Contacts of the helix formed by residues 173 - 179 (chain A) in PDB entry 3UZC
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 PRO 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO* 4.6 3.4 - - + -
143A TRP* 3.0 43.7 - - + +
144A ASN* 3.4 22.7 - - + +
145A ASN* 3.7 19.7 - - - +
171A VAL 3.8 0.4 - - - +
172A VAL* 1.3 91.6 - - + +
174A MET* 1.3 58.7 + - - +
175A ASN* 3.1 21.5 - - - +
176A TYR* 4.0 3.0 + - + +
177A MET* 3.1 27.0 + - - +
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 4.9 1.0 - - - +
168A PHE* 6.2 2.5 - - - -
169A GLU* 5.2 16.6 - - - +
172A VAL 4.7 6.3 - - - +
173A PRO* 1.3 73.7 - - - +
175A ASN* 1.3 62.5 + - - +
176A TYR 3.1 2.0 - - - -
177A MET* 3.2 11.2 + - + +
178A VAL* 3.0 37.5 + - + +
253A ASN* 4.0 43.5 - - + +
256A THR* 4.9 14.6 - - + -
257A PHE* 3.7 24.9 - - + -
330A T4E 5.4 6.1 - - - +
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Residues in contact with ASN 175 (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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143A TRP* 3.0 37.9 + - + +
173A PRO* 3.1 13.1 - - - +
174A MET* 1.3 74.8 - - - +
176A TYR* 1.3 64.2 + - - -
178A VAL 4.0 0.2 - - - -
179A TYR* 3.1 42.6 + - + +
180A PHE* 3.8 0.7 + - - +
257A PHE* 3.8 20.8 - - + -
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Residues in contact with TYR 176 (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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85A LEU* 3.9 16.4 - - + +
135A ILE* 2.6 29.1 + - - +
136A GLY* 3.9 6.2 + - - -
138A THR* 3.5 24.7 - - + -
139A PRO* 3.5 30.0 - - + +
143A TRP* 3.4 32.3 - + + +
172A VAL* 4.8 1.1 - - + -
173A PRO* 4.0 8.7 - - + +
174A MET 3.1 0.2 - - - -
175A ASN* 1.3 78.6 + - - +
177A MET* 1.3 71.2 + - + +
178A VAL 3.0 5.3 + - - -
180A PHE* 3.2 43.5 + + + -
181A ASN* 2.7 48.8 + - + +
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Residues in contact with MET 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.1 6.1 - - + -
168A PHE* 3.7 27.1 - - + -
172A VAL* 3.7 22.0 - - + +
173A PRO 3.1 18.4 - - - +
174A MET* 3.2 18.3 + - - +
176A TYR* 1.3 88.8 - - - +
178A VAL* 1.3 60.5 + - + +
181A ASN* 3.6 26.7 + - - +
182A PHE* 3.2 23.7 + - - +
250A HIS* 4.5 4.5 + - - -
253A ASN* 4.5 12.4 + - - +
330A T4E 3.8 32.8 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A MET* 3.0 24.5 + - + +
176A TYR 3.0 1.4 + - - -
177A MET* 1.3 79.4 - - + +
179A TYR* 1.3 73.3 + - + +
182A PHE* 3.2 6.8 + - - +
183A PHE* 3.0 43.7 + - + -
253A ASN* 4.1 15.9 - - + +
254A CYS* 5.1 4.7 - - - +
257A PHE* 3.8 26.5 - - + -
258A PHE* 3.3 35.0 - - + -
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Residues in contact with TYR 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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175A ASN* 3.1 26.8 + - + +
178A VAL* 1.3 85.4 - - + +
180A PHE* 1.3 69.1 + - - +
183A PHE* 3.5 15.0 - + + +
184A ALA* 3.2 18.7 + - - +
257A PHE* 3.3 40.2 - + - -
258A PHE* 3.8 20.0 - + - -
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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