Contacts of the strand formed by residues 157 - 166 (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 SER 157 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97J LYS* 3.3 29.1 + - - +
98J ALA 3.4 13.9 - - - -
99J PHE* 3.8 23.3 - - - +
150J VAL* 5.2 1.1 - - - -
151J PRO* 3.4 17.2 - - - +
156J ALA* 1.3 75.2 - - - +
158J LEU* 1.3 59.8 + - - +
159J TYR 4.0 0.2 - - - -
187J PRO* 3.5 0.5 - - - +
188J VAL* 2.9 40.0 + - - +
372J TYR* 4.1 1.1 - - - -
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Residues in contact with LEU 158 (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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52J THR* 3.9 15.0 - - + -
97J LYS* 3.2 5.1 - - - -
98J ALA* 2.9 41.3 + - + +
143J VAL* 4.4 12.6 - - + -
146J ASP 4.5 6.5 - - - +
149J TRP* 4.0 12.6 - - + +
150J VAL* 3.7 38.6 - - + +
151J PRO* 3.8 0.8 - - - +
157J SER* 1.3 73.4 - - - +
159J TYR* 1.3 67.9 + - - +
160J ILE* 3.6 1.7 + - - +
185J LEU* 3.9 29.4 - - + -
186J SER 3.6 12.8 - - - +
187J PRO 3.6 22.7 - - - -
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Residues in contact with TYR 159 (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* 3.9 17.7 - - + -
47J PHE* 3.8 23.8 - + + -
93J PHE* 5.0 0.7 - - - -
95J GLY* 3.2 35.7 - - - -
96J LEU 3.7 8.1 - - - -
97J LYS* 4.1 18.2 - - + -
157J SER 3.9 1.8 + - - -
158J LEU* 1.3 72.7 - - - +
160J ILE* 1.3 61.6 + - - +
161J ARG* 2.8 44.8 + - + -
184J LEU 3.9 0.3 - - - +
185J LEU* 3.4 5.7 - - - +
186J SER* 2.8 49.5 + - - +
188J VAL* 4.0 12.9 - - + +
220J LYS* 5.9 0.2 - - - -
331J THR* 4.2 8.7 - - + -
332J ALA 5.2 0.9 - - - -
4401J CBC 3.2 25.8 + - - -
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Residues in contact with ILE 160 (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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95J GLY* 3.4 4.9 - - - -
96J LEU* 2.7 60.6 + - + +
97J LYS 4.0 8.7 - - - -
98J ALA* 4.0 2.5 - - + +
108J LEU* 3.8 30.1 - - + -
139J ILE* 3.9 16.2 - - + -
143J VAL* 4.0 15.5 - - + -
158J LEU* 3.8 7.2 - - + +
159J TYR* 1.3 78.5 - - - +
161J ARG* 1.3 62.2 + - - +
162J PRO* 3.3 8.6 - - + +
183J VAL* 3.7 22.9 - - + -
184J LEU 3.6 2.7 - - - -
185J LEU* 3.9 14.4 - - + -
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Residues in contact with ARG 161 (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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87G HIS* 3.1 44.2 + - + -
88G TYR* 3.0 36.3 + - - -
171G LEU* 3.8 29.9 - - + +
93J PHE* 3.4 32.1 - - - -
94J GLU 2.9 20.0 + - - -
159J TYR* 2.8 31.5 + - + -
160J ILE* 1.3 71.7 - - - +
162J PRO* 1.3 67.2 - - - +
163J ALA* 3.5 2.9 + - - +
182J PHE 3.8 0.2 - - - +
183J VAL* 3.5 2.6 - - - -
184J LEU* 2.8 42.2 + - + +
4401J CBC 4.0 8.7 - - - -
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Residues in contact with PRO 162 (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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93J PHE* 3.3 5.5 - - - +
94J GLU* 2.9 52.4 + - + +
96J LEU* 3.9 14.4 - - + -
115J MET* 4.8 1.8 - - + -
118J MET* 3.8 27.1 - - + +
135J LEU* 5.2 0.7 - - + -
139J ILE* 4.0 18.4 - - + -
160J ILE* 3.3 15.0 - - + +
161J ARG* 1.3 85.0 - - - +
163J ALA* 1.3 59.4 + - - +
182J PHE 3.4 6.1 - - - +
183J VAL* 3.9 14.8 - - + -
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Residues in contact with ALA 163 (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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86G LEU 5.3 4.3 - - - +
87G HIS* 4.0 20.2 - - + +
92J LEU 3.6 8.3 - - - +
93J PHE* 4.8 0.7 - - + -
118J MET* 4.2 2.0 - - - +
161J ARG* 4.3 2.9 - - - +
162J PRO* 1.3 75.8 - - - +
164J PHE* 1.3 60.4 + - - +
165J ILE* 4.2 1.1 - - + -
181J LEU* 3.4 3.5 - - - +
182J PHE* 2.6 77.9 + - + +
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Residues in contact with PHE 164 (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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66J TRP* 3.5 23.3 - + - -
91J GLU* 3.1 5.2 - - - +
92J LEU* 2.9 67.9 + - + +
118J MET* 4.0 4.7 - - + -
122J ALA* 3.9 11.2 - - + -
127J LEU* 3.6 16.3 - - + +
128J PRO* 3.2 51.6 - - + -
130J PHE* 4.0 14.4 - + - -
163J ALA* 1.3 74.4 - - - +
165J ILE* 1.3 61.7 + - - +
179J ALA* 4.0 13.2 - - + -
180J LEU 3.5 12.1 - - - -
181J LEU* 3.9 15.7 - - + -
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Residues in contact with ILE 165 (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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86G LEU* 3.7 37.5 - - + +
77J LEU* 4.4 0.7 - - + -
79J LEU* 4.0 23.6 - - + -
85J ALA* 3.7 13.5 - - + -
90J VAL 3.6 2.5 - - - -
91J GLU* 4.0 5.8 - - + -
127J LEU* 3.9 4.5 - - - -
163J ALA* 5.4 0.2 - - + -
164J PHE* 1.3 79.7 - - - +
166J GLY* 1.3 59.4 + - - +
167J THR* 3.8 18.4 - - + -
179J ALA* 3.3 5.2 - - - +
180J LEU* 2.8 59.3 + - + +
182J PHE* 4.0 27.4 - - + -
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Residues in contact with GLY 166 (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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83J SER* 3.9 1.9 - - - -
84J SER* 3.6 16.6 + - - -
85J ALA* 3.0 26.5 + - - +
90J VAL* 2.8 27.0 + - - -
127J LEU* 3.8 8.2 - - - +
165J ILE* 1.3 70.8 - - - +
167J THR* 1.3 62.8 + - - +
168J GLU 3.5 2.5 - - - -
176J PRO* 4.4 1.8 - - - -
178J LYS 3.8 6.3 - - - -
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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