Contacts of the helix formed by residues 159 - 166 (chain A) in PDB entry 2N8A
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 HIS 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A CYS* 3.1 21.3 - - + +
128A CYS* 3.8 8.1 - - - -
130A GLU* 3.8 15.5 - - + -
131A LYS 4.0 8.4 + - - -
132A ILE* 3.5 27.2 - - + +
136A GLN* 4.5 11.2 + - + -
137A VAL 4.8 3.4 - - - -
138A ARG* 5.0 0.2 - - - +
158A TYR* 1.3 74.7 - - - +
160A PRO* 1.3 72.4 - - + +
161A GLY* 4.3 1.8 - - - +
162A CYS* 3.1 11.5 + - - +
163A PHE* 2.8 26.6 + - - +
1001A ZN 2.0 37.7 - - - -
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Residues in contact with PRO 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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137A VAL* 3.3 34.1 - - + +
138A ARG* 4.5 0.9 - - - -
139A LEU* 3.7 24.5 - - + -
158A TYR 3.6 1.5 - - - +
159A HIS* 1.3 87.0 - - + +
161A GLY* 1.3 63.2 + - - +
163A PHE* 3.3 1.4 + - - +
164A VAL* 2.9 29.3 + - - +
195A LEU* 4.3 10.3 - - + -
198A GLN* 3.8 18.2 - - - +
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Residues in contact with GLY 161 (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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159A HIS* 3.2 2.7 - - - +
160A PRO* 1.3 82.4 - - - +
162A CYS* 1.3 63.3 + - - +
164A VAL* 3.1 9.7 + - - +
165A LYS* 3.1 22.4 + - - +
198A GLN* 4.2 3.8 - - - +
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Residues in contact with CYS 162 (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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125A CYS* 3.6 10.3 - - - -
127A GLY* 4.8 8.1 - - - -
128A CYS* 4.0 10.3 - - - -
158A TYR* 4.6 3.3 - - + -
159A HIS* 3.1 14.7 + - - +
161A GLY* 1.3 74.0 - - - +
163A PHE* 1.3 63.0 + - - +
165A LYS* 3.3 23.9 + - - +
166A ASN* 3.1 25.7 + - - +
1001A ZN 2.3 36.8 - - - -
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Residues in contact with PHE 163 (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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113A PHE* 3.9 13.7 - + - -
139A LEU* 3.7 30.7 - - + -
140A SER 4.0 25.6 - - - -
141A LYS* 4.1 5.2 - - + -
158A TYR* 3.9 20.8 - + + +
159A HIS 2.8 20.2 + - - +
160A PRO 3.4 5.6 - - - +
162A CYS* 1.3 74.2 - - - +
164A VAL* 1.3 68.5 + - + +
166A ASN 3.2 5.4 + - - -
167A ARG* 3.1 16.8 + - + -
170A LEU* 3.8 23.6 - - + +
172A PHE* 3.6 47.1 - + + -
181A LEU* 5.2 3.6 - - + -
199A LEU* 4.6 9.4 - - + -
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Residues in contact with VAL 164 (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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160A PRO 2.9 17.4 + - - +
161A GLY* 3.5 8.5 - - - +
163A PHE* 1.3 78.8 - - + +
165A LYS* 1.3 64.4 + - - +
167A ARG* 3.0 30.0 - - + +
198A GLN* 2.9 50.9 - - + +
199A LEU* 4.4 13.9 - - + -
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Residues in contact with LYS 165 (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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127A GLY 6.4 0.2 - - - -
128A CYS* 6.1 2.0 - - - +
161A GLY 3.1 12.1 + - - +
162A CYS* 3.4 23.9 - - - +
163A PHE 3.2 0.2 - - - -
164A VAL* 1.3 77.8 - - - +
166A ASN* 1.3 72.4 + - - +
167A ARG* 3.7 3.1 + - - +
168A GLU* 5.2 0.3 + - - +
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Residues in contact with ASN 166 (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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127A GLY* 4.8 14.9 - - - -
158A TYR* 5.6 3.7 - - + -
162A CYS* 3.1 22.1 + - - +
163A PHE 3.2 4.9 + - - -
164A VAL 3.1 0.4 - - - -
165A LYS* 1.3 94.0 - - - +
167A ARG* 1.3 63.6 + - - -
168A GLU* 3.1 4.0 + - - -
169A GLU* 3.3 12.5 + - + +
170A LEU* 3.0 40.8 + - + +
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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