Contacts of the strand formed by residues 157 - 166 (chain D) in PDB entry 2ABJ
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 SER 157 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D LYS* 3.2 32.5 + - - +
98D ALA 3.3 14.1 - - - -
99D PHE* 3.6 23.8 - - - +
150D VAL* 5.3 0.2 - - - -
151D PRO* 3.4 16.0 - - - +
156D ALA* 1.3 76.4 - - - +
158D LEU* 1.3 60.0 + - - +
187D PRO* 3.7 0.2 - - - +
188D VAL* 2.9 37.4 + - - +
372D TYR* 4.2 0.4 - - - -
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Residues in contact with LEU 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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52D THR* 3.9 13.9 - - + -
97D LYS* 3.3 4.9 - - - -
98D ALA* 2.9 39.8 + - + +
143D VAL* 4.2 12.6 - - + -
146D ASP 4.8 5.2 - - - +
149D TRP* 3.9 14.8 - - + +
150D VAL* 3.7 35.9 - - + +
151D PRO* 3.7 1.4 - - - +
157D SER* 1.3 71.2 - - - +
159D TYR* 1.3 70.4 + - - +
160D ILE* 3.6 2.4 + - + +
185D LEU* 3.8 31.0 - - + -
186D SER 3.7 10.5 - - - +
187D PRO* 3.6 23.8 - - + -
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Residues in contact with TYR 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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171A LEU* 3.9 24.0 - - + -
47D PHE* 3.9 20.9 - + - -
48D GLY* 6.0 0.2 - - - -
93D PHE* 5.0 0.9 - - - -
95D GLY* 3.3 30.6 - - - -
96D LEU 3.7 11.9 - - - -
97D LYS* 4.1 14.8 - - + -
157D SER 3.9 2.0 + - - -
158D LEU* 1.3 73.1 - - - +
160D ILE* 1.3 63.6 + - - +
161D ARG* 2.7 41.9 + - + -
184D LEU 3.9 0.2 - - - +
185D LEU* 3.4 5.2 - - - -
186D SER* 2.7 46.1 + - - +
188D VAL* 3.7 17.8 - - + +
220D LYS* 5.9 0.2 - - - -
331D THR* 4.2 9.4 - - + -
332D ALA 5.3 0.4 - - - -
2401D CBC 3.2 28.4 + - - -
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Residues in contact with ILE 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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95D GLY* 3.6 4.5 - - - -
96D LEU* 2.7 52.4 + - + +
97D LYS 4.0 3.6 - - - -
98D ALA* 4.0 13.2 - - + +
108D LEU* 3.7 29.8 - - + -
139D ILE* 4.0 17.7 - - + -
143D VAL* 4.0 14.6 - - + -
158D LEU* 3.8 7.0 - - + +
159D TYR* 1.3 78.9 - - - +
161D ARG* 1.3 62.9 + - - +
162D PRO* 3.4 9.0 - - + +
183D VAL* 3.7 22.7 - - + -
184D LEU 3.7 2.5 - - - -
185D LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 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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87A HIS* 2.9 43.4 + - + +
88A TYR* 2.4 47.7 + - - -
171A LEU* 4.1 23.2 + - + +
93D PHE* 3.5 20.9 - - - +
94D GLU 3.2 12.1 - - - -
159D TYR* 2.7 47.9 + - + +
160D ILE* 1.3 74.2 - - - +
162D PRO* 1.3 67.9 - - - +
163D ALA* 3.6 2.6 + - - +
182D PHE* 3.8 0.9 - - - +
183D VAL* 3.4 3.1 - - - -
184D LEU* 2.8 41.3 + - + +
2401D CBC 4.6 2.8 - - - -
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Residues in contact with PRO 162 (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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93D PHE* 3.2 6.4 - - - +
94D GLU* 2.9 46.4 + - + +
96D LEU* 3.8 18.2 - - + -
115D MET* 4.8 1.8 - - + -
118D MET* 3.7 28.7 - - + -
135D LEU* 5.2 1.1 - - + -
139D ILE* 4.0 20.2 - - + -
160D ILE* 3.4 14.4 - - + +
161D ARG* 1.3 85.7 - - - +
163D ALA* 1.3 59.3 + - - +
181D LEU* 5.4 0.2 - - + -
182D PHE 3.4 6.5 - - - +
183D VAL* 3.9 11.0 - - + -
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Residues in contact with ALA 163 (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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86A LEU 5.4 2.0 - - - +
87A HIS* 3.9 20.0 - - + +
92D LEU 3.5 8.5 - - - +
93D PHE* 4.7 0.7 - - + -
118D MET* 4.2 1.5 - - - +
161D ARG 4.3 1.1 - - - +
162D PRO* 1.3 76.7 - - - +
164D PHE* 1.3 60.7 + - - +
165D ILE* 4.3 2.5 - - + -
180D LEU 3.9 0.3 - - - +
181D LEU* 3.4 4.5 - - - +
182D PHE* 2.7 73.5 + - + +
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Residues in contact with PHE 164 (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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66D TRP* 3.5 28.9 - + - -
91D GLU* 3.1 4.5 - - - -
92D LEU* 2.9 70.8 + - + +
118D MET* 4.1 4.7 - - + -
122D ALA* 3.9 14.4 - - + -
127D LEU* 3.7 12.2 - - + +
128D PRO* 3.2 38.8 - - + -
130D PHE* 3.9 15.5 - + - -
163D ALA* 1.3 75.8 - - - +
165D ILE* 1.3 65.2 + - - +
179D ALA* 3.9 20.4 - - + -
180D LEU 3.5 9.2 - - - -
181D LEU* 4.0 15.9 - - + -
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Residues in contact with ILE 165 (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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86A LEU* 3.9 46.2 - - + +
77D LEU* 4.5 1.3 - - + -
79D LEU* 4.2 15.5 - - + -
83D SER* 6.3 0.2 - - - -
85D ALA* 3.7 13.2 - - + -
90D VAL 3.5 3.1 - - - -
91D GLU* 4.0 6.5 - - + -
127D LEU* 4.0 5.6 - - - -
163D ALA* 5.1 0.4 - - + -
164D PHE* 1.3 82.7 - - - +
166D GLY* 1.3 59.7 + - - +
167D THR* 3.8 19.5 - - + -
179D ALA* 3.2 5.7 - - - +
180D LEU* 2.8 57.0 + - + +
182D PHE* 4.2 22.0 - - + -
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Residues in contact with GLY 166 (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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83D SER* 3.8 1.7 - - - -
84D SER* 3.5 15.7 + - - -
85D ALA* 3.0 27.9 + - - +
90D VAL* 2.8 26.8 + - - -
127D LEU* 3.9 6.3 - - - +
165D ILE* 1.3 71.4 - - - +
167D THR* 1.3 59.8 + - - +
168D GLU 3.5 3.8 - - - -
176D PRO* 4.3 1.1 - - - -
178D LYS 3.6 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