Contacts of the helix formed by residues 169 - 177 (chain D) in PDB entry 4UN7
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 ASP 169 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLY 3.9 13.4 - - - +
147D VAL* 4.2 17.3 - - + -
148D ARG* 2.8 65.5 + - - +
166D SER* 3.0 11.2 + - - +
167D LEU 2.9 0.6 - - - -
168D ARG* 1.3 79.8 - - - +
170D ARG* 1.3 67.7 + - - +
171D ILE 3.2 2.9 - - - -
172D LYS* 2.9 23.9 + - + +
173D PHE* 3.0 12.7 + - - +
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Residues in contact with ARG 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 4.3 18.6 + - - -
123D LYS 5.1 2.5 + - - -
125D LEU* 3.8 19.1 - - + -
166D SER 3.4 3.6 + - - -
167D LEU* 3.3 38.8 + - - +
168D ARG 3.7 0.2 - - - -
169D ASP* 1.3 74.8 - - - +
171D ILE* 1.3 79.7 + - + +
173D PHE* 3.3 1.0 + - - +
174D VAL* 2.9 45.0 + - + +
4E T 3.8 27.1 + - - -
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D LEU 5.9 0.2 - - - +
169D ASP 3.0 1.2 + - - -
170D ARG* 1.3 104.7 - - + +
172D LYS* 1.3 67.6 + - - +
174D VAL* 4.4 2.6 - - - +
175D HIS* 3.1 30.5 + - + +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU 3.4 15.9 + - - +
146D GLY* 3.1 39.2 + - - +
147D VAL* 3.7 9.0 - - + -
169D ASP* 2.9 16.1 + - + +
171D ILE* 1.3 80.8 - - - +
173D PHE* 1.3 58.1 + - - +
175D HIS* 5.2 0.4 - - - -
176D THR* 2.8 54.9 + - + +
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Residues in contact with PHE 173 (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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110D ILE* 4.3 11.9 - - + -
114D TYR* 3.8 30.1 - + - -
125D LEU* 3.6 27.1 - - + -
127D ILE* 5.3 0.4 - - + -
142D LEU* 4.0 15.3 - - + -
147D VAL* 4.1 27.6 - - + -
165D ILE* 3.8 28.5 - - + -
169D ASP 3.0 12.3 + - - +
170D ARG 3.7 5.8 - - - +
172D LYS* 1.3 78.5 - - - +
174D VAL* 1.3 66.7 + - + +
177D ILE* 3.2 48.9 + - + +
178D LEU* 3.3 26.6 + - + -
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 4.5 18.8 - - + -
125D LEU* 4.3 16.8 - - + -
170D ARG* 2.9 26.6 + - + +
171D ILE* 4.4 3.1 - - - +
173D PHE* 1.3 88.7 - - + +
175D HIS* 1.3 57.9 + - + +
178D LEU* 3.4 21.5 - - + +
179D SER* 3.1 27.5 + - - +
189D ALA* 6.5 0.2 - - + -
192D LEU* 4.8 12.8 - - + -
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Residues in contact with HIS 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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171D ILE* 3.1 23.3 + - + +
172D LYS* 5.2 0.4 - - - -
174D VAL* 1.3 80.7 - - + +
176D THR* 1.3 67.3 + - - +
177D ILE 3.3 0.4 - - - -
179D SER* 3.3 38.3 + - - +
180D SER* 4.7 0.5 - - - -
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Residues in contact with THR 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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103D MET* 5.6 3.6 - - + -
107D ILE* 4.5 13.4 - - + +
145D LEU* 5.3 13.7 - - + +
172D LYS* 2.8 37.1 + - + +
175D HIS* 1.3 75.5 + - - +
177D ILE* 1.3 67.7 + - + +
180D SER* 3.6 19.4 - - - -
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Residues in contact with ILE 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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107D ILE* 3.6 24.6 - - + +
110D ILE* 3.8 29.2 - - + -
111D LYS* 3.3 15.1 - - - +
142D LEU* 3.5 31.0 - - + -
145D LEU* 3.7 24.9 - - + -
147D VAL* 4.4 11.2 - - + -
172D LYS 4.7 0.2 - - - +
173D PHE* 3.2 28.0 + - + +
176D THR* 1.3 88.2 - - + +
178D LEU* 1.3 71.5 + - + +
179D SER 3.2 1.8 + - - -
180D SER 3.3 7.4 + - - -
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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