Contacts of the strand formed by residues 153 - 161 (chain D) in PDB entry 3C6Q
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 GLU 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A PRO* 3.9 23.9 - - - +
303A ILE 5.3 0.9 + - - -
122D GLY 3.0 12.3 + - - +
123D LYS* 3.5 38.9 - - + +
124D GLY* 3.7 10.8 + - - +
152D SER* 1.3 75.3 - - - +
154D ILE* 1.3 60.2 + - - +
155D GLU* 3.7 5.9 + - - +
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Residues in contact with ILE 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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116D MET* 4.8 1.3 - - + -
117D LYS* 3.8 29.8 - - + +
120D LEU* 3.6 22.4 - - + -
122D GLY* 3.4 4.7 - - - -
123D LYS 3.4 25.8 - - - +
124D GLY 3.4 14.4 - - - +
126D VAL* 4.3 19.3 - - + -
145D PHE* 5.7 0.2 - - + -
149D ILE* 3.4 43.3 - - + +
150D LYS* 5.8 0.3 - - - -
152D SER* 3.1 15.5 - - - +
153D GLU* 1.3 77.0 - - - +
155D GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 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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124D GLY 2.9 18.0 + - - +
125D LYS* 3.5 23.4 - - + +
126D VAL* 3.1 24.8 + - - +
153D GLU 3.7 5.3 + - - +
154D ILE* 1.3 76.1 - - - +
156D ILE* 1.3 64.1 + - - +
157D VAL* 3.6 20.8 + - - +
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Residues in contact with ILE 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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126D VAL* 3.6 11.4 - - + +
128D ILE* 3.7 25.4 - - + -
145D PHE* 3.9 20.4 - - + -
146D LYS* 3.5 35.0 - - + -
149D ILE* 3.7 26.9 - - + -
155D GLU* 1.3 73.1 - - - +
157D VAL* 1.3 62.7 + - - +
158D ASP 3.9 13.7 - - - +
159D ILE* 4.0 12.1 - - + -
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Residues in contact with VAL 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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125D LYS* 3.8 36.3 - - + -
126D VAL 3.0 15.6 + - - +
127D VAL* 3.9 17.9 - - + -
155D GLU* 3.8 18.2 - - - +
156D ILE* 1.3 73.7 - - - +
158D ASP* 1.3 73.0 + - + +
180D HIS* 3.8 30.7 + - + +
183D LEU* 4.3 6.1 - - + -
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Residues in contact with ASP 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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126D VAL 3.7 0.6 + - - -
127D VAL* 3.5 20.9 - - + -
128D ILE* 2.6 34.5 + - - +
156D ILE* 3.5 3.6 - - - +
157D VAL* 1.3 91.1 - - + +
159D ILE* 1.3 66.1 + - - +
160D LEU* 3.8 22.5 - - + +
176D ALA* 5.5 2.7 - - + +
180D HIS* 3.7 18.8 + - + +
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Residues in contact with ILE 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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128D ILE* 3.7 29.2 - - + -
130D THR* 4.4 10.3 - - + -
133D LEU* 4.6 13.5 - - + +
142D ILE* 4.2 25.1 - - + -
146D LYS* 4.3 24.9 - - - +
156D ILE* 4.0 8.7 - - + -
158D ASP* 1.3 81.8 + - - +
160D LEU* 1.3 62.7 + - - +
161D ASN* 3.8 2.8 + - - +
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Residues in contact with LEU 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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127D VAL* 3.5 27.6 - - + -
128D ILE 2.9 13.1 + - - +
129D GLY* 3.6 5.1 - - - -
130D THR* 2.9 28.2 + - - +
158D ASP* 3.8 25.8 - - + +
159D ILE* 1.3 72.5 - - - +
161D ASN* 1.3 60.1 + - - +
162D ASP* 3.7 1.8 + - - +
172D LEU* 3.7 55.8 - - + +
173D ALA* 5.1 1.1 - - - -
176D ALA* 3.8 7.4 - - + -
186D PHE* 5.6 0.2 - - + -
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Residues in contact with ASN 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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130D THR* 3.4 8.5 - - + -
131D GLY 3.0 17.0 - - - +
132D SER* 4.0 14.7 - - - +
133D LEU* 4.0 33.1 - - + +
159D ILE 3.8 3.8 + - - +
160D LEU* 1.3 69.5 - - - +
162D ASP* 1.3 58.8 + - - +
163D CYS* 2.8 46.5 + - - -
168D ARG* 5.2 2.3 + - - +
172D LEU* 4.0 8.7 - - - +
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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