Contacts of the helix formed by residues 231 - 241 (chain D) in PDB entry 6UZA
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 GLU 231 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D ILE 4.0 11.8 - - - +
170D SER 4.4 2.9 - - - +
171D LYS 4.5 1.0 - - - -
172D GLY* 3.6 31.9 + - - +
174D VAL* 5.6 1.9 - - - +
226D ALA* 3.3 13.1 + - - +
229D CYS* 3.5 32.1 - - + +
230D GLN* 1.3 73.9 - - - +
232D TYR* 1.3 60.6 + - - +
233D GLU 3.4 1.6 - - - -
234D ILE* 3.9 25.1 - - + +
235D VAL* 3.0 30.1 + - - +
284D ALA* 4.5 0.6 - - - +
874D LYS* 4.6 5.6 + - - +
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Residues in contact with TYR 232 (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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131A TYR* 5.0 3.3 - - + +
230D GLN* 3.5 13.8 + - - -
231D GLU* 1.3 71.9 - - - +
233D GLU* 1.3 58.7 + - - +
235D VAL* 3.5 1.5 + - - -
236D HIS* 3.0 28.9 + - - +
283D PRO* 3.8 20.3 - - - +
284D ALA* 3.7 27.5 + - + -
287D SER* 3.8 12.3 - - - -
288D LEU* 3.6 17.6 - - + +
866D TYR* 4.0 4.5 - + - -
867D VAL* 4.0 27.4 - - + -
870D ALA* 3.3 32.7 - - + +
871D GLN* 3.8 24.9 - - + +
874D LYS* 3.3 30.5 - - - +
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Residues in contact with GLU 233 (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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107A GLU* 5.5 4.8 - - - +
108A TYR* 5.2 4.6 + - - -
131A TYR* 3.6 40.2 + - + +
174D VAL* 3.6 38.5 - - + +
231D GLU 3.4 0.4 - - - -
232D TYR* 1.3 77.2 - - - +
234D ILE* 1.3 60.0 + - - +
236D HIS* 3.4 5.0 + - - +
237D THR* 2.9 37.6 + - - +
871D GLN* 5.0 1.7 - - - +
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Residues in contact with ILE 234 (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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169D ILE* 3.9 34.8 - - + +
172D GLY* 4.4 16.8 - - - -
174D VAL* 4.4 20.9 - - + -
177D VAL* 4.2 31.2 - - + -
226D ALA* 4.0 12.1 - - + -
231D GLU* 3.6 31.5 + - + +
232D TYR 3.4 0.2 - - - -
233D GLU* 1.3 74.6 - - + +
235D VAL* 1.3 61.2 + - - +
237D THR* 3.7 5.7 - - - -
238D LEU* 2.9 36.6 + - + +
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Residues in contact with VAL 235 (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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223D ILE* 4.4 11.4 - - + +
226D ALA* 3.3 32.8 - - + +
227D ALA* 3.9 12.3 - - + +
231D GLU 3.0 22.4 + - - +
232D TYR* 3.8 3.4 - - - +
234D ILE* 1.3 77.2 - - - +
236D HIS* 1.3 57.2 + - - +
238D LEU* 3.8 1.2 - - - +
239D LEU* 2.9 45.0 + - + +
284D ALA* 3.4 30.3 - - + +
285D TYR* 4.6 5.2 - - + -
288D LEU* 3.8 7.6 - - + -
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Residues in contact with HIS 236 (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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87A MET* 3.8 22.4 - - + +
88A PHE* 2.9 30.7 + + - -
89A SER* 4.2 8.3 + - - -
131A TYR* 3.5 50.0 + + + +
132A MET* 5.6 0.2 - - + -
232D TYR 3.0 18.7 + - - +
233D GLU 3.7 4.5 - - - +
234D ILE 3.3 0.2 - - - -
235D VAL* 1.3 77.0 - - - +
237D THR* 1.3 56.7 + - - +
239D LEU* 3.5 5.9 + - + +
240D ARG* 3.0 44.9 + - - +
288D LEU* 4.3 22.4 - - + -
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Residues in contact with THR 237 (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 VAL* 5.6 2.4 - - - +
177D VAL* 5.5 4.3 - - + -
178D GLU* 5.9 5.8 - - + -
181D LEU* 4.1 15.0 - - + -
233D GLU* 2.9 24.2 + - - +
234D ILE* 3.7 7.9 - - - -
236D HIS* 1.3 77.3 + - - +
238D LEU* 1.3 62.2 + - + +
240D ARG* 3.3 36.0 + - - +
241D LYS* 3.4 35.4 - - - +
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Residues in contact with LEU 238 (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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169D ILE* 4.0 8.1 - - + -
181D LEU* 4.1 20.0 - - + -
192D LEU* 3.9 38.6 - - + -
222D PRO* 3.6 34.5 - - + +
223D ILE* 4.1 15.5 - - + -
226D ALA* 3.9 12.6 - - + -
234D ILE* 2.9 31.1 + - + +
235D VAL 4.1 0.2 - - - +
237D THR* 1.3 74.2 - - - +
239D LEU* 1.3 64.2 + - - +
241D LYS* 3.4 9.8 + - - +
242D GLY 3.7 0.3 + - - -
243D ALA* 3.3 28.4 + - + +
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Residues in contact with LEU 239 (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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87A MET* 3.3 25.5 - - + +
223D ILE* 4.5 2.9 - - + -
235D VAL* 2.9 39.8 + - + +
236D HIS* 3.9 5.6 - - + +
238D LEU* 1.3 75.8 - - - +
240D ARG* 1.3 62.7 + - - +
242D GLY* 3.3 9.9 + - - -
243D ALA 3.4 20.0 - - - +
244D ARG* 3.6 39.1 + - - +
285D TYR* 4.1 15.5 - - + -
288D LEU* 3.8 33.7 - - + +
289D SER* 4.1 6.5 - - - -
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Residues in contact with ARG 240 (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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87A MET* 3.7 20.1 - - + +
131A TYR* 4.9 8.7 - - - +
236D HIS* 3.0 41.2 + - - +
237D THR* 3.5 30.8 + - - +
238D LEU 3.3 0.4 - - - -
239D LEU* 1.3 76.4 - - - +
241D LYS* 1.3 70.9 + - + +
242D GLY 3.4 1.7 + - - -
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Residues in contact with LYS 241 (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 LEU* 3.8 36.7 + - + +
186D PHE 5.6 4.3 - - - +
188D GLU 4.7 3.1 - - - +
189D GLY* 4.2 21.2 - - - +
192D LEU* 3.8 30.3 - - + +
237D THR* 3.4 23.3 - - - +
238D LEU* 3.4 4.3 + - - +
239D LEU 3.2 0.8 - - - -
240D ARG* 1.3 91.6 - - + +
242D GLY* 1.3 63.9 + - - +
243D ALA 3.7 1.1 - - - -
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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