Contacts of the strand formed by residues 178 - 188 (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 LYS 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D GLU* 4.3 18.9 + - + +
60D TRP* 3.7 17.7 - - - +
61D SER* 4.6 8.9 - - - -
166D GLY* 3.6 0.2 - - - -
167D THR* 2.9 46.3 + - - +
168D GLU* 3.5 19.9 + - - +
169D PRO* 4.5 9.2 - - + -
176D PRO* 3.3 11.9 - - - +
177D THR* 1.3 85.0 + - - +
179D ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 179 (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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59D GLU* 3.6 7.6 - - - +
60D TRP* 3.0 39.8 + - + +
127D LEU* 3.8 19.5 - - + -
128D PRO* 3.9 13.9 - - + -
164D PHE* 3.9 14.1 - - + -
165D ILE 3.2 12.8 - - - +
167D THR* 3.3 7.7 + - - -
176D PRO* 5.3 0.4 - - + -
178D LYS* 1.3 74.1 - - - +
180D LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 180 (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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57D THR* 4.0 12.3 - - + -
58D VAL 3.3 27.1 - - - +
59D GLU* 4.0 20.9 - - - +
77D LEU* 4.0 27.1 - - + -
79D LEU* 5.0 4.5 - - + -
163D ALA 3.9 0.9 - - - +
164D PHE* 3.5 4.1 - - - -
165D ILE* 2.8 52.0 + - + +
167D THR* 4.0 10.5 + - + -
179D ALA* 1.3 74.5 - - - +
181D LEU* 1.3 70.1 + - - +
182D PHE* 3.6 31.1 + - + -
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Residues in contact with LEU 181 (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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23D PHE* 4.3 8.1 - - + -
56D LEU* 4.0 1.3 - - + +
57D THR* 3.3 2.3 - - - -
58D VAL* 2.7 55.6 + - + +
66D TRP* 4.0 27.1 - - + -
118D MET* 4.0 21.5 - - + -
130D PHE* 4.2 12.8 - - + -
135D LEU* 3.8 30.1 - - + -
163D ALA 3.4 9.0 - - - +
164D PHE* 4.0 18.7 - - + -
179D ALA 4.3 0.2 - - - -
180D LEU* 1.3 72.5 - - - +
182D PHE* 1.3 71.8 + - - +
183D VAL* 4.4 4.3 - - + -
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Residues in contact with PHE 182 (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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81A PRO* 3.2 37.7 - - + -
86A LEU* 4.4 7.2 - - + -
87A HIS* 4.2 4.0 - + - -
55D MET* 4.3 3.8 - - + -
56D LEU 3.0 14.1 - - - +
57D THR* 4.1 12.8 - - + -
77D LEU* 3.7 18.6 - - + -
161D ARG 3.8 0.4 - - - +
163D ALA* 2.7 70.0 + - + +
165D ILE* 4.2 21.1 - - + -
180D LEU* 3.6 21.5 - - + -
181D LEU* 1.3 75.5 - - - +
183D VAL* 1.3 66.1 + - - +
184D LEU* 3.9 26.5 - - + -
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Residues in contact with VAL 183 (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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55D MET* 3.4 12.1 - - - +
56D LEU* 2.9 51.8 + - + -
135D LEU* 4.5 0.4 - - + -
139D ILE* 4.1 18.2 - - + -
142D LEU* 3.8 24.0 - - + +
160D ILE* 3.7 29.6 - - + -
161D ARG 3.4 7.2 - - - +
162D PRO* 3.9 13.5 - - + -
181D LEU* 4.4 7.0 - - + -
182D PHE* 1.3 79.6 - - - +
184D LEU* 1.3 68.5 + - - +
185D LEU* 4.5 0.2 - - + -
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Residues in contact with LEU 184 (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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81A PRO* 3.7 55.6 - - + +
82A GLY* 3.9 7.2 - - - +
87A HIS* 4.4 8.5 - - + +
171A LEU* 4.7 2.5 - - + -
51D PHE* 3.9 31.6 - - + -
54D HIS 5.4 0.9 - - - -
55D MET* 3.8 20.0 - - + -
74D LEU* 3.9 11.4 - - + -
159D TYR 3.9 0.3 - - - +
160D ILE* 3.7 2.6 - - - -
161D ARG* 2.8 42.3 + - + +
182D PHE* 3.9 10.5 - - + -
183D VAL* 1.3 78.7 - - - +
185D LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 185 (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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51D PHE* 3.4 10.1 - - - +
52D THR* 3.2 50.1 + - + +
54D HIS 4.8 3.7 + - - +
74D LEU* 6.3 0.2 - - - +
139D ILE* 5.7 0.2 - - + -
142D LEU* 4.0 37.7 - - + +
143D VAL* 4.0 12.8 - - + -
146D ASP* 3.8 21.3 - - + +
158D LEU* 3.8 21.3 - - + -
159D TYR 3.4 1.8 - - - -
160D ILE* 3.9 30.3 - - + -
183D VAL 4.4 0.2 + - - -
184D LEU* 1.3 83.3 - - - +
186D SER* 1.3 61.5 + - - +
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Residues in contact with SER 186 (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* 4.4 13.7 - - - -
47D PHE 3.5 16.6 + - - -
48D GLY* 3.6 10.7 - - - -
50D VAL 2.7 18.4 + - - -
51D PHE* 4.3 12.8 - - - -
158D LEU* 3.7 4.6 - - - +
159D TYR* 2.7 46.0 + - - +
184D LEU 5.7 0.2 - - - -
185D LEU* 1.3 75.1 - - - +
187D PRO* 1.4 64.5 + - - +
188D VAL* 3.2 1.1 + - - +
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Residues in contact with PRO 187 (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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40D PRO* 4.1 13.2 - - + -
45D LEU* 3.8 32.5 - - + +
46D VAL 4.5 1.7 - - - +
47D PHE 3.5 6.8 - - - +
50D VAL* 3.2 23.8 - - + +
52D THR* 4.1 8.5 - - + -
149D TRP* 3.7 39.9 - - + +
151D PRO* 4.4 4.3 - - + -
157D SER 3.7 7.2 - - - +
158D LEU* 3.6 10.5 - - + -
186D SER* 1.4 84.7 + - - +
188D VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 188 (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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45D LEU* 3.5 7.9 - - - -
47D PHE* 2.7 55.0 - - + +
97D LYS* 3.8 21.3 - - - +
156D ALA* 3.3 3.5 - - - +
157D SER* 2.9 54.2 + - - +
159D TYR* 3.7 15.5 - - + -
186D SER* 3.2 16.4 + - - +
187D PRO* 1.3 70.5 - - - +
189D GLY* 1.3 64.5 + - - +
332D ALA 5.8 0.2 - - - +
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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