Contacts of the strand formed by residues 166 - 173 (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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A SER 4.5 0.2 - - - +
163A ALA* 3.0 26.6 + - - +
164A LYS 3.5 1.4 - - - -
165A ASP* 1.3 79.5 - - - +
167A VAL* 1.3 57.7 + - - -
181A LYS* 3.3 15.2 + - - +
182A LEU 3.1 15.0 - - - -
183A SER* 4.1 3.8 - - - -
197A ILE* 3.3 19.1 - - - +
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Residues in contact with VAL 167 (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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137A VAL* 4.4 30.1 - - + -
160A ILE* 3.9 22.9 - - + -
161A SER 3.4 14.4 - - - +
162A CYS* 4.3 7.6 - - + +
166A GLY* 1.3 74.8 - - - +
168A LYS* 1.3 64.3 + - - +
169A PHE* 3.9 21.1 - - + -
180A ILE 4.0 0.4 - - - +
181A LYS* 3.2 5.8 - - - +
182A LEU* 2.8 52.2 + - + +
195A VAL* 4.8 2.2 - - + -
197A ILE* 4.5 4.5 - - + -
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Residues in contact with LYS 168 (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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159A VAL 3.3 4.4 - - - +
160A ILE* 3.4 3.5 - - - +
161A SER* 2.8 57.5 + - - +
167A VAL* 1.3 77.3 - - - +
169A PHE* 1.3 63.6 + - - +
170A SER* 3.5 9.8 + - - +
179A ASN* 2.9 47.1 + - - +
180A ILE 3.4 9.9 - - - +
181A LYS* 4.0 21.5 - - + +
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Residues in contact with PHE 169 (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* 3.3 26.9 - - + -
144A PHE* 4.2 20.9 - + - -
147A ILE* 3.7 35.4 - - + -
148A CYS* 6.3 0.9 - - - -
151A LEU* 3.6 22.1 - - + +
158A VAL* 3.9 7.9 - - + -
159A VAL 3.9 2.9 - - - -
160A ILE* 3.8 34.5 - - + -
167A VAL* 3.9 17.5 - - + -
168A LYS* 1.3 74.1 - - - +
170A SER* 1.3 63.3 + - - +
179A ASN* 3.5 0.3 - - - +
180A ILE* 2.7 49.7 + - + +
182A LEU* 3.8 15.9 - - + -
227A LEU* 4.2 4.9 - - + -
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Residues in contact with SER 170 (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* 4.4 2.2 - - - -
157A ALA 3.8 0.2 - - - +
158A VAL* 3.2 11.1 - - - +
159A VAL* 2.9 46.3 + - - +
168A LYS* 3.5 16.5 + - - +
169A PHE* 1.3 74.8 - - - +
171A ALA* 1.3 61.6 + - - +
172A SER* 6.0 0.2 - - - -
178A GLY 3.2 13.7 - - - -
179A ASN* 2.7 22.5 + - - -
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Residues in contact with ALA 171 (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* 3.9 39.5 - - + +
154A ILE* 4.2 4.5 - - + -
155A GLY* 4.0 9.0 - - - +
157A ALA 3.8 16.4 - - - +
159A VAL* 6.0 0.9 - - - -
170A SER* 1.3 76.4 - - - +
172A SER* 1.3 67.3 + - - +
177A ASN* 3.2 2.8 - - - +
178A GLY 2.8 29.8 + - - +
209A LEU* 4.6 0.7 - - + -
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Residues in contact with SER 172 (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 3.7 4.3 - - - -
155A GLY* 3.6 13.6 - - - -
156A ASP 4.6 1.6 + - - -
157A ALA 4.8 1.4 + - - -
170A SER* 6.0 0.3 - - - -
171A ALA* 1.3 80.3 + - - +
173A GLY* 1.3 59.2 + - - +
176A GLY 3.7 6.1 - - - -
177A ASN* 3.6 13.8 - - - +
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Residues in contact with GLY 173 (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 3.2 16.7 + - - -
155A GLY* 4.8 0.7 - - - -
172A SER* 1.3 75.9 - - - +
174A GLU* 1.3 61.1 + - - +
175A LEU 3.0 11.4 + - - -
176A GLY 2.7 17.9 + - - +
117E LYS* 3.7 10.0 + - - -
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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