Contacts of the strand formed by residues 143 - 150 (chain A) in PDB entry 2YD7
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 ALA 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 5.7 1.3 - - + -
137A VAL* 3.7 28.7 - - + -
141A ARG 3.5 1.2 + - - -
142A THR* 1.3 73.3 - - - +
144A THR* 1.3 61.3 + - - +
145A MET* 4.2 1.6 - - + -
186A LEU 3.5 1.2 - - - +
187A GLN* 3.3 2.8 - - - -
188A ILE* 2.7 49.6 + - + +
191A SER* 4.6 1.1 - - - -
217A LEU* 3.8 30.1 - - + -
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Residues in contact with THR 144 (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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135A LYS* 3.6 31.7 + - - +
142A THR* 4.1 14.1 + - - +
143A ALA* 1.3 76.6 + - - +
145A MET* 1.3 71.4 + - - +
146A LEU* 4.0 17.6 + - + +
185A ALA* 4.1 18.4 - - + -
186A LEU 3.3 5.6 - - - +
187A GLN* 4.6 5.9 - - + +
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Residues in contact with MET 145 (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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132A PRO* 4.2 5.8 - - + -
133A GLN 3.4 21.1 - - - +
135A LYS* 3.8 26.9 - - - +
143A ALA 4.2 0.6 - - - -
144A THR* 1.3 75.0 - - - +
146A LEU* 1.3 60.8 + - - +
159A TRP* 3.7 22.0 - - + -
185A ALA* 3.3 6.2 - - - +
186A LEU* 2.8 42.1 + - + +
188A ILE* 5.1 6.7 - - + -
199A TYR* 4.2 27.4 - - + -
215A ALA* 3.7 29.8 - - + +
216A ASN 4.2 9.0 - - - +
217A LEU* 4.3 13.0 - - + -
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Residues in contact with LEU 146 (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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130A MET* 4.8 2.9 - - + -
131A GLY 3.6 2.7 - - - +
132A PRO* 3.0 33.5 - - + +
133A GLN 5.4 1.8 - - - +
135A LYS* 5.4 10.9 - - - +
144A THR* 4.0 15.9 + - + +
145A MET* 1.3 75.8 - - - +
147A CYS* 1.3 60.0 + - - +
159A TRP* 3.9 1.1 - - - -
183A ILE* 4.3 24.2 - - + -
184A GLY 3.7 0.9 - - - -
185A ALA* 3.9 24.7 - - + -
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Residues in contact with CYS 147 (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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128A ILE* 4.1 16.6 - - - -
130A MET 3.5 10.8 - - - -
132A PRO* 4.6 1.6 - - + -
146A LEU* 1.3 77.2 - - - +
148A ALA* 1.3 63.4 + - - +
149A ALA* 4.6 2.5 - - - -
157A ILE* 3.6 5.2 - - + +
159A TRP* 3.7 5.8 - - + -
182A SER 3.6 1.2 - - - +
183A ILE* 4.5 3.4 - - - -
184A GLY* 2.6 46.5 + - - +
201A CYS* 2.0 54.3 - - + -
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Residues in contact with ALA 148 (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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128A ILE* 3.5 4.3 - - - +
129A ASP* 2.7 35.8 + - + -
130A MET* 2.8 39.3 + - + +
146A LEU 4.4 0.2 - - - -
147A CYS* 1.3 72.6 - - - +
149A ALA* 1.3 55.2 + - - +
182A SER* 3.2 16.4 - - - +
183A ILE* 3.8 19.2 - - + +
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Residues in contact with ALA 149 (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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127A THR 3.1 13.5 - - - +
128A ILE* 4.0 7.6 - - + -
129A ASP* 3.5 4.7 + - - -
147A CYS* 3.9 1.7 + - - -
148A ALA* 1.3 75.6 - - - +
150A SER* 1.3 60.6 + - - +
155A PRO* 4.3 5.0 - - + +
157A ILE* 3.9 17.5 - - + -
179A ARG* 4.3 7.1 + - - -
182A SER* 2.8 32.6 + - - +
203A ALA* 3.7 26.0 - - + -
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Residues in contact with SER 150 (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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126A PRO* 3.1 5.9 - - - +
127A THR* 2.8 50.4 + - - +
129A ASP* 2.9 18.1 + - - -
149A ALA* 1.3 76.0 - - - +
151A GLY* 1.3 59.4 + - - +
154A ASP* 6.2 0.2 - - - -
155A PRO* 3.7 12.4 - - - +
182A SER* 4.7 5.6 - - - -
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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