Contacts of the strand formed by residues 156 - 163 (chain P) in PDB entry 2ZCH
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 GLN 156 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16P ILE* 3.9 17.4 + - + -
19P GLY* 4.0 6.7 + - - +
20P TRP* 3.2 26.2 + - - +
21P GLU* 3.6 13.2 - - - +
22P CYS* 3.3 9.4 - - - -
139P SER* 3.1 23.9 - - - -
140P GLY 3.2 14.1 + - - +
144P ILE* 3.7 31.9 - - + +
152P PRO* 3.9 10.1 - - + +
154P LYS* 3.3 16.9 + - - +
155P LEU* 1.3 87.7 - - - +
157P CYS* 1.3 58.0 + - - +
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Residues in contact with CYS 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P ILE* 4.1 1.8 - - - -
19P GLY* 3.1 4.0 - - - -
20P TRP* 2.7 63.3 + - + +
22P CYS* 2.1 46.0 - - - -
26P SER* 5.0 0.4 - - - -
27P GLN* 3.9 18.2 - - - -
137P TYR* 5.8 4.3 - - + -
138P ALA 3.4 7.2 - - - +
139P SER* 3.9 11.9 - - - -
156P GLN* 1.3 73.7 - - - +
158P VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P ILE* 3.4 27.4 - - + -
17P VAL 4.3 0.9 - - - +
18P GLY 4.3 1.8 - - - +
19P GLY* 4.1 11.9 - - - -
20P TRP* 3.5 10.5 - - + -
137P TYR* 3.2 5.6 - - - +
138P ALA* 2.9 41.4 + - + +
157P CYS* 1.3 77.5 - - - +
159P ASP* 1.3 77.3 + - - +
160P LEU* 4.0 22.1 + - + -
188P LYS* 3.8 29.6 - - + -
189P SER 4.5 7.0 - - - +
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Residues in contact with ASP 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P TRP* 3.3 19.1 - - + -
135P THR* 4.3 10.3 - - + +
136P CYS 3.4 6.7 - - - +
137P TYR* 3.6 27.0 + - + +
158P VAL* 1.3 74.0 - - - +
160P LEU* 1.3 66.8 + - - +
161P HIS* 5.3 2.5 - - + -
185P ARG* 2.9 49.4 + - - +
188P LYS* 3.8 11.7 + - - -
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P THR* 3.4 5.7 - - - +
136P CYS* 2.7 35.5 + - - +
138P ALA* 4.3 15.3 - - + -
158P VAL* 4.2 22.2 - - + +
159P ASP* 1.3 83.0 - - - +
161P HIS* 1.3 63.8 + - - +
183P ALA* 4.5 5.2 - - + -
184P GLY* 3.9 20.4 - - - +
185P ARG* 3.8 11.7 - - + +
188P LYS 3.7 25.1 - - - +
189P SER* 4.2 5.8 - - - -
190P THR 4.4 6.7 - - - +
199P LEU* 4.5 7.0 - - + -
228P TYR* 3.4 29.2 - - + +
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Residues in contact with HIS 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P GLY* 4.5 10.2 + - - +
134P THR 3.4 5.1 + - - +
135P THR* 3.3 30.3 + - + -
136P CYS* 5.5 0.7 - - - -
159P ASP* 5.3 2.5 - - - -
160P LEU* 1.3 76.8 + - - +
162P VAL* 1.3 67.4 + - - +
163P ILE* 3.4 9.1 + - + +
183P ALA* 3.1 7.0 - - - -
184P GLY 2.9 35.6 + - - +
185P ARG* 3.3 42.8 + - - -
186P TRP 6.0 0.2 - - - -
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Residues in contact with VAL 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P PRO* 4.3 17.7 - - + +
131P ALA 3.7 24.7 - - - +
132P LEU* 3.7 17.3 - - + +
133P GLY* 2.7 29.9 + - - +
134P THR* 3.0 16.4 + - - +
136P CYS* 3.7 28.5 - - - -
161P HIS* 1.3 71.7 - - - +
163P ILE* 1.3 63.1 + - - +
181P LEU* 3.7 27.8 - - + -
182P CYS 3.7 4.3 - - - +
183P ALA* 4.4 3.4 - - + -
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Residues in contact with ILE 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P LEU* 3.7 6.1 - - - +
161P HIS* 3.6 17.3 - - + +
162P VAL* 1.3 77.2 - - - +
164P SER* 1.3 69.1 + - - +
165P ASN* 3.8 1.4 + - - +
167P VAL* 3.9 32.3 - - + -
181P LEU* 5.1 0.3 - - - +
182P CYS* 3.0 33.5 + - - +
183P ALA* 4.2 0.9 - - - -
184P GLY 4.0 27.1 - - - +
186P TRP* 4.6 22.4 - - + +
225P PRO* 4.1 15.5 - - + -
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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