Contacts of the strand formed by residues 153 - 161 (chain D) in PDB entry 2I2X
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 ASN 153 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D THR* 3.8 30.8 - - + +
124D GLY 3.2 10.0 + - - +
125D THR* 3.4 21.8 + - - +
126D VAL* 3.0 27.2 + - - +
152D TYR* 1.3 72.0 - - - +
154D VAL* 1.3 67.4 + - - +
155D VAL* 4.9 1.4 + - - +
173D GLU* 5.4 2.4 - - - +
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 3.5 5.2 - - + +
128D CYS* 3.8 26.7 - - - -
144D THR* 4.0 20.0 - - + +
147D LEU* 3.7 30.3 - - + -
148D ARG* 3.4 45.8 + - + +
152D TYR* 3.6 5.0 + - + +
153D ASN* 1.3 84.3 + - - +
155D VAL* 1.3 66.6 + - - +
156D ASP* 3.4 7.4 + - + +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 3.9 14.2 - - + +
126D VAL 3.1 5.9 + - - +
127D VAL* 3.4 29.7 - - + +
128D CYS 3.1 22.0 + - - +
153D ASN* 4.1 2.7 + - - +
154D VAL* 1.3 71.5 - - - +
156D ASP* 1.3 64.0 + - - +
157D LEU* 3.5 19.0 + - + -
169D ALA* 5.5 2.0 - - + -
173D GLU* 4.0 27.1 - - + +
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D CYS* 4.0 5.2 - - - -
140D LYS* 3.2 35.6 + - - +
141D ASN* 4.2 3.3 - - - +
144D THR* 3.8 17.7 + - - +
148D ARG* 4.3 17.6 + - - +
154D VAL* 3.4 7.9 + - + -
155D VAL* 1.3 74.2 - - - +
157D LEU* 1.3 59.1 + - - +
158D GLY* 2.7 21.2 + - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 4.5 7.1 + - - -
127D VAL* 3.4 31.0 - - + -
128D CYS 2.8 19.2 + - - +
129D HIS* 3.9 12.6 - - + -
155D VAL* 3.9 17.9 - - + -
156D ASP* 1.3 71.0 - - - +
158D GLY* 1.3 58.2 + - - +
159D ARG 4.0 0.2 + - - -
161D VAL* 3.1 22.4 - - + +
165D GLU* 3.9 40.4 - - + +
166D VAL* 5.2 2.5 - - + -
169D ALA* 3.8 18.6 - - + -
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Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 5.3 1.1 - - - -
128D CYS 4.5 0.4 + - - -
129D HIS* 4.0 1.4 - - - -
130D VAL* 3.3 15.9 + - - +
140D LYS* 4.0 13.2 - - - +
156D ASP* 2.7 24.4 + - - -
157D LEU* 1.3 73.8 - - - +
159D ARG* 1.3 67.7 + - - +
161D VAL* 3.2 6.8 - - - +
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Residues in contact with ARG 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLU* 2.7 36.2 + - - -
132C ASN 3.6 9.1 + - - -
133C ARG* 2.8 38.8 + - - +
134C GLU 3.7 15.2 + - - -
135C PHE* 4.4 2.2 - - - +
130D VAL* 2.7 27.2 - - + +
134D ASP 3.8 12.3 - - - +
135D VAL* 3.5 32.1 - - + +
137D ASP* 3.4 39.9 + - - +
157D LEU 4.0 0.2 + - - -
158D GLY* 1.3 70.3 - - - +
160D ASP* 1.3 56.2 + - + +
161D VAL* 2.5 26.0 + - - +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 3.4 45.7 + - + +
132D GLU* 3.3 11.2 - - - +
133D GLY* 2.7 33.5 + - - +
134D ASP 3.8 11.6 + - - +
135D VAL* 5.7 5.2 - - + -
159D ARG* 1.3 72.5 - - + +
161D VAL* 1.3 57.0 + - - +
162D PRO* 3.4 10.0 - - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 4.8 4.0 - - - +
129D HIS* 4.1 13.5 - - + -
130D VAL 3.4 11.1 + - - +
132D GLU* 3.1 20.9 + - - +
157D LEU* 3.1 39.0 - - + +
158D GLY 3.2 13.0 - - - +
159D ARG 2.5 24.0 + - - +
160D ASP* 1.3 70.3 - - - +
162D PRO* 1.3 69.1 - - + +
163D ALA 3.3 6.1 + - - -
165D GLU* 4.3 11.4 - - + -
166D VAL* 3.6 26.5 - - + -
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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