Contacts of the strand formed by residues 178 - 186 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ILE* 3.4 23.6 - - + +
174A GLU 3.7 7.9 - - - -
175A GLU* 3.1 40.5 + - + +
177A PHE* 1.3 80.2 - - - +
179A GLU* 1.3 67.1 + - - +
180A GLY 3.6 15.7 - - - -
182A LEU* 3.2 31.6 - - + +
310A PHE* 3.7 30.1 - + + -
323A ALA* 4.1 10.8 - - + -
324A VAL 3.1 14.4 - - - +
326A LYS* 3.8 5.9 - - - +
203B LYS* 2.8 53.6 + - + -
204B THR* 3.8 4.3 - - - -
205B SER 4.2 1.2 + - - -
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Residues in contact with GLU 179 (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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178A TYR* 1.3 81.1 - - - +
180A GLY* 1.3 64.7 + - - +
181A GLU 5.1 0.3 - - - +
323A ALA* 4.7 1.0 - - - +
324A VAL* 2.6 45.9 + - + +
325A ALA 4.4 8.3 - - - +
326A LYS* 3.2 45.4 + - + +
327A ASN* 4.5 6.2 + - - +
203B LYS* 4.5 4.3 - - - -
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Residues in contact with GLY 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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178A TYR* 3.6 12.3 - - - -
179A GLU* 1.3 76.4 - - - +
181A GLU* 1.3 65.5 + - - -
202B GLY 4.6 0.4 - - - -
203B LYS* 3.6 26.4 - - - +
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Residues in contact with GLU 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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179A GLU 5.1 0.3 - - - +
180A GLY* 1.3 76.7 - - - -
182A LEU* 1.3 64.1 + - - +
183A THR* 3.9 6.3 + - - +
322A PHE 4.3 0.2 - - - +
323A ALA* 4.1 9.1 - - - +
200B ASN* 2.6 36.6 + - - +
202B GLY* 2.3 42.0 - - - +
203B LYS 4.7 0.9 - - - -
256B THR* 4.1 11.3 + - - +
258B GLU* 2.4 44.7 - - - +
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Residues in contact with LEU 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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173A ILE* 4.4 17.5 - - + -
178A TYR* 3.2 36.8 - - + +
181A GLU* 1.3 76.1 - - - +
183A THR* 1.3 65.0 + - - +
184A TYR* 3.9 33.4 - - + +
310A PHE* 5.0 2.5 - - + -
312A VAL* 3.8 28.5 - - + -
321A GLY* 5.2 1.3 - - - -
322A PHE 3.1 9.9 - - - +
323A ALA* 3.8 14.4 - - + -
200B ASN* 3.6 21.0 + - - +
203B LYS 3.9 6.3 - - - +
205B SER* 4.1 13.7 - - - +
260B LYS* 6.2 0.3 - - - +
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Residues in contact with THR 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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181A GLU 4.7 4.9 + - - +
182A LEU* 1.3 77.8 - - - +
184A TYR* 1.3 63.0 + - - +
264A ASN* 3.2 28.9 - - + +
266A TYR* 2.9 33.7 + - - -
321A GLY* 3.3 2.9 - - - -
322A PHE* 2.6 36.0 + - - +
323A ALA* 5.4 0.3 - - - -
200B ASN* 5.9 0.7 - - - +
260B LYS* 4.7 11.0 - - + +
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Residues in contact with TYR 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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173A ILE* 5.3 5.3 - - + +
182A LEU* 3.9 42.0 - - + +
183A THR* 1.3 81.4 - - - +
185A GLU* 1.3 77.7 - - - +
264A ASN* 3.5 7.4 + - - +
312A VAL* 5.3 7.6 - - + -
314A ASP* 5.6 4.0 - - + -
317A LYS* 4.6 11.3 + - + -
319A SER* 3.7 8.3 - - - +
320A ILE 3.2 4.9 - - - -
321A GLY* 3.7 17.5 - - - -
322A PHE* 4.4 0.4 - - - -
198B ASP* 4.7 11.7 - - + +
200B ASN* 5.3 1.3 - - - -
205B SER* 4.4 14.7 + - - -
206B MET* 4.4 4.1 - - - -
207B GLU* 2.5 70.4 + - + +
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Residues in contact with GLU 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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184A TYR* 1.3 79.5 - - - +
186A LYS* 1.3 62.3 + - - +
195A VAL* 3.9 22.4 - - + -
196A ASP 4.5 3.6 - - - +
197A LEU* 4.1 16.2 - - + +
261A SER* 2.9 38.2 + - - -
264A ASN* 2.9 15.2 + - - -
266A TYR* 3.3 16.6 + - + +
319A SER* 3.0 4.0 + - - -
320A ILE* 2.8 33.0 + - - +
322A PHE* 3.7 20.0 - - + -
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Residues in contact with LYS 186 (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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185A GLU* 1.3 74.4 + - - +
187A LEU* 1.3 71.7 + - - +
188A ASN* 3.2 3.3 + - - +
195A VAL* 3.9 10.9 - - - +
196A ASP* 4.7 2.6 + - - +
317A LYS 4.7 7.4 - - - -
318A GLU* 4.0 7.4 - - + +
319A SER* 3.7 17.3 - - - -
198B ASP* 5.3 5.9 + - - -
207B GLU* 5.2 8.4 + - - +
208B LYS* 4.2 34.1 - - - +
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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