Contacts of the helix formed by residues 184 - 192 (chain C) in PDB entry 1P4D
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 GLY 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A GLU* 5.2 9.0 - - - -
122C SER* 4.9 1.1 - - - -
124C ARG* 5.6 0.2 - - - -
133C THR* 4.4 12.3 - - - -
177C SER* 6.3 2.2 - - - -
182C LYS 3.2 5.1 + - - -
183C THR* 1.3 73.2 - - - +
185C PHE* 1.3 62.5 + - - +
186C ILE* 3.8 1.3 - - - -
187C GLU* 3.4 10.6 + - - +
188C ASN* 2.4 35.5 + - - -
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Residues in contact with PHE 185 (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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271A GLU* 5.6 1.4 + - - -
80C TYR* 3.1 44.4 - + + +
82C LEU* 5.7 0.9 - - + -
117C VAL* 3.7 23.8 - - + -
120C LEU* 3.8 9.6 - - + -
121C ALA* 3.5 35.7 - - + -
122C SER* 4.2 18.9 + - - +
133C THR* 5.2 0.4 - - - +
139C LEU* 4.4 12.3 - - + -
162C VAL* 4.4 11.0 - - + -
175C LEU* 4.2 31.5 + - + +
184C GLY* 1.3 65.1 - - - -
186C ILE* 1.3 58.7 + - - +
187C GLU 2.9 3.6 - - - -
188C ASN* 2.5 35.5 + - - +
189C VAL* 3.0 29.6 + - + +
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Residues in contact with ILE 186 (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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271A GLU* 3.6 46.4 - - + +
272A ILE* 4.2 14.4 - - + -
275A ALA* 5.0 1.3 - - + -
4C ILE* 4.1 19.1 - - + -
5C ALA 5.7 0.2 - - - +
80C TYR* 3.4 53.8 + - + +
82C LEU* 5.4 0.4 - - + -
184C GLY* 5.4 0.4 - - - -
185C PHE* 1.3 81.4 - - - +
187C GLU* 1.3 63.4 + - + +
189C VAL* 3.4 12.5 + - + +
190C TYR* 3.0 37.1 + - + -
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Residues in contact with GLU 187 (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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271A GLU* 6.2 1.1 - - + +
275A ALA* 4.5 18.7 - - + +
278A MET* 4.9 10.7 - - - +
282A LYS* 5.7 2.1 + - - -
183C THR* 3.5 38.7 - - + +
184C GLY* 3.5 14.3 - - - +
185C PHE 2.7 2.6 + - - -
186C ILE* 1.3 82.5 - - + +
188C ASN* 1.3 60.1 + - - +
190C TYR* 3.5 5.4 + - - +
191C ALA* 2.9 32.4 + - - +
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Residues in contact with ASN 188 (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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120C LEU* 3.8 32.0 + - + +
122C SER* 5.1 3.6 + - - -
133C THR* 6.2 0.6 - - - +
135C LEU* 6.1 2.0 - - - +
183C THR* 4.3 16.7 + - - -
184C GLY* 2.4 32.4 + - - -
185C PHE* 2.5 18.4 + - - +
187C GLU* 1.3 70.5 - - - +
189C VAL* 1.3 64.5 + - - +
191C ALA* 3.2 7.3 + - - +
192C ASN* 3.1 29.8 + - - +
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Residues in contact with VAL 189 (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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2C MET* 3.5 17.5 - - + -
4C ILE* 3.5 20.6 - - + -
82C LEU* 4.1 17.5 - - + -
117C VAL* 4.6 7.4 - - + -
120C LEU* 4.2 3.6 - - + +
185C PHE* 3.0 46.1 + - + +
186C ILE* 3.6 13.0 - - + +
187C GLU 3.3 0.2 - - - -
188C ASN* 1.3 77.3 - - - +
190C TYR* 1.3 60.7 + - - +
192C ASN* 3.1 5.9 + - - +
193C GLN* 3.0 20.1 + - - -
196C PHE* 4.2 13.5 - - + -
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Residues in contact with TYR 190 (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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272A ILE* 3.9 16.4 - - + +
275A ALA* 3.5 32.3 - - + +
276A GLU* 3.0 41.5 + - + +
279A GLN* 3.1 40.1 - - + +
4C ILE* 3.3 53.1 + - + +
5C ALA* 4.8 0.3 - - - -
186C ILE* 3.0 30.8 + - + +
187C GLU* 3.7 7.0 - - - +
189C VAL* 1.3 77.2 - - - +
191C ALA* 1.3 61.9 + - - +
192C ASN 3.2 0.9 + - - -
193C GLN* 3.2 23.5 + - - +
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Residues in contact with ALA 191 (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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282A LYS* 5.5 9.4 - - - +
187C GLU* 2.9 29.5 + - - +
188C ASN* 3.2 7.8 + - - +
190C TYR* 1.3 76.0 - - - +
192C ASN* 1.3 72.9 + - - +
193C GLN 3.9 0.3 + - - -
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Residues in contact with ASN 192 (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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120C LEU* 5.1 5.3 - - - +
188C ASN* 3.2 16.0 + - - +
189C VAL 3.1 7.1 + - - +
191C ALA* 1.3 93.4 + - - +
193C GLN* 1.3 64.4 + - - +
194C ILE 3.4 2.0 - - - -
195C ALA* 3.3 17.8 + - + +
196C PHE* 2.8 43.7 + - + +
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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