Contacts of the helix formed by residues 174 - 185 (chain D) in PDB entry 1D1T
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 CYS 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D CYS* 3.7 2.0 - - - -
67D HIS* 3.6 11.9 - - + -
68D GLU* 3.5 11.1 + - + +
93D PHE* 3.9 4.5 - - + -
171D LEU 3.2 2.2 + - - -
172D ILE 3.3 2.4 + - - -
173D GLY* 1.3 82.5 - - - +
175D GLY* 1.3 60.2 + - - +
176D PHE 3.6 0.9 - - - -
177D SER* 3.4 2.4 + - - -
178D THR* 2.6 37.5 + - - -
319D PHE* 3.6 8.5 - - - -
376D ZN 2.1 39.5 - - - -
511D ACT 2.8 10.5 - - - -
4377D NAD 3.2 17.9 - - - -
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Residues in contact with GLY 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLU* 2.8 11.2 + - - -
171D LEU* 3.4 1.1 + - - -
174D CYS* 1.3 79.4 - - - +
176D PHE* 1.3 62.4 + - - +
178D THR* 3.9 1.2 - - - -
179D GLY 3.3 14.4 + - - -
202D GLY 4.8 1.3 - - - -
203D VAL* 3.9 17.5 - - - -
206D SER* 3.5 9.6 + - - -
369D ARG* 3.3 26.5 - - - -
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Residues in contact with PHE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.1 32.5 + - + +
172D ILE* 4.6 7.9 - - + +
175D GLY* 1.3 69.8 - - - -
177D SER* 1.3 75.9 + - - +
179D GLY 3.3 1.0 + - - -
180D TYR* 2.9 72.3 + + + +
206D SER* 3.3 20.9 + - - +
209D MET* 4.0 19.5 - - + -
331D LEU* 4.4 6.7 - - + -
340D PHE* 3.6 42.4 - + - -
342D LEU* 3.4 25.8 - - + -
345D LEU* 3.9 9.1 - - + +
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU 3.9 1.2 + - - -
172D ILE* 2.6 34.4 + - - +
174D CYS 3.4 2.1 + - - -
176D PHE* 1.3 82.0 - - - +
178D THR* 1.3 54.8 + - - +
180D TYR* 4.7 1.3 - - - -
181D GLY* 2.7 33.1 + - - -
319D PHE* 3.6 24.4 - - - +
320D GLY* 3.8 2.4 - - - -
322D LEU* 3.7 14.8 - - - +
328D VAL* 5.1 0.2 - - - +
331D LEU* 3.3 21.2 - - - +
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Residues in contact with THR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D CYS* 2.6 27.6 + - - -
175D GLY 3.9 3.4 - - - -
177D SER* 1.3 72.4 - - - +
179D GLY* 1.3 53.7 + - - +
182D ALA* 2.7 37.4 + - - +
203D VAL* 4.1 1.1 - - + -
292D VAL* 3.7 17.5 - - + -
317D CYS* 4.9 1.6 - - - -
319D PHE* 3.7 14.2 - - - -
320D GLY* 3.3 19.9 - - - +
4377D NAD 3.3 50.6 - - + +
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Residues in contact with GLY 179 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D GLY 3.3 8.7 + - - -
178D THR* 1.3 81.0 - - - +
180D TYR* 1.3 62.6 + - - +
182D ALA* 3.3 8.9 + - - +
183D ALA* 3.4 3.6 + - - +
203D VAL* 3.7 8.7 - - - +
206D SER* 3.6 12.8 - - - -
207D VAL* 3.2 43.2 - - - +
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Residues in contact with TYR 180 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D PHE* 2.9 54.0 + + + +
177D SER 4.2 0.9 - - - +
179D GLY* 1.3 74.0 - - - +
181D GLY* 1.3 65.7 + - - +
183D ALA* 3.4 2.9 + - - +
184D VAL* 3.1 33.5 + - + +
206D SER 3.6 10.8 + - - +
209D MET* 3.9 6.1 - - + -
210D GLY* 3.5 19.1 - - - -
213D SER* 3.6 37.5 + - - -
322D LEU* 6.5 0.2 - - + -
331D LEU* 4.1 24.9 - - + -
334D GLU* 4.5 7.5 + - - -
339D LYS* 5.4 2.6 + - - +
340D PHE* 4.2 18.1 - + + -
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D SER 2.7 22.8 + - - -
180D TYR* 1.3 76.4 - - - +
182D ALA* 1.3 59.6 - - - +
184D VAL* 5.0 0.9 - - - -
185D LYS* 2.7 32.7 + - - -
186D THR 3.1 2.3 + - - -
320D GLY 3.0 22.1 - - - +
322D LEU* 4.5 11.4 - - - -
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D THR 2.7 23.1 + - - +
179D GLY* 3.4 9.2 - - - +
181D GLY* 1.3 70.7 - - - +
183D ALA* 1.3 56.9 + - - +
186D THR* 3.5 4.0 - - - -
187D GLY 2.8 26.5 + - - -
207D VAL* 4.4 4.5 - - + -
266D PHE* 3.5 13.3 - - + -
290D VAL* 4.4 1.6 - - + +
292D VAL* 3.9 22.2 - - + -
317D CYS* 3.8 25.6 - - - -
320D GLY* 3.5 1.4 - - - -
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D GLY 3.4 1.6 + - - +
180D TYR 3.4 1.6 + - - +
181D GLY 3.1 0.8 - - - -
182D ALA* 1.3 78.8 - - - +
184D VAL* 1.3 61.1 + - - +
188D LYS 2.9 23.0 + - - -
189D VAL* 3.1 17.2 + - + +
207D VAL* 3.8 13.7 - - + +
210D GLY* 3.8 5.4 - - - -
211D CYS* 3.6 39.7 - - - +
266D PHE* 3.8 13.5 - - + -
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D TYR* 3.1 29.1 + - + +
181D GLY* 5.0 0.4 - - - -
183D ALA* 1.3 75.6 - - - +
185D LYS* 1.3 76.9 + - + +
188D LYS* 3.7 16.0 - - - +
189D VAL 5.0 0.9 - - - +
210D GLY* 3.7 12.3 - - - +
213D SER* 3.2 27.1 - - - +
214D ALA* 4.7 9.0 - - + -
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Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLY* 2.7 17.9 + - - +
184D VAL* 1.3 89.1 - - + +
186D THR* 1.3 60.8 + - - +
187D GLY 3.5 0.9 - - - -
188D LYS* 2.9 31.2 + - - +
320D GLY 3.6 7.6 - - - +
321D GLY* 4.2 13.7 - - - +
322D LEU* 3.3 31.9 - - + +
327D ASP* 4.1 19.0 + - - +
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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