Contacts of the strand formed by residues 178 - 186 (chain B) in PDB entry 2ANL
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 TYR 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B ILE* 3.4 24.5 - - + +
174B GLU 3.7 8.3 - - - -
175B GLU* 3.2 55.9 + - + +
177B PHE* 1.3 79.6 - - - +
179B GLU* 1.3 68.2 + - - +
180B GLY 3.6 21.0 - - - +
182B LEU* 3.2 35.6 - - + +
310B PHE* 3.7 29.6 - + + -
323B ALA* 4.1 10.1 - - + -
324B VAL 3.1 13.9 - - - +
326B LYS* 3.8 5.8 - - - +
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Residues in contact with GLU 179 (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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178B TYR* 1.3 80.5 - - - +
180B GLY* 1.3 64.6 + - - +
181B GLU 5.1 0.5 - - - +
323B ALA* 4.7 1.0 - - - +
324B VAL* 2.6 47.4 + - + +
325B ALA 4.4 9.6 - - - +
326B LYS* 3.2 45.5 + - + +
327B ASN* 4.5 6.8 + - - +
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Residues in contact with GLY 180 (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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178B TYR* 3.6 19.3 - - - +
179B GLU* 1.3 79.0 - - - +
181B GLU* 1.3 60.8 + - - -
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Residues in contact with GLU 181 (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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179B GLU 5.1 0.2 - - - +
180B GLY* 1.3 75.7 - - - -
182B LEU* 1.3 70.9 + - - +
183B THR* 3.9 10.8 + - + +
322B PHE 4.3 0.5 - - - +
323B ALA* 4.1 9.6 - - - +
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Residues in contact with LEU 182 (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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173B ILE* 4.4 17.3 - - + -
178B TYR* 3.2 36.8 - - + +
181B GLU* 1.3 83.8 - - - +
183B THR* 1.3 65.7 + - - +
184B TYR* 3.9 36.4 - - + +
310B PHE* 5.0 2.0 - - + -
312B VAL* 3.8 28.5 - - + -
321B GLY* 5.2 1.1 - - - -
322B PHE 3.1 9.9 - - - +
323B ALA* 3.8 14.4 - - + -
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Residues in contact with THR 183 (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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181B GLU* 4.7 11.3 + - + +
182B LEU* 1.3 77.4 - - - +
184B TYR* 1.3 63.5 + - - +
264B ASN* 3.2 28.7 - - + +
266B TYR* 2.9 33.9 + - - -
321B GLY* 3.3 2.8 - - - -
322B PHE* 2.6 36.7 + - - +
323B ALA* 5.4 0.2 - - - -
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Residues in contact with TYR 184 (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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173B ILE* 5.3 6.3 - - + +
182B LEU* 3.9 41.1 - - + +
183B THR* 1.3 82.2 - - - +
185B GLU* 1.3 77.3 - - - +
186B LYS* 6.4 0.2 - - + -
264B ASN* 3.5 8.4 + - - +
312B VAL* 5.3 7.6 - - + -
314B ASP* 5.7 2.7 - - + -
317B LYS* 3.7 38.8 + - + -
319B SER* 3.7 20.4 - - - +
320B ILE 3.2 4.0 - - - -
321B GLY* 3.7 17.3 - - - -
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Residues in contact with GLU 185 (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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184B TYR* 1.3 78.1 - - - +
186B LYS* 1.3 62.1 + - - +
195B VAL* 3.9 22.0 - - + -
196B ASP 4.5 4.0 - - - +
197B LEU* 4.1 16.4 - - + +
261B SER* 2.9 38.5 + - - -
264B ASN* 2.9 14.9 + - - -
266B TYR* 3.3 16.3 + - + +
319B SER* 3.0 3.7 + - - -
320B ILE* 2.8 32.8 + - - +
322B PHE* 3.7 21.1 - - + -
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Residues in contact with LYS 186 (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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185B GLU* 1.3 74.9 + - - +
187B LEU* 1.3 70.8 + - - +
188B ASN* 3.2 3.1 + - - -
195B VAL* 3.9 10.5 - - - +
196B ASP* 4.7 2.6 + - - +
317B LYS* 4.7 9.4 - - - -
318B GLU* 4.0 7.9 - - + +
319B SER* 3.7 16.8 - - - -
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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