Contacts of the strand formed by residues 178 - 188 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59J GLU* 4.6 14.1 + - - +
60J TRP* 3.4 13.0 - - - +
61J SER* 5.1 5.2 - - - -
167J THR* 2.8 54.5 + - - +
168J GLU* 3.3 15.7 + - - +
169J PRO* 4.6 11.2 - - + -
176J PRO* 3.4 9.1 - - - +
177J THR* 1.3 84.1 + - - +
179J ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J GLU* 3.6 8.1 - - - +
60J TRP* 3.0 35.8 + - + +
127J LEU* 3.8 9.2 - - + -
128J PRO* 3.8 35.7 - - + -
164J PHE* 4.0 5.2 - - + -
165J ILE 3.3 13.2 - - - +
167J THR* 3.2 7.8 + - - -
176J PRO* 5.3 0.7 - - + -
178J LYS* 1.3 75.5 - - - +
180J LEU* 1.3 59.9 + - - +
181J LEU 4.3 0.2 - - - -
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Residues in contact with LEU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J THR* 4.1 13.0 - - + -
58J VAL 3.4 20.9 - - - +
59J GLU* 4.2 19.1 - - - +
77J LEU* 4.0 21.8 - - + -
79J LEU* 4.7 8.5 - - + -
163J ALA 3.9 0.7 - - - +
164J PHE* 3.5 5.0 - - - -
165J ILE* 2.8 56.5 + - + +
167J THR* 4.0 8.3 + - + -
179J ALA* 1.3 75.0 - - - +
181J LEU* 1.3 82.0 + - - +
182J PHE* 3.6 23.5 + - + -
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Residues in contact with LEU 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.3 8.1 - - + -
56J LEU* 4.6 0.8 - - + -
57J THR* 3.5 0.7 - - - -
58J VAL* 2.8 47.2 + - + +
66J TRP* 4.1 17.2 - - + -
118J MET* 4.1 18.8 - - + -
130J PHE* 4.1 19.5 - - + -
135J LEU* 3.8 29.4 - - + -
163J ALA 3.4 8.1 - - - +
164J PHE* 3.9 29.4 - - + -
179J ALA 4.3 0.2 - - - -
180J LEU* 1.3 76.2 - - - +
182J PHE* 1.3 72.2 + - - +
183J VAL* 4.3 6.7 - - + -
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Residues in contact with PHE 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G PRO* 3.3 33.9 - - + -
86G LEU* 4.5 6.1 - - + -
87G HIS* 4.3 5.2 - - - -
55J MET* 4.2 7.0 - - + -
56J LEU* 3.1 14.8 - - - +
57J THR* 4.1 13.0 - - + -
77J LEU* 3.7 18.8 - - + -
161J ARG 5.4 0.4 - - - -
163J ALA* 2.6 71.1 + - + +
165J ILE* 4.0 24.9 - - + -
180J LEU* 3.6 22.4 - - + -
181J LEU* 1.3 75.4 - - - +
183J VAL* 1.3 64.7 + - - +
184J LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J MET* 3.4 12.5 - - - +
56J LEU* 2.9 52.9 + - + -
135J LEU* 4.6 0.4 - - + -
139J ILE* 4.0 17.0 - - + -
142J LEU* 3.8 22.8 - - + +
160J ILE* 3.7 29.8 - - + -
161J ARG 3.5 7.9 - - - +
162J PRO* 3.9 13.7 - - + -
181J LEU* 4.3 7.4 - - + -
182J PHE* 1.3 79.9 - - - +
184J LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G PRO* 3.7 52.3 - - + +
82G GLY* 3.9 6.3 - - - +
87G HIS* 4.4 5.2 - - + +
171G LEU* 4.4 7.2 - - + -
51J PHE* 3.9 33.0 - - + -
54J HIS 5.4 0.9 - - - -
55J MET* 3.9 12.1 - - + -
74J LEU* 4.3 9.0 - - + -
159J TYR 3.9 0.2 - - - +
161J ARG* 2.8 43.1 + - + +
182J PHE* 3.7 15.3 - - + -
183J VAL* 1.3 82.4 - - - +
185J LEU* 1.3 68.8 + - - +
186J SER* 5.8 0.2 - - - -
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Residues in contact with LEU 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PHE* 3.4 10.6 - - - +
52J THR* 3.2 49.7 + - + +
54J HIS 4.8 3.1 + - - +
142J LEU* 3.8 37.9 - - + +
143J VAL* 3.9 23.8 - - + -
146J ASP* 3.8 21.5 - - + +
158J LEU* 3.9 17.5 - - + -
159J TYR 3.4 2.5 - - - +
160J ILE* 3.9 22.2 - - + -
184J LEU* 1.3 83.8 - - - +
186J SER* 1.3 61.6 + - - +
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Residues in contact with SER 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G LEU* 4.8 7.0 - - - -
48J GLY* 3.5 29.3 + - - -
49J THR 4.0 0.7 + - - -
50J VAL 2.7 19.0 + - - -
51J PHE* 4.2 13.5 - - - -
158J LEU* 3.6 4.3 - - - +
159J TYR* 2.8 44.8 + - - +
184J LEU* 6.2 0.2 - - - -
185J LEU* 1.3 76.6 - - - +
187J PRO* 1.3 70.7 + - - +
188J VAL* 4.4 0.2 - - - +
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Residues in contact with PRO 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J PRO* 4.1 5.6 - - + -
45J LEU* 3.6 31.5 - - + +
46J VAL 4.6 7.8 - - - +
48J GLY 4.8 1.2 + - - -
50J VAL* 3.3 32.8 + - + +
52J THR* 4.3 7.9 - - + -
149J TRP* 3.9 35.4 - - + +
151J PRO* 4.3 5.4 - - + -
157J SER 3.5 7.4 - - - +
158J LEU* 3.6 8.2 - - + -
186J SER* 1.3 91.2 + - - +
188J VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J LEU* 3.5 7.3 - - - +
47J PHE* 3.6 41.3 - - + +
48J GLY 5.5 0.2 - - - +
97J LYS* 3.6 21.5 - - - +
156J ALA* 3.3 5.5 - - - +
157J SER* 2.9 57.5 + - - +
159J TYR* 4.0 13.0 - - + -
186J SER 4.4 1.8 - - - +
187J PRO* 1.3 74.8 - - - +
189J GLY* 1.3 72.7 + - - +
191J TYR* 4.1 12.1 - - + -
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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