Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 1U5Y
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 ARG 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ARG 4.0 0.2 - - - +
176A GLU* 3.4 5.9 - - - +
177A GLY 3.0 32.5 + - - +
178A GLN* 3.4 22.7 + - - +
179A GLY* 1.3 82.6 - - - +
181A ARG* 1.3 66.2 + - - +
182A GLU* 4.1 4.5 - - + +
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Residues in contact with ARG 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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172A VAL* 5.9 1.0 - - - +
174A SER* 4.1 20.8 + - - -
175A ARG 3.8 3.4 - - - -
176A GLU* 4.2 21.1 - - + +
180A ARG* 1.3 77.3 - - - +
182A GLU* 1.3 62.2 + - - +
183A THR* 3.0 29.5 + - - +
217A THR* 5.8 0.4 - - - +
219A LYS* 5.8 9.2 - - - +
232B HIS* 6.1 0.6 - - - -
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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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174A SER* 3.0 6.7 - - - -
175A ARG* 2.8 77.4 + - - +
180A ARG* 4.1 4.7 - - + -
181A ARG* 1.3 74.3 - - - +
183A THR* 1.3 72.3 + - - +
184A LEU* 3.7 11.6 + - + +
208A PHE* 5.7 1.4 - - - -
232B HIS* 5.8 0.7 - - - +
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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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172A VAL* 3.8 28.0 - - + +
173A VAL 3.9 5.2 - - - +
174A SER* 3.9 2.6 - - - -
181A ARG* 3.0 29.4 + - - +
182A GLU* 1.3 80.0 - - - +
184A LEU* 1.3 60.7 + - - +
185A PHE 4.0 5.8 - - - +
186A ARG* 5.0 8.9 + - + +
232B HIS* 2.9 61.6 + - + +
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Residues in contact with LEU 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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156A LEU* 3.8 28.7 - - + -
173A VAL* 2.9 19.3 + - + +
174A SER 4.5 0.4 - - - -
175A ARG* 4.1 39.5 - - + +
182A GLU* 4.0 21.3 - - - +
183A THR* 1.3 79.6 - - - +
185A PHE* 1.3 70.2 - - + +
208A PHE* 3.5 50.8 - - + -
210A LEU* 4.4 8.1 - - + -
216A ILE* 4.7 1.8 - - + -
110B HIS* 4.9 1.0 + - - -
231B PRO 4.4 4.2 - - - +
232B HIS* 3.9 11.1 - - - -
235B PHE* 5.1 0.2 - - - -
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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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156A LEU* 3.7 32.8 - - + -
158A SER* 4.2 10.1 - - - -
171A GLN* 5.6 1.6 - - + -
172A VAL* 3.8 0.3 - - - -
173A VAL* 2.9 62.8 + - + +
183A THR* 3.7 4.4 - - - +
184A LEU* 1.3 84.1 - - + +
186A ARG* 1.3 65.5 + - - +
187A CYS 5.0 0.4 - - - -
204A SER* 3.1 45.3 - - - -
205A ALA* 4.0 0.9 - - - -
206A GLY 4.1 3.8 - - - -
208A PHE* 3.6 27.1 - + + -
232B HIS* 3.4 14.8 - - - +
235B PHE* 3.7 17.7 - + + -
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Residues in contact with ARG 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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170A GLY 6.2 0.7 - - - -
171A GLN 3.4 9.6 - - - +
172A VAL* 3.7 37.8 - - + +
183A THR* 5.0 8.0 + - + +
185A PHE* 1.3 83.1 - - - +
187A CYS* 1.3 63.5 + - - +
188A ILE* 3.5 36.3 + - + +
204A SER* 4.3 0.4 + - - -
221A PRO* 4.6 12.5 - - - +
159B GLN* 2.9 25.6 + - - +
161B LEU* 5.7 1.1 - - + -
201B SER* 4.5 0.7 - - - -
232B HIS* 3.0 20.2 + - + +
233B GLY* 4.6 3.2 - - - -
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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