VAL 4.9 0.8 + - - -
182A GLY* 4.1 21.7 - - - +
356A GLU* 3.1 46.1 + - + +
354B LYS* 2.5 29.6 + - - +
359B SER* 5.6 2.2 - - - -
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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