Contacts of the helix formed by residues 170 - 182 (chain D) in PDB entry 6A5T
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 ASN 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D GLU* 4.9 5.6 - - + +
169D VAL* 1.3 78.2 - - - +
171D LEU* 1.3 54.7 + - - +
172D GLN* 3.6 1.8 - - - -
173D ARG* 3.0 39.6 + - - +
174D ILE* 2.9 35.6 + - + +
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Residues in contact with LEU 171 (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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145D LEU* 4.7 14.1 - - + -
153D VAL* 3.5 22.9 - - + +
156D ALA* 4.1 17.3 - - + -
163D LEU* 4.7 20.4 - - + -
169D VAL* 2.8 25.9 - - + +
170D ASN* 1.3 74.3 - - - +
172D GLN* 1.3 62.0 + - - +
173D ARG 3.3 0.2 - - - -
174D ILE* 3.1 31.2 - - + +
175D LEU* 2.8 51.6 + - + +
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Residues in contact with GLN 172 (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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151D GLU* 2.8 31.4 + - - +
152D ASP* 2.9 18.7 - - - +
153D VAL* 4.6 4.9 - - + +
169D VAL* 4.4 6.4 - - + +
171D LEU* 1.3 79.1 - - - +
173D ARG* 1.3 64.0 + - - +
175D LEU* 3.3 0.9 + - - +
176D ASP* 2.3 60.5 + - - +
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Residues in contact with ARG 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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170D ASN* 3.0 36.6 + - - +
172D GLN* 1.3 80.2 - - - +
174D ILE* 1.3 57.4 + - - +
176D ASP* 4.7 4.0 - - - -
177D GLU* 2.8 40.5 + - + +
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Residues in contact with ILE 174 (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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127D LEU* 5.5 13.4 - - + +
128D LEU* 4.5 23.3 - - + -
145D LEU* 5.5 5.4 - - + -
169D VAL 3.9 5.2 - - - +
170D ASN* 2.9 39.7 + - + +
171D LEU* 3.0 38.1 + - + +
173D ARG* 1.3 76.7 - - - +
175D LEU* 1.3 63.6 + - + +
177D GLU* 3.7 4.5 - - - +
178D LEU* 2.9 50.6 + - + +
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Residues in contact with LEU 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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145D LEU* 5.9 4.7 - - + -
148D LEU 3.9 7.4 - - - +
149D GLY* 3.7 13.1 - - - -
150D CYS* 3.1 54.9 + - + +
151D GLU 3.9 15.3 - - - +
152D ASP 4.4 4.0 - - - +
156D ALA* 5.6 2.7 - - + -
171D LEU* 2.8 43.5 + - + +
172D GLN 4.0 2.5 - - - +
174D ILE* 1.3 82.0 - - + +
176D ASP* 1.3 58.7 + - - +
178D LEU* 3.6 9.9 - - + +
179D ASN* 2.9 34.0 + - - -
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Residues in contact with ASP 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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150D CYS 4.8 3.3 - - - +
151D GLU* 5.0 7.6 - - - +
172D GLN* 2.3 45.4 + - - +
173D ARG* 4.2 4.0 - - - +
175D LEU* 1.3 75.4 - - - +
177D GLU* 1.3 59.1 + - - +
179D ASN* 3.3 16.6 + - - +
180D ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 177 (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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127D LEU* 5.2 18.4 - - + -
173D ARG* 2.8 26.1 + - + +
174D ILE* 3.7 4.7 - - - +
176D ASP* 1.3 76.0 - - - +
178D LEU* 1.3 57.7 + - - +
180D ARG* 2.3 43.4 + - - +
181D LEU* 2.9 44.5 + - + +
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Residues in contact with LEU 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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114D ARG* 3.0 25.4 + - - +
115D PHE* 3.8 24.7 - - + -
124D VAL* 5.2 0.9 - - + -
127D LEU* 3.8 28.7 - - + -
128D LEU* 5.0 7.0 - - + -
145D LEU* 3.4 22.4 - - + +
146D SER* 6.3 0.2 - - - -
149D GLY* 5.4 1.6 - - - -
174D ILE* 2.9 37.6 + - + +
175D LEU* 3.6 14.6 - - + +
176D ASP 3.2 0.2 - - - -
177D GLU* 1.3 75.8 - - + +
179D ASN* 1.3 56.1 + - - +
181D LEU* 3.0 1.9 + - + -
182D GLU* 2.3 41.6 + - - +
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Residues in contact with ASN 179 (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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114D ARG* 4.7 0.7 + - - +
149D GLY* 5.0 10.2 - - - +
150D CYS 3.7 20.6 + - - +
151D GLU* 5.2 6.1 + - - -
175D LEU* 2.9 27.8 + - - +
176D ASP* 3.3 15.6 + - - +
178D LEU* 1.3 72.4 - - - +
180D ARG* 1.3 62.5 + - - +
182D GLU* 2.7 42.1 - - - +
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Residues in contact with ARG 180 (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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176D ASP 2.9 16.2 + - - +
177D GLU* 2.3 41.7 + - - +
179D ASN* 1.3 77.0 - - - +
181D LEU* 1.3 87.7 + - - +
182D GLU 3.2 10.2 - - - +
183D ASP* 5.0 0.5 - - - -
184D PRO* 5.9 0.3 - - - +
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Residues in contact with LEU 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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114D ARG 4.6 0.2 - - - +
115D PHE* 3.5 30.3 - - + -
120D THR* 3.7 31.2 - - + +
123D ALA* 5.8 1.6 - - + -
124D VAL* 5.8 0.9 - - + -
127D LEU* 5.6 7.4 - - + -
177D GLU* 2.9 36.3 + - + +
178D LEU* 4.0 1.3 - - + +
180D ARG* 1.3 100.6 - - - +
182D GLU* 1.3 60.0 + - - +
183D ASP* 2.9 14.8 + - - +
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Residues in contact with GLU 182 (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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114D ARG* 4.6 31.4 + - + +
115D PHE* 4.3 4.7 - - - -
178D LEU 2.3 31.2 + - - +
179D ASN* 2.7 40.9 + - - +
180D ARG 3.1 10.6 - - - +
181D LEU* 1.3 65.2 - - - +
183D ASP* 1.3 71.9 + - - +
184D PRO* 3.7 2.8 - - - +
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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