Contacts of the helix formed by residues 181 - 186 (chain C) in PDB entry 2ZXX
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 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A HIS* 3.4 31.6 - - + +
113B GLU* 3.9 6.3 - - - +
180C ALA* 1.3 85.5 - - - +
182C ALA* 1.3 55.7 + - - +
183C TYR* 3.4 20.2 - - + +
184C GLN* 2.7 53.2 + - + +
185C ARG* 3.1 9.8 + - - -
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Residues in contact with ALA 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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111A LEU* 3.6 13.5 - - + +
114A ASN* 3.2 23.3 - - - +
109B GLU 5.5 0.2 - - - +
110B ALA* 4.2 12.1 - - - -
113B GLU* 3.0 20.9 + - - +
180C ALA 3.5 2.2 + - - -
181C PRO* 1.3 69.6 - - - +
183C TYR* 1.3 62.3 + - - +
184C GLN 3.0 1.2 + - - -
185C ARG* 4.0 8.7 - - - +
186C PHE* 3.0 41.7 + - + -
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Residues in contact with TYR 183 (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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111A LEU* 3.7 35.8 - - + +
114A ASN* 2.9 31.4 + - - +
115A GLU* 3.2 44.9 - - + +
118A HIS* 3.8 15.5 - + + +
119A LYS* 4.9 8.7 + - - +
181C PRO* 3.1 27.0 + - + +
182C ALA* 1.3 71.5 - - - +
184C GLN* 1.3 77.9 + - + +
187C HIS* 3.5 22.5 - - - +
201C TYR* 3.6 34.2 + + - -
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Residues in contact with GLN 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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180C ALA* 5.1 4.2 - - + +
181C PRO* 2.7 31.7 + - + +
183C TYR* 1.3 104.9 + - + +
185C ARG* 1.3 60.0 + - - +
186C PHE 3.2 1.1 - - - -
187C HIS* 2.9 20.3 + - - +
201C TYR* 3.1 47.9 + - + +
202C LYS* 5.1 5.7 - - - +
350C ASP* 3.1 16.0 - - - +
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Residues in contact with ARG 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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109B GLU* 4.0 24.2 + - - +
113B GLU* 3.3 23.4 + - - -
179C LYS 4.1 7.4 + - - -
180C ALA* 2.9 41.2 + - + +
181C PRO 3.1 6.4 + - - +
182C ALA* 3.7 11.1 - - - +
184C GLN* 1.3 77.7 - - - +
186C PHE* 1.3 100.8 + - + +
189C LEU* 5.6 0.3 - - - +
348C ASN* 4.6 5.4 - - - +
350C ASP* 3.3 25.8 - - - +
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Residues in contact with PHE 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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107A LEU* 4.1 4.8 - - + +
111A LEU* 3.9 20.5 - - + +
106B ALA* 3.7 38.8 - - + -
109B GLU* 3.9 22.9 - - + -
110B ALA* 4.3 2.9 - - + -
182C ALA* 3.0 34.5 + - + +
185C ARG* 1.3 120.9 - - + +
187C HIS* 1.3 67.6 + - - +
188C ALA 3.2 2.5 - - - -
189C LEU* 3.0 29.6 + - + +
190C ALA 3.6 2.8 + - - -
350C ASP* 3.7 1.6 - - - -
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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