Contacts of the helix formed by residues 181 - 190 (chain C) in PDB entry 4W9K
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 VAL 181 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASN* 4.7 8.1 - - - +
180C ILE* 1.3 74.0 - - - +
182C ARG* 1.3 68.1 + - - +
183C SER* 3.1 22.2 - - - +
184C LEU* 2.7 35.8 + - + +
185C TYR 3.4 4.9 + - - -
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Residues in contact with ARG 182 (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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176C ARG* 5.0 6.7 + - - +
180C ILE 3.4 3.7 + - - -
181C VAL* 1.3 71.4 - - - +
183C SER* 1.3 55.7 + - - +
185C TYR* 2.9 27.7 + - + +
186C GLU* 3.0 24.4 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASN* 4.9 5.0 + - - -
181C VAL* 2.7 27.1 + - - +
182C ARG* 1.3 75.6 - - - +
184C LEU* 1.3 55.9 + - - +
186C GLU* 3.6 17.2 - - - +
187C ASP* 2.9 34.2 + - - +
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Residues in contact with LEU 184 (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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104B LEU* 4.0 33.2 - - + -
105B MET* 4.3 20.6 - - + -
108B ASN* 3.8 31.9 - - + +
159C LYS* 4.3 4.5 - - - -
163C LEU* 4.8 0.4 - - + -
180C ILE* 3.5 26.7 - - + -
181C VAL* 2.7 33.8 + - + +
183C SER* 1.3 73.8 + - - +
185C TYR* 1.3 58.9 + - - +
186C GLU 3.3 0.2 - - - -
187C ASP* 3.5 19.1 - - + +
188C LEU* 2.9 33.6 + - - +
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Residues in contact with TYR 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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175C TYR* 4.8 12.7 - - + +
176C ARG* 3.3 30.1 - - - +
180C ILE* 3.6 15.0 - - + +
181C VAL 3.4 3.2 + - - +
182C ARG* 2.9 15.1 + - - +
184C LEU* 1.3 77.2 - - - +
186C GLU* 1.3 63.5 + - - +
188C LEU* 3.2 8.8 + - - +
189C GLU* 2.9 30.0 + - - +
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Residues in contact with GLU 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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176C ARG* 5.3 8.0 + - - +
182C ARG* 3.0 18.7 + - - +
183C SER* 3.6 22.1 + - - +
185C TYR* 1.3 75.5 - - + +
187C ASP* 1.3 53.8 + - - +
189C GLU* 3.1 11.1 + - - +
190C ASP* 2.8 36.9 + - - +
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Residues in contact with ASP 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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108B ASN* 4.3 0.7 - - - +
159C LYS* 3.1 32.6 + - - -
163C LEU* 4.0 20.7 - - + +
167C ARG* 3.0 21.6 + - - -
183C SER* 2.9 29.1 + - - +
184C LEU* 3.5 17.3 - - - +
185C TYR 3.3 0.6 - - - -
186C GLU* 1.3 76.0 - - - +
188C LEU* 1.3 60.8 + - - +
190C ASP* 3.4 13.6 + - - +
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Residues in contact with LEU 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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101B LEU* 6.3 0.2 - - + -
104B LEU* 5.0 2.7 - - + -
163C LEU* 3.5 32.1 - - + +
166C VAL* 3.7 39.0 - - + -
167C ARG* 2.9 32.8 + - + +
175C TYR* 3.8 27.5 - - + -
178C LEU* 4.1 12.1 - - + -
180C ILE* 4.0 19.7 - - + -
184C LEU 2.9 21.6 + - - +
185C TYR* 3.4 7.4 - - - +
187C ASP* 1.3 71.7 - - - +
189C GLU* 1.3 62.1 + - - +
190C ASP 3.4 0.5 + - - -
191C HIS* 3.3 10.6 + - - -
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Residues in contact with GLU 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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172C PRO 5.7 0.4 - - - +
175C TYR* 3.8 26.9 - - + +
176C ARG* 2.7 39.5 + - - +
185C TYR* 2.9 19.7 + - - +
186C GLU* 3.1 11.6 + - - +
188C LEU* 1.3 76.0 - - - +
190C ASP* 1.3 58.2 + - - +
191C HIS* 2.8 20.9 + - - -
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Residues in contact with ASP 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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167C ARG* 3.4 12.8 + - - -
186C GLU 2.8 20.8 + - - +
187C ASP* 3.6 10.3 - - - +
188C LEU 3.2 1.3 - - - -
189C GLU* 1.3 69.8 - - - +
191C HIS* 1.3 63.1 + - - +
192C PRO 3.7 0.2 - - - -
196C LYS* 3.3 31.6 + - - +
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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