Contacts of the strand formed by residues 178 - 188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLU* 4.4 15.0 + - - +
60A TRP* 3.5 14.3 + - - +
61A SER* 5.2 4.2 - - - -
80A HIS* 6.3 2.2 - - - -
167A THR* 2.9 52.9 + - - +
168A GLU* 3.4 14.3 + - - +
169A PRO* 4.4 13.7 - - + -
176A PRO* 3.3 10.0 - - - +
177A THR* 1.3 83.7 - - - +
179A ALA* 1.3 64.3 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.6 8.7 - - - +
60A TRP* 3.0 37.0 + - + +
127A LEU* 3.8 19.7 - - + -
128A PRO* 3.8 22.7 - - + -
164A PHE* 3.9 7.6 - - + -
165A ILE 3.3 11.7 - - - +
167A THR* 3.2 9.7 + - - -
176A PRO* 5.4 0.4 - - + -
178A LYS* 1.3 74.4 - - - +
180A LEU* 1.3 58.4 + - - +
181A LEU 4.3 0.4 - - - -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 4.1 13.2 - - + -
58A VAL 3.3 26.9 - - - +
59A GLU* 4.2 19.5 - - - +
77A LEU* 4.0 27.1 - - + -
79A LEU* 4.8 7.9 - - + -
163A ALA 3.9 0.7 - - - +
164A PHE* 3.5 4.9 - - - -
165A ILE* 2.8 52.8 + - + +
167A THR* 4.0 8.7 + - + -
179A ALA* 1.3 74.1 - - - +
181A LEU* 1.3 75.5 + - - +
182A PHE* 3.7 24.6 + - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.3 8.1 - - + -
56A LEU* 4.6 4.7 - - + -
57A THR* 3.5 0.7 - - - -
58A VAL* 2.8 40.9 + - + +
66A TRP* 4.2 17.7 - - + -
118A MET* 4.1 19.5 - - + -
130A PHE* 4.3 8.5 - - + -
135A LEU* 3.8 33.9 - - + -
163A ALA 3.4 8.1 - - - +
164A PHE* 3.9 34.1 - - + -
179A ALA 4.3 0.2 - - - -
180A LEU* 1.3 75.8 - - - +
182A PHE* 1.3 71.5 + - - +
183A VAL* 4.3 7.2 - - + -
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A MET* 4.2 7.6 - - + -
56A LEU 3.1 14.6 - - - +
57A THR* 4.1 13.5 - - + -
77A LEU* 3.8 18.4 - - + -
162A PRO* 3.4 1.9 - - - +
163A ALA* 2.6 71.3 + - + +
165A ILE* 4.1 22.9 - - + -
180A LEU* 3.7 22.0 - - + -
181A LEU* 1.3 75.5 - - - +
183A VAL* 1.3 62.8 + - - +
184A LEU* 3.7 29.6 - - + -
81D PRO* 3.3 30.5 - - + -
86D LEU* 4.6 7.6 - - + -
87D HIS* 4.3 3.6 - - - -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A MET* 3.5 11.6 - - - +
56A LEU* 2.9 51.0 + - + -
135A LEU* 4.6 0.7 - - + -
139A ILE* 4.1 15.9 - - + -
142A LEU* 3.6 25.1 - - + +
160A ILE* 3.7 29.4 - - + -
161A ARG 3.4 6.1 - - - +
162A PRO* 3.9 16.2 - - + -
181A LEU* 4.3 7.2 - - + -
182A PHE* 1.3 79.2 - - - +
184A LEU* 1.3 67.0 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 4.2 26.5 - - + -
54A HIS 5.4 0.9 - - - -
55A MET* 3.8 13.5 - - + -
74A LEU* 4.2 9.9 - - + -
161A ARG* 2.8 43.1 + - + +
182A PHE* 3.7 17.9 - - + -
183A VAL* 1.3 79.7 - - - +
185A LEU* 1.3 68.4 + - - +
81D PRO* 3.7 51.1 - - + +
82D GLY* 4.0 6.3 - - - +
87D HIS* 4.1 13.5 - - + -
171D LEU* 4.5 2.9 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.4 9.3 - - - +
52A THR* 3.2 48.4 + - + +
54A HIS 4.8 3.4 + - - +
74A LEU* 6.3 0.4 - - - +
142A LEU* 3.7 39.5 - - + +
143A VAL* 3.9 14.6 - - + -
146A ASP* 3.9 20.2 - - + -
158A LEU* 4.0 18.6 - - + -
159A TYR 3.4 1.8 - - - +
160A ILE* 3.8 33.2 - - + -
184A LEU* 1.3 83.9 - - - +
186A SER* 1.3 63.4 + - - +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 3.5 28.0 + - - -
49A THR 4.0 0.5 + - - -
50A VAL 2.7 19.0 + - - -
51A PHE* 4.2 12.1 - - - -
158A LEU* 3.6 4.8 - - - +
159A TYR* 2.7 47.8 + - - +
184A LEU 5.7 0.2 - - - -
185A LEU* 1.3 76.4 - - - +
187A PRO* 1.4 71.0 + - - +
188A VAL* 4.4 0.2 - - - +
171D LEU* 4.9 6.7 - - - -
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 4.1 5.6 - - + -
45A LEU* 3.8 31.7 - - + +
46A VAL 4.5 8.3 - - - +
48A GLY 4.7 0.9 + - - -
50A VAL* 3.3 30.0 + - + +
52A THR* 4.4 7.0 - - + -
149A TRP* 3.8 32.3 - - + +
151A PRO* 4.2 11.9 - - + -
157A SER 3.5 7.4 - - - +
158A LEU* 3.6 8.0 - - + -
186A SER* 1.4 90.8 + - - +
188A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.5 6.5 - - - -
47A PHE* 3.6 40.4 - - + +
48A GLY 5.4 0.4 - - - +
97A LYS* 3.7 20.2 - - - +
156A ALA* 3.3 4.0 - - - +
157A SER* 2.8 59.7 + - - +
159A TYR* 4.0 13.7 - - + -
186A SER 4.4 2.0 - - - +
187A PRO* 1.3 74.1 - - - +
189A GLY* 1.3 73.0 + - - +
191A TYR* 4.2 11.7 - - + -
332A ALA 4.8 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