Contacts of the helix formed by residues 156 - 160 (chain A) in PDB entry 2YZ5
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 ASP 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.1 9.1 - - + -
137A PHE* 4.3 11.4 - - + -
155A LEU* 1.3 73.4 - - - +
157A LEU* 1.3 61.7 + - - +
158A PRO* 2.9 13.2 - - - +
159A LYS* 2.8 36.4 + - + +
170A LEU* 4.3 4.7 - - + +
203A TYR* 3.4 14.5 - - - -
204A PRO* 3.2 17.9 - - - +
205A ALA* 2.8 32.6 + - - +
208A LEU* 4.0 15.7 - - + +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL 3.4 24.7 - - - +
108A HIS* 4.0 5.8 - - + -
115A LEU* 4.2 8.3 - - + -
116A ASP* 3.7 35.3 - - + +
124A TYR* 4.8 0.9 + - - -
136A TYR* 3.2 23.1 - - + +
154A HIS* 3.2 35.6 + - + +
155A LEU 3.4 0.8 + - - -
156A ASP* 1.3 73.5 - - - +
158A PRO* 1.3 63.9 - - + +
159A LYS 3.0 2.2 + - - -
160A LYS* 3.0 24.6 + - + +
203A TYR* 3.8 24.0 - - + +
2001A PO4 6.0 2.0 - - - +
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Residues in contact with PRO 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.0 7.9 - - + -
124A TYR* 3.5 31.4 + - + +
132A VAL* 4.3 14.4 - - + -
133A PHE* 3.4 33.5 - - + -
136A TYR* 3.6 41.3 - - + -
156A ASP* 3.0 8.5 - - - -
157A LEU* 1.3 92.5 - - + +
159A LYS* 1.3 57.3 + - - +
160A LYS 3.2 2.7 + - - -
161A PHE 4.8 0.5 + - - -
163A HIS* 3.8 10.2 + - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.7 6.7 - - + -
156A ASP* 2.8 46.5 + - + +
157A LEU 3.0 1.8 + - - -
158A PRO* 1.3 75.9 - - - +
160A LYS* 1.3 65.5 + - - +
161A PHE 3.3 2.0 - - - -
162A GLY* 2.9 17.0 + - - -
163A HIS 3.1 20.6 - - - +
164A ARG* 3.7 16.3 - - + -
199A ALA* 3.1 17.6 - - + +
201A GLU* 2.6 39.8 + - - +
202A VAL 2.9 23.9 + - - -
203A TYR* 3.7 16.2 - - + -
205A ALA* 3.2 6.0 - - + +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 2.9 48.7 + - + +
118A PRO* 4.5 6.6 - - - +
124A TYR* 5.7 0.9 - - - +
157A LEU* 3.0 18.0 + - + +
158A PRO 3.2 1.4 - - - -
159A LYS* 1.3 78.5 - - - +
161A PHE* 1.3 82.8 + - + +
197A ARG* 3.4 34.8 - - + +
198A PRO* 3.3 9.2 - - - +
199A ALA* 3.1 23.2 + - - -
203A TYR* 3.3 25.4 - - - +
2001A PO4 4.8 10.7 + - - -
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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