Contacts of the helix formed by residues 176 - 181 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 2.9 23.5 + - + +
147A PRO* 3.9 39.3 - - + +
148A ASN 4.7 1.8 - - - -
149A ASN* 3.5 13.8 + - + -
173A ASP 5.1 0.4 + - - -
174A GLU* 3.1 1.0 - - - +
175A ALA* 1.3 80.6 - - + +
177A TYR* 1.3 65.5 + - - +
178A GLU 3.4 2.7 - - - -
179A PHE* 2.9 25.7 + + + +
180A HIS 3.5 3.3 + - - -
202A LYS* 2.9 34.6 + - + -
280A ARG 4.1 1.0 - - - +
281A GLY* 4.2 7.2 - - - -
282A ASN* 3.1 31.2 - - - -
283A PHE* 4.0 14.1 - + - -
1335A PMP 2.6 40.8 + + + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 4.4 8.1 - + - -
147A PRO* 3.9 10.3 - - - +
174A GLU* 3.2 27.6 + - + +
175A ALA 3.5 0.6 - - - -
176A TYR* 1.3 75.6 - - - +
178A GLU* 1.3 84.6 + - - +
180A HIS* 2.6 25.2 + - - -
181A GLY* 2.8 43.9 + - - -
182A GLU 3.6 19.1 - - - -
183A SER* 3.8 17.5 - - - -
198A ARG* 3.1 41.9 + - - +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 2.7 37.3 + - - +
174A GLU 4.9 1.6 - - - +
175A ALA 4.4 11.4 - - - +
176A TYR 3.2 0.6 + - - -
177A TYR* 1.3 98.0 + - + +
179A PHE* 1.3 65.9 + - + +
180A HIS 3.6 0.2 + - - -
181A GLY* 4.4 4.7 + - - +
198A ARG* 4.4 5.9 - - - -
199A THR 4.3 11.1 + - - +
202A LYS* 6.0 0.2 - - - +
203A ALA* 3.3 35.8 + - + +
204A PHE* 4.3 8.0 - - + -
213A TYR* 4.5 1.0 + - - -
255A THR* 3.4 18.8 - - + +
259A VAL* 5.3 0.2 - - - +
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Residues in contact with PHE 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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29A ASN* 4.8 2.9 - - - -
175A ALA 5.2 0.9 - - - -
176A TYR* 2.9 21.3 + + - +
177A TYR 2.8 0.2 + - - -
178A GLU* 1.3 80.5 - - + +
180A HIS* 1.3 61.6 + - - +
202A LYS* 3.7 27.1 - - + -
203A ALA* 3.8 29.4 - - + -
255A THR* 3.6 27.8 - - + -
258A ILE* 3.9 24.5 - - + -
259A VAL* 3.8 16.3 - - + +
262A ARG* 3.5 15.2 + - - +
280A ARG* 3.3 19.3 - - - +
281A GLY 3.7 11.0 - - - +
282A ASN* 3.7 36.8 - - + -
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Residues in contact with HIS 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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146A ASN* 5.3 2.3 + - - -
147A PRO* 3.6 27.5 - - + +
154A VAL* 3.3 47.3 - - + +
176A TYR 3.5 0.6 + - - -
177A TYR* 2.6 14.5 + - - +
178A GLU 4.8 0.4 - - - -
179A PHE* 1.3 77.2 - - - +
181A GLY* 1.3 56.9 + - - +
182A GLU* 3.6 39.0 + - + +
184A TYR* 5.3 3.4 - + - -
280A ARG* 3.5 29.3 + - + +
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Residues in contact with GLY 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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177A TYR* 2.8 34.1 + - - -
178A GLU 4.4 3.7 + - - -
180A HIS* 1.3 74.0 - - - +
182A GLU* 1.3 61.3 + - - +
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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