Contacts of the helix formed by residues 176 - 180 (chain B) in PDB entry 1UU1
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 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 2.9 22.6 + - + -
147B PRO* 3.6 44.7 - - + +
149B ASN* 3.5 12.1 + - + -
173B ASP 4.9 0.2 + - - -
174B GLU 3.1 1.2 - - - -
175B ALA* 1.3 86.1 - - + +
177B TYR* 1.3 66.0 + - - +
178B GLU 3.2 2.7 - - - -
179B PHE* 3.0 21.5 + + + +
180B HIS* 3.7 4.7 + - - +
202B LYS* 3.7 25.5 - - + -
280B ARG 4.4 0.2 - - - +
281B GLY* 4.1 7.0 - - - -
282B ASN* 3.3 31.4 - - - -
283B PHE* 3.6 20.4 - + - -
1335B PMP 2.5 43.9 + - + -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 4.4 10.1 - + - -
146B ASN 5.3 0.2 - - - -
147B PRO* 4.5 7.8 - - - +
174B GLU* 3.0 27.1 + - + +
175B ALA 3.4 0.8 - - - -
176B TYR* 1.3 75.6 - - - +
178B GLU* 1.3 78.3 + - - +
180B HIS* 2.4 37.0 + - - +
181B GLY 3.0 17.8 + - - -
182B GLU 2.9 29.6 - - - -
183B SER* 3.5 18.3 - - - -
198B ARG* 3.6 36.1 - - - +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 2.8 39.2 + - - +
174B GLU 4.5 1.4 - - - +
175B ALA 4.5 7.4 - - - +
176B TYR 3.1 0.4 + - - -
177B TYR* 1.3 97.2 + - + +
179B PHE* 1.3 65.6 + - + +
180B HIS 3.2 4.9 + - - +
198B ARG* 4.8 3.2 - - - -
199B THR 4.6 11.1 + - - +
202B LYS* 6.1 0.5 - - - +
203B ALA* 3.4 34.7 + - + +
204B PHE* 4.2 10.6 - - + -
213B TYR* 4.2 5.9 + - - -
255B THR* 3.2 20.8 - - + +
259B VAL* 5.2 0.3 - - - +
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 4.7 2.7 - - - -
175B ALA 5.2 0.2 - - - -
176B TYR* 3.0 21.2 + + - +
178B GLU* 1.3 76.6 - - + +
180B HIS* 1.3 56.0 + - - +
202B LYS* 3.5 30.7 - - + -
203B ALA* 3.8 29.6 - - + -
255B THR* 3.9 21.3 - - + -
258B ILE* 3.7 42.0 - - + -
259B VAL* 3.4 17.4 - - + +
262B ARG* 2.8 30.1 + - - +
280B ARG 3.2 14.4 - - - +
281B GLY 3.7 9.6 - - - +
282B ASN* 3.7 27.4 - - + -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 5.3 2.6 + - - -
147B PRO* 3.8 21.3 - - + +
154B VAL* 3.6 34.1 - - + +
176B TYR 4.2 0.2 - - - +
177B TYR* 2.4 27.0 + - - +
178B GLU* 3.7 5.9 - - - +
179B PHE* 1.3 77.8 - - - +
181B GLY* 1.3 68.8 + - - +
182B GLU* 3.4 45.6 + - + -
280B ARG* 3.3 46.1 + - + +
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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
------------------------------------------------------------
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