Contacts of the strand formed by residues 181 - 189 (chain A) in PDB entry 2G1Y
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A SER* 3.9 11.3 - - - -
177A ASP 3.3 21.1 - - - -
178A PRO* 3.2 48.6 + - + +
180A HIS* 1.3 78.7 - - - +
182A GLU* 1.3 65.6 + - - +
183A GLY 4.1 12.8 - - - -
184A ASN* 5.6 0.2 - - - -
185A PHE* 3.5 30.5 - + - -
319A TYR* 3.7 28.3 - + + -
332A ALA* 4.0 17.9 - - + -
333A LEU 3.1 13.5 - - - +
335A ARG* 3.2 16.5 + - - +
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Residues in contact with GLU 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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181A TYR* 1.3 76.7 - - - +
183A GLY* 1.3 69.7 + - - +
184A ASN 4.8 0.2 - - - +
332A ALA* 4.0 5.0 - - - +
333A LEU* 2.9 61.4 + - + +
334A ALA 4.9 1.6 - - - +
335A ARG* 3.3 43.5 + - + +
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Residues in contact with GLY 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 TYR* 4.1 13.9 - - - -
182A GLU* 1.3 81.7 - - - +
184A ASN* 1.3 69.3 + - - -
333A LEU* 6.0 0.4 - - - -
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Residues in contact with ASN 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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181A TYR* 5.6 0.2 - - - -
182A GLU 4.8 0.2 - - - +
183A GLY* 1.3 83.1 + - - -
185A PHE* 1.3 66.7 + - - +
186A HIS* 3.0 28.1 + - + -
331A PHE 3.8 3.5 - - - +
332A ALA* 4.1 8.4 - - - +
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Residues in contact with PHE 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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176A SER* 3.6 25.6 - - - -
181A TYR* 3.5 36.3 - + - -
184A ASN* 1.3 81.6 - - - +
186A HIS* 1.3 63.1 + - - +
187A TYR* 3.5 39.0 + - + -
319A TYR* 3.7 26.0 - + - -
321A GLU* 3.7 20.6 - - + -
330A GLY* 3.6 20.0 - - - -
331A PHE 3.2 17.5 - - - +
332A ALA* 3.8 8.1 - - + -
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Residues in contact with HIS 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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184A ASN* 3.0 35.1 + - + -
185A PHE* 1.3 74.1 - - - +
187A TYR* 1.3 65.4 + - - +
188A ILE* 4.3 4.6 - - + +
268A GLY 6.1 0.9 - - - +
270A LYS* 3.3 44.6 - - + -
272A TYR* 3.3 24.2 + - - +
329A ILE 3.9 0.5 - - - +
330A GLY* 3.6 0.9 - - - -
331A PHE* 2.9 27.4 + - - +
332A ALA* 5.6 0.6 - - - -
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Residues in contact with TYR 187 (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 PHE* 3.5 33.7 - - + +
186A HIS* 1.3 71.9 - - - +
188A ILE* 1.3 71.0 + - - +
189A ASN* 5.5 2.2 - - - +
268A GLY* 4.7 7.8 - - - +
321A GLU* 2.7 30.6 + - + -
323A ASP* 4.8 1.3 - - + -
328A ARG* 3.2 65.2 + - + +
329A ILE 3.3 5.6 - - - -
330A GLY* 3.7 20.9 - - - -
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Residues in contact with ILE 188 (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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186A HIS* 4.3 4.5 - - + +
187A TYR* 1.3 81.1 - - - +
189A ASN* 1.3 76.3 + - - +
198A ILE* 3.6 34.7 - - + +
199A GLN* 4.5 7.6 - - + +
201A LYS* 5.5 0.9 - - - +
267A LEU* 3.2 36.3 - - + +
268A GLY* 3.6 24.7 - - - +
272A TYR* 5.0 2.0 - - + +
328A ARG* 3.3 1.3 - - - -
329A ILE* 2.9 32.9 + - + +
331A PHE* 4.0 16.6 - - + -
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Residues in contact with ASN 189 (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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187A TYR* 5.5 1.6 - - - +
188A ILE* 1.3 81.2 - - - +
190A LEU* 1.3 67.9 + - - +
191A ILE* 3.5 2.6 + - - +
198A ILE* 3.8 9.6 - - - +
199A GLN* 4.9 2.3 + - - +
326A ASN 4.6 4.2 + - - -
327A ASN 3.9 4.7 + - - +
328A ARG* 3.7 22.2 - - - +
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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