Contacts of the strand formed by residues 176 - 183 (chain A) in PDB entry 1AXC
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.9 7.1 - - - +
172A SER* 5.3 0.4 - - - -
173A GLY* 2.7 36.2 + - - +
175A LEU* 1.3 84.9 - - - +
177A ASN* 1.3 61.4 + - - -
115E GLU 2.9 13.9 - - - -
117E LYS* 3.6 13.2 - - - +
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Residues in contact with ASN 177 (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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154A ILE* 3.9 8.0 - - - +
171A ALA 3.2 14.6 - - - +
172A SER* 3.6 15.7 - - - +
175A LEU* 5.2 0.4 - - - +
176A GLY* 1.3 78.4 - - - -
178A GLY* 1.3 63.6 + - - +
179A ASN* 5.6 2.3 - - - +
78E ILE* 5.7 1.0 - - - +
113E ASP* 4.9 6.4 - - - +
114E TYR* 3.4 6.3 - - - +
115E GLU* 3.1 58.6 + - - +
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Residues in contact with GLY 178 (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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151A LEU* 4.3 9.6 - - - -
154A ILE* 3.8 4.8 - - - +
170A SER* 3.2 8.3 - - - -
171A ALA 2.8 30.9 + - - +
177A ASN* 1.3 78.0 - - - +
179A ASN* 1.3 63.0 + - - +
113E ASP 3.5 5.4 - - - -
114E TYR* 3.6 19.5 - - - -
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Residues in contact with ASN 179 (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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151A LEU* 4.7 0.6 - - - +
168A LYS* 2.9 39.8 - - - +
169A PHE 3.5 1.1 - - - +
170A SER* 2.7 27.9 + - - -
177A ASN* 5.6 2.9 - - - +
178A GLY* 1.3 75.6 - - - +
180A ILE* 1.3 62.0 + - - +
181A LYS* 4.0 2.0 + - - +
111E VAL 3.6 1.7 - - - +
112E SER* 3.2 3.1 - - - -
113E ASP* 2.9 54.6 + - + +
114E TYR* 4.6 3.2 - - - -
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Residues in contact with ILE 180 (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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147A ILE* 3.9 35.2 - - + +
150A ASP* 4.8 5.4 - - + +
151A LEU* 3.8 28.0 - - + -
168A LYS* 3.4 3.6 - - - -
169A PHE* 2.7 47.1 + - + +
179A ASN* 1.3 74.3 + - - +
181A LYS* 1.3 62.5 + - - +
182A LEU* 4.8 1.1 - - + -
110E LYS* 3.3 37.9 - - + +
111E VAL 3.5 2.2 - - - -
112E SER* 3.7 11.7 - - - +
114E TYR* 3.7 24.5 - - - +
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Residues in contact with LYS 181 (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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161A SER 5.5 0.2 + - - -
163A ALA* 5.6 4.0 - - - +
165A ASP* 5.0 6.1 - - - +
166A GLY* 3.3 34.8 + - - +
167A VAL 3.2 13.3 + - - +
168A LYS* 4.0 25.4 - - + +
179A ASN* 4.0 2.4 + - - +
180A ILE* 1.3 72.3 - - - +
182A LEU* 1.3 72.7 + - - +
183A SER* 4.1 8.0 + - - +
109E GLU 3.5 1.9 - - - +
110E LYS* 3.5 3.8 - - - -
111E VAL* 2.9 42.7 + - + +
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Residues in contact with LEU 182 (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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139A MET* 3.7 36.1 - - + -
143A GLU* 4.3 19.3 - - + +
147A ILE* 3.9 14.1 - - + -
166A GLY* 3.1 3.3 - - - -
167A VAL* 2.8 44.2 + - + +
169A PHE* 3.8 13.7 - - + -
180A ILE* 3.9 1.3 + - + -
181A LYS* 1.3 78.3 - - - +
183A SER* 1.3 60.9 + - - +
195A VAL* 4.5 20.9 - - + -
109E GLU* 3.3 4.9 - - + +
110E LYS* 3.7 33.7 - - + -
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Residues in contact with SER 183 (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 ASP 4.0 7.4 - - - -
166A GLY* 4.1 0.9 - - - -
181A LYS* 4.8 10.4 + - - +
182A LEU* 1.3 75.0 - - - +
184A GLN* 1.3 70.9 + - - +
185A THR* 3.3 8.5 + - - +
195A VAL* 3.6 16.7 - - - +
108E GLN 4.4 7.1 + - - -
109E GLU* 3.0 25.0 + - - +
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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