Contacts of the strand formed by residues 179 - 185 (chain A) in PDB entry 4AY1
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 LEU 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A HIS* 4.4 26.9 - - + +
96A LYS* 4.5 18.6 - - + -
98A LEU* 4.4 17.0 - - + -
138A ASP* 2.8 22.9 + - + +
139A GLY* 3.1 4.2 - - - -
140A LEU 2.8 25.2 + - - -
166A PHE* 3.4 7.6 - - - -
177A ARG* 4.3 14.6 - - - +
178A LEU* 1.3 73.2 - - - +
180A LEU* 1.3 59.5 + - - +
181A THR* 4.9 2.2 - - + -
205A ASP* 3.4 27.1 - - + +
206A PHE* 5.2 4.9 - - + -
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Residues in contact with LEU 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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140A LEU* 3.3 30.7 - - + +
142A VAL* 4.2 4.3 - - + -
159A ILE* 3.7 16.2 - - + +
162A LEU* 3.8 13.2 - - + -
163A ALA* 3.6 33.2 - - - +
166A PHE* 4.0 20.6 - - + -
177A ARG* 5.7 0.9 - - - +
179A LEU* 1.3 74.5 - - - +
181A THR* 1.3 68.6 + - - +
203A ASP 4.0 14.1 - - - +
204A LEU* 3.7 16.1 - - + -
205A ASP* 2.9 38.4 + - - +
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Residues in contact with THR 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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60A ILE* 4.7 0.3 - - - +
98A LEU* 3.6 16.3 - - + +
140A LEU 2.8 8.3 + - - +
141A ASP* 2.7 33.6 + - - +
142A VAL* 2.9 23.0 + - - +
179A LEU* 4.9 1.6 - - + -
180A LEU* 1.3 85.0 - - - +
182A ALA* 1.3 63.4 + - - +
204A LEU* 4.0 5.8 - - - +
205A ASP* 4.6 2.2 - - + -
206A PHE* 3.4 53.2 - - + +
208A ASN* 3.6 9.9 + - - -
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Residues in contact with ALA 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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141A ASP* 3.5 4.3 - - - -
142A VAL* 3.1 18.2 - - + +
155A PHE* 4.5 13.5 - - + -
159A ILE* 4.9 0.9 - - + -
181A THR* 1.3 78.8 - - - +
183A GLY* 1.3 61.8 + - - +
184A VAL* 3.5 15.9 + - + +
204A LEU* 3.6 24.4 - - + +
206A PHE 3.5 5.3 + - - -
207A ILE* 3.5 5.0 - - - -
208A ASN 2.9 22.1 + - - -
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Residues in contact with GLY 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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32A TYR* 4.0 2.2 - - - -
141A ASP* 3.4 3.8 + - - -
142A VAL 3.3 2.6 + - - +
143A SER* 3.3 39.9 + - - -
144A TRP 4.3 2.6 + - - +
145A ILE* 4.4 2.8 - - - +
155A PHE* 6.0 0.7 - - - -
182A ALA* 1.3 72.0 - - - +
184A VAL* 1.3 60.4 + - - +
195A TYR* 4.4 2.3 + - - -
208A ASN* 3.1 18.8 - - - -
210A LEU* 3.7 15.9 - - - +
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Residues in contact with VAL 184 (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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145A ILE* 5.7 0.2 - - - -
155A PHE* 5.1 1.3 - - + -
182A ALA* 3.8 21.8 - - + +
183A GLY* 1.3 79.7 - - - +
185A SER* 1.3 63.8 + - - +
195A TYR* 3.4 24.5 - - + +
200A LEU* 4.6 4.7 - - + -
207A ILE* 3.8 33.2 - - + -
208A ASN 3.0 7.4 + - - +
209A LEU* 4.1 3.8 - - - -
210A LEU* 2.9 33.1 + - - +
252A TRP* 3.4 34.3 - - + +
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Residues in contact with SER 185 (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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145A ILE* 5.7 0.2 - - - +
146A TYR* 3.7 29.0 + - - -
184A VAL* 1.3 74.4 - - - +
186A ALA* 1.3 56.3 + - - +
187A GLY* 3.0 18.1 + - - -
190A MET* 3.4 28.3 - - - +
191A ILE* 3.3 6.6 - - - +
195A TYR* 3.0 18.4 + - - -
209A LEU* 3.7 0.4 - - - +
210A LEU* 4.5 4.8 - - - +
252A TRP* 3.0 25.1 + - - -
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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