Contacts of the helix formed by residues 182 - 187 (chain X) in PDB entry 4HSC
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 ASN 182 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123X VAL 4.1 9.9 - - - -
124X LEU* 3.9 0.2 - - - +
180X LEU* 3.2 26.9 + - - +
181X ALA* 1.3 75.5 - - - +
183X LYS* 1.3 68.2 + - - +
184X GLY* 3.4 5.3 + - - -
185X PHE* 2.8 33.8 + - - +
186X THR* 3.3 6.5 + - - +
191X ASP* 2.8 29.2 + - - +
333X GLU 4.5 4.3 - - - +
334X ALA* 4.2 12.6 - - + +
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Residues in contact with LYS 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X VAL 4.8 1.4 + - - -
182X ASN* 1.3 73.6 - - - +
184X GLY* 1.3 62.6 + - - +
186X THR* 2.4 32.1 + - - +
187X GLU* 3.2 32.4 + - - +
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Residues in contact with GLY 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X ASN* 3.2 8.7 + - - -
183X LYS* 1.3 77.5 - - - +
185X PHE* 1.3 63.7 + - - +
187X GLU* 2.9 18.0 + - - -
189X LYS* 2.9 41.8 + - - -
191X ASP* 5.4 2.2 - - - -
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Residues in contact with PHE 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LEU* 3.7 26.9 - - + -
163X ILE* 3.9 28.1 - - + +
179X GLN* 3.3 17.7 - - - -
180X LEU 3.7 17.3 - - - +
182X ASN* 2.8 25.5 + - - +
184X GLY* 1.3 69.9 - - - +
186X THR* 1.3 58.2 + - - +
188X ASN* 2.9 20.4 + - - -
189X LYS 3.9 1.8 + - - -
190X PRO* 4.1 13.1 - - + +
337X LEU* 3.6 23.1 - - + -
433X TYR* 3.1 28.7 + + - -
435X SER* 4.0 15.5 - - - -
444X ALA* 5.4 4.5 - - + -
446X VAL* 3.9 22.4 - - + -
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Residues in contact with THR 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X VAL 5.0 0.2 - - - +
124X LEU* 3.5 44.6 - - + +
125X ALA 4.2 6.7 + - - +
126X LYS* 2.8 38.6 + - - +
163X ILE* 6.0 1.2 - - - +
182X ASN 3.8 9.9 - - - +
183X LYS* 2.4 35.7 + - - +
185X PHE* 1.3 78.3 - - - +
187X GLU* 1.3 62.2 + - - +
188X ASN* 3.4 5.2 + - - +
446X VAL* 4.1 18.0 - - + +
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Residues in contact with GLU 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X LYS* 4.4 11.0 - - + +
166X ILE* 4.6 1.6 - - - +
183X LYS* 3.2 44.2 + - - +
184X GLY* 2.9 9.0 + - - +
186X THR* 1.3 82.1 + - - +
188X ASN* 1.3 77.4 + - - +
189X LYS* 3.1 39.0 + - - +
270X ASN* 4.2 11.6 + - - +
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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