Contacts of the helix formed by residues 168 - 174 (chain C) in PDB entry 3ULA
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 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C LEU* 3.8 7.4 - - + +
142C GLU* 3.6 50.0 - - + +
166C LYS* 3.5 13.5 - - - +
167C LEU* 1.3 86.0 - - - +
169C GLU* 1.3 68.2 + - - +
170C TYR* 3.2 22.9 - - + +
171C PHE* 2.9 38.3 + - + +
197C VAL* 4.1 2.3 - - - +
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PRO* 1.3 72.6 - - - +
170C TYR* 1.3 51.5 + - - +
171C PHE* 2.6 13.7 + - - +
172C SER* 2.6 33.6 + - - +
197C VAL* 3.7 19.8 - - + +
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Residues in contact with TYR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 2.4 47.6 + - - +
142C GLU 4.0 10.1 - - - -
144C PHE* 3.7 14.7 + - - +
146C ILE* 3.5 27.4 - - + +
147C GLY* 3.9 30.2 - - - +
168C PRO* 3.0 21.8 + - + +
169C GLU* 1.3 75.3 - - - +
171C PHE* 1.3 85.6 + + - +
172C SER* 3.0 2.4 + - - -
173C ASN* 3.2 23.0 + - - +
174C LEU* 3.9 8.2 - - + +
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 4.0 13.7 - - + -
146C ILE* 5.5 3.1 - - + -
155C LEU* 5.6 3.1 - - + -
167C LEU* 3.6 37.2 - - + -
168C PRO* 2.9 40.5 + - + +
169C GLU 2.6 6.7 + - - -
170C TYR* 1.3 94.4 - + - +
172C SER* 1.3 52.7 + - - +
174C LEU* 2.7 59.8 + - + +
177C LEU* 3.8 23.3 - - + -
180C LEU* 3.8 16.6 - - + -
197C VAL* 4.1 15.7 - - + -
198C LEU* 6.3 2.7 - - + -
201C MET* 3.6 13.3 - - - +
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Residues in contact with SER 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU* 2.6 29.4 + - - +
170C TYR 4.6 0.2 - - - -
171C PHE* 1.3 74.5 - - - +
173C ASN* 1.3 68.8 + - - +
174C LEU 2.8 6.4 + - - -
175C THR* 3.5 5.2 + - - -
197C VAL* 5.0 8.8 + - - +
200C GLN* 6.1 3.8 - - - -
201C MET* 2.9 31.2 - - - +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLY 3.4 22.5 + - - +
150C LYS* 3.5 36.9 - - + +
170C TYR* 3.2 10.2 + - - +
172C SER* 1.3 78.5 - - - +
174C LEU* 1.3 57.3 + - - +
175C THR* 2.9 20.4 + - - +
406C NAG 3.0 46.4 + - - -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ILE* 4.4 21.3 - - + +
147C GLY 4.6 2.7 - - - +
149C LEU 3.5 24.5 - - - +
150C LYS 4.7 4.3 - - - -
152C LEU* 4.7 15.9 - - + +
155C LEU* 6.1 0.7 - - + -
170C TYR* 3.9 14.8 - - + +
171C PHE* 2.7 68.8 + - + +
172C SER 2.8 0.2 + - - -
173C ASN* 1.3 71.0 - - - +
175C THR* 1.3 50.3 + - - +
176C ASN 2.6 18.3 + - - -
177C LEU* 2.9 29.5 + - + +
201C MET* 3.9 10.7 - - + +
204C LEU* 4.1 3.1 - - - +
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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
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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