Contacts of the strand formed by residues 143 - 150 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 4.2 3.8 - - - +
137B VAL* 3.6 20.9 - - + -
141B ARG 3.4 1.8 + - - -
142B THR* 1.3 72.1 - - - +
144B THR* 1.3 60.6 + - - +
145B MET* 4.1 1.7 + - - -
186B LEU 3.5 2.8 - - - +
187B GLN* 3.5 0.7 - - - -
188B ILE* 2.7 44.1 + - + +
191B SER* 3.4 16.8 - - - +
217B LEU* 3.7 26.7 - - + -
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LYS* 3.4 35.8 + - - +
142B THR* 3.9 10.6 + - - +
143B ALA* 1.3 73.9 - - - +
145B MET* 1.3 71.8 + - - +
146B LEU* 4.1 14.4 + - + +
185B ALA* 4.2 15.0 - - + -
186B LEU 3.3 6.7 - - - +
187B GLN* 3.9 20.6 - - + +
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 4.4 3.8 - - + -
133B GLN 3.6 20.9 - - - +
135B LYS* 3.8 24.7 - - - -
143B ALA 4.1 0.4 - - - -
144B THR* 1.3 73.6 - - - +
146B LEU* 1.3 60.1 + - - +
159B TRP* 3.7 20.6 - - + -
185B ALA* 3.2 5.7 - - - +
186B LEU* 2.7 46.6 + - + +
188B ILE* 5.1 7.6 - - + -
199B TYR* 4.1 28.7 - - + -
215B ALA* 3.7 30.1 - - + +
216B ASN 4.1 9.9 - - - +
217B LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B MET* 4.3 21.3 - - + +
131B GLY 3.7 2.3 - - - +
132B PRO* 3.0 33.0 - - + +
133B GLN 5.4 1.6 - - - +
144B THR* 4.1 13.6 + - + +
145B MET* 1.3 76.0 - - - +
147B CYS* 1.3 60.9 + - - +
159B TRP* 3.9 1.8 - - - -
183B ILE* 3.9 26.0 - - + -
184B GLY 3.8 0.4 - - - -
185B ALA* 3.4 26.0 - - + -
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 4.2 11.7 - - - -
130B MET* 3.4 11.2 - - - -
132B PRO* 4.7 1.3 - - + -
146B LEU* 1.3 75.9 - - - +
148B ALA* 1.3 69.9 + - - +
149B ALA* 4.1 3.4 - - - -
157B ILE* 4.3 3.0 - - + +
159B TRP* 3.8 5.2 - - + -
182B SER 3.8 0.2 - - - +
183B ILE* 3.5 6.3 - - - +
184B GLY 2.6 49.4 + - - +
201B CYS* 2.0 54.1 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 3.4 4.3 - - - +
129B ASP* 2.6 34.6 + - + -
130B MET* 2.8 40.2 + - + +
147B CYS* 1.3 72.8 - - - +
149B ALA* 1.3 56.9 + - - +
182B SER* 3.3 20.0 - - - +
183B ILE* 3.9 16.2 - - + -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR 3.2 13.5 - - - +
128B ILE* 4.1 6.7 - - + -
129B ASP* 3.6 4.3 - - - -
147B CYS* 4.1 2.4 + - - -
148B ALA* 1.3 74.6 - - - +
150B SER* 1.3 62.1 + - - +
155B PRO* 4.1 8.7 - - + +
157B ILE* 4.0 19.1 - - + -
179B ARG* 4.4 5.5 + - - -
182B SER* 2.8 27.4 + - - +
203B ALA* 3.8 24.7 - - + -
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE 4.3 0.2 - - - +
126B PRO* 3.2 5.0 - - - +
127B THR* 2.9 49.6 + - - +
129B ASP* 2.9 20.5 + - - -
149B ALA* 1.3 73.7 - - - +
151B GLY* 1.3 60.7 + - - +
154B ASP* 5.7 1.6 - - - -
155B PRO* 3.6 10.8 - - - +
182B SER* 5.2 3.6 - - - -
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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