Contacts of the strand formed by residues 156 - 163 (chain B) in PDB entry 4MNY
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 LYS 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 2.9 37.9 + - + +
18B GLY* 2.7 34.6 + - - +
19B GLY 4.7 0.9 + - - -
20B GLU* 3.3 15.7 - - - +
21B PHE* 3.6 27.4 - - + -
22B THR* 3.7 3.8 - - - -
139B THR* 3.2 8.5 - - - +
140B GLY 2.9 36.2 + - - +
144B GLU* 3.0 39.4 + - + +
152B PRO* 4.4 6.1 - - + -
154B GLN 3.7 3.8 - - - +
155B LEU* 1.3 73.0 - - - +
157B MET* 1.3 61.4 + - - +
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Residues in contact with MET 157 (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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16B ILE* 4.3 4.2 - - - +
19B GLY* 3.4 1.6 - - - -
20B GLU* 2.9 50.6 + - + +
22B THR* 3.2 32.2 - - + +
26B ASN* 3.7 17.7 - - + +
27B GLN* 3.4 28.0 - - + +
137B GLU* 3.9 30.7 - - - +
138B ILE 3.1 11.7 - - - +
139B THR* 3.6 5.2 - - - +
156B LYS* 1.3 76.2 - - - +
158B THR* 1.3 63.4 + - - +
159B VAL* 6.2 1.6 - - + -
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Residues in contact with THR 158 (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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16B ILE* 3.7 13.7 - - + +
19B GLY* 3.4 16.4 - - - -
137B GLU* 3.3 7.3 - - - +
138B ILE* 2.9 59.2 + - + +
157B MET* 1.3 77.6 - - - +
159B VAL* 1.3 74.2 + - - +
160B VAL* 4.6 0.7 - - + -
188B THR* 2.7 35.3 + - - +
189B ASP 4.2 4.9 - - - +
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Residues in contact with VAL 159 (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 SER* 3.7 29.2 - - - +
136B CYS 3.3 12.1 - - - +
137B GLU* 4.5 13.2 - - + -
157B MET* 6.2 1.6 - - + -
158B THR* 1.3 84.4 + - - +
160B VAL* 1.3 72.7 + - - +
161B LYS* 5.8 0.9 - - + -
185B ASP* 5.1 2.4 - - - +
188B THR* 3.7 16.5 - - - +
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Residues in contact with VAL 160 (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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134B THR 3.7 0.2 - - - +
135B SER* 3.5 1.5 - - - -
136B CYS* 2.8 36.4 + - - +
138B ILE* 4.0 29.8 - - + -
158B THR* 4.6 1.3 - - + -
159B VAL* 1.3 79.6 - - - +
161B LYS* 1.3 63.0 + - - +
162B LEU 4.1 0.2 + - - -
183B ALA* 3.6 22.6 - - + +
184B ALA* 3.8 24.9 - - - +
185B ASP* 4.1 1.6 - - - +
188B THR 4.1 18.2 - - - +
189B ASP* 4.5 4.3 - - - +
199B LEU* 4.0 18.2 - - + -
228B TYR* 4.4 2.7 - - - +
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Residues in contact with LYS 161 (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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133B GLY* 3.6 29.1 + - - +
134B THR 3.2 3.8 - - - +
135B SER* 3.6 22.4 - - - +
159B VAL* 5.8 1.1 - - + -
160B VAL* 1.3 73.9 - - - +
162B LEU* 1.3 67.3 + - - +
163B ILE* 3.6 4.4 + - + +
183B ALA* 3.2 2.9 - - - -
184B ALA 2.8 37.3 + - - +
185B PRO* 3.9 30.6 - - - +
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Residues in contact with LEU 162 (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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129B ASP* 5.9 0.2 - - + -
130B PRO* 3.5 50.7 - - + +
131B GLN 4.2 2.0 - - - +
132B PHE* 3.9 7.0 - - - +
133B GLY* 2.8 32.8 + - - +
134B THR* 2.9 19.0 + - - +
136B CYS* 4.0 14.1 - - + -
161B LYS* 1.3 75.3 - - - +
163B ILE* 1.3 63.1 + - - +
181B LEU* 5.1 15.0 - - + -
182B CYS 3.6 6.5 - - - +
183B ALA* 4.0 11.9 - - + -
199B LEU* 3.9 27.6 - - + -
201B CYS* 4.3 0.9 - - - -
210B THR* 4.9 2.5 - - + -
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Residues in contact with ILE 163 (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 PHE* 4.2 2.7 - - - -
161B LYS* 3.8 6.5 - - + +
162B LEU* 1.3 78.8 - - - +
164B SER* 1.3 75.5 + - - +
165B HIS* 3.6 1.0 + - - -
167B GLU* 3.6 32.5 - - + +
168B CYS* 4.1 9.9 - - + +
171B TYR* 4.3 9.4 - - + -
181B LEU* 5.6 4.2 - - - +
182B CYS* 2.9 27.1 + - + +
183B ALA 4.1 0.7 - - - -
184B ALA* 3.7 26.2 - - + +
186B TRP* 4.6 3.6 - - + -
225B PRO* 3.5 30.3 - - + -
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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