Contacts of the helix formed by residues 176 - 181 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D ASN* 2.7 26.2 + - + +
147D PRO* 3.8 36.1 - - + +
148D ASN 5.1 0.2 - - - -
149D ASN* 3.6 13.7 + - + -
173D ASP 5.0 0.6 + - - -
174D GLU* 3.0 1.2 - - - +
175D ALA* 1.3 83.1 - - + +
177D TYR* 1.3 62.6 + - - +
178D GLU 3.5 1.8 - - - -
179D PHE* 3.3 22.5 + + + +
180D HIS 3.5 7.1 + - - -
202D LYS* 2.9 29.3 + - + -
280D ARG 4.0 0.7 - - - +
281D GLY* 4.0 16.8 - - - -
282D ASN* 3.1 31.2 - - - -
283D PHE* 3.8 12.1 - + - -
1335D PMP 2.7 40.6 + + + -
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Residues in contact with TYR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 4.2 11.2 - + - -
147D PRO* 4.4 4.0 - - - +
174D GLU* 2.9 23.2 + - + +
175D ALA 3.4 1.2 + - - -
176D TYR* 1.3 76.5 - - - +
178D GLU* 1.3 99.7 + - + +
180D HIS* 2.9 17.6 + - - +
181D GLY* 3.0 43.4 + - - -
182D GLU 3.3 24.7 - - - -
183D SER* 4.0 7.4 - - - -
198D ARG* 3.5 38.3 + - - +
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 2.8 37.1 + - - +
174D GLU 4.7 1.0 - - - +
175D ALA 4.3 8.7 - - - +
176D TYR 3.5 0.8 - - - -
177D TYR* 1.3 100.2 + - + +
179D PHE* 1.3 61.8 + - + +
180D HIS 4.8 1.6 - - - -
181D GLY* 4.8 2.0 + - - -
198D ARG* 4.3 5.1 + - - +
199D THR 4.6 9.7 + - - +
202D LYS* 6.2 0.2 - - - +
203D ALA* 3.4 34.0 - - + +
204D PHE* 4.2 11.3 - - + -
213D TYR* 4.6 1.7 + - - -
255D THR* 3.3 21.8 - - + +
259D VAL* 5.1 0.3 - - - +
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Residues in contact with PHE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASN* 6.2 0.2 - - - -
175D ALA 5.2 0.7 - - - -
176D TYR* 3.3 19.9 + + - +
177D TYR 3.0 1.2 - - - -
178D GLU* 1.3 77.0 - - + +
180D HIS* 1.3 63.8 + - - +
202D LYS* 3.7 26.9 - - + -
203D ALA* 3.7 28.7 - - + -
255D THR* 3.5 28.0 - - + -
258D ILE* 4.0 28.7 - - + -
259D VAL* 3.6 16.8 - - + +
262D ARG* 3.4 18.4 + - - +
280D ARG 3.4 11.7 - - - +
281D GLY 3.8 11.2 - - - +
282D ASN* 3.7 40.2 - - + -
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Residues in contact with HIS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN* 5.2 5.8 + - - -
147D PRO* 3.6 32.2 - - + +
154D VAL* 3.5 42.2 - - + +
176D TYR 3.5 1.7 + - - +
177D TYR* 2.9 6.5 + - - +
178D GLU 4.8 0.9 - - - -
179D PHE* 1.3 82.3 - - - +
181D GLY* 1.3 58.4 + - - +
182D GLU* 3.6 45.1 + - + +
184D TYR* 6.3 0.9 - + - -
280D ARG* 3.4 27.3 + - + +
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TYR* 3.0 31.0 + - - -
178D GLU 5.3 2.0 - - - -
180D HIS* 1.3 80.8 - - - +
182D GLU* 1.3 65.6 + - - +
183D SER 4.3 0.2 + - - -
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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