Contacts of the strand formed by residues 157 - 166 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G LYS* 3.3 33.7 + - - +
98G ALA 3.3 14.4 - - - -
99G PHE* 3.6 23.5 - - - +
150G VAL* 5.3 0.4 - - - -
151G PRO* 3.3 16.3 - - - +
156G ALA* 1.3 76.9 - - - +
158G LEU* 1.3 60.5 + - - +
187G PRO* 3.7 0.2 - - - +
188G VAL* 2.9 33.0 + - - +
189G GLY 5.6 0.3 + - - -
372G TYR* 4.3 0.2 - - - -
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G THR* 3.8 19.5 - - + -
97G LYS* 3.2 6.7 - - - -
98G ALA* 2.8 41.6 + - + +
143G VAL* 4.0 13.5 - - + -
146G ASP 4.7 4.7 - - - +
149G TRP* 3.9 15.3 - - + +
150G VAL* 3.8 35.4 - - + +
151G PRO* 3.7 1.2 - - - +
157G SER* 1.3 70.2 - - - +
159G TYR* 1.3 63.0 + - - +
160G ILE* 3.7 3.0 + - + +
185G LEU* 3.9 33.9 - - + -
186G SER 3.7 5.6 - - - +
187G PRO* 3.6 23.6 - - + -
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Residues in contact with TYR 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G PHE* 4.0 21.3 - + - -
93G PHE* 5.0 1.2 - - - -
95G GLY* 3.3 30.9 - - - -
96G LEU 3.6 12.1 - - - -
97G LYS* 4.1 15.7 - - + +
157G SER 3.9 2.0 + - - -
158G LEU* 1.3 72.9 - - - +
160G ILE* 1.3 62.9 + - - +
161G ARG* 2.7 46.3 + - + -
184G LEU 3.9 0.2 - - - +
185G LEU* 3.4 5.7 - - - -
186G SER* 2.9 42.7 + - - +
188G VAL* 3.8 17.6 - - + +
220G LYS* 6.0 0.2 - - - -
331G THR* 4.3 9.2 - - + -
332G ALA 5.4 0.4 - - - -
3401G CBC 3.3 26.9 + - - -
171J LEU* 4.0 19.5 - - + -
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Residues in contact with ILE 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G GLY* 3.5 5.0 - - - -
96G LEU* 2.6 54.9 + - + +
97G LYS 4.0 3.8 - - - -
98G ALA* 4.0 15.7 - - + +
108G LEU* 3.8 29.2 - - + -
139G ILE* 4.0 22.7 - - + -
143G VAL* 5.2 4.3 - - + -
158G LEU* 3.8 7.2 - - + +
159G TYR* 1.3 78.9 - - - +
161G ARG* 1.3 61.7 + - - +
162G PRO* 3.4 9.1 - - + +
183G VAL* 3.7 22.9 - - + -
184G LEU 3.7 2.7 - - - -
185G LEU* 3.8 16.8 - - + -
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Residues in contact with ARG 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G PHE* 3.5 21.1 - - - -
94G GLU 3.2 12.6 - - - -
159G TYR* 2.7 45.0 + - + -
160G ILE* 1.3 74.2 - - - +
162G PRO* 1.4 65.9 - - - +
163G ALA* 3.5 2.8 + - - +
182G PHE* 3.6 1.2 - - - +
183G VAL* 3.4 2.8 - - - -
184G LEU* 2.8 40.5 + - + +
3401G CBC 4.6 3.0 - - - -
87J HIS* 2.9 42.3 + - + +
88J TYR* 2.4 47.5 + - - -
171J LEU* 4.1 26.0 + - + +
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Residues in contact with PRO 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G PHE* 3.2 6.6 - - - +
94G GLU* 2.9 45.3 + - + +
96G LEU* 3.8 17.0 - - + -
115G MET* 4.7 2.2 - - + -
118G MET* 3.7 29.2 - - + -
135G LEU* 5.1 0.9 - - + -
139G ILE* 4.1 20.4 - - + -
160G ILE* 3.4 15.5 - - + +
161G ARG* 1.4 84.8 - - - +
163G ALA* 1.3 58.3 + - - +
182G PHE 3.3 6.7 - - - +
183G VAL* 4.0 11.2 - - + -
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Residues in contact with ALA 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LEU 3.5 8.3 - - - +
93G PHE* 4.7 1.1 - - + -
118G MET* 4.5 1.7 - - - +
161G ARG 4.3 1.1 - - - +
162G PRO* 1.3 76.2 - - - +
164G PHE* 1.3 62.5 + - - +
165G ILE* 4.3 3.4 - - + -
181G LEU* 3.3 5.5 - - - +
182G PHE* 2.7 72.7 + - + +
86J LEU 5.3 2.2 - - - +
87J HIS* 3.9 20.4 - - + +
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Residues in contact with PHE 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G TRP* 3.6 28.3 - + - -
91G GLU* 3.1 5.2 - - - -
92G LEU* 2.9 65.2 + - + +
118G MET* 4.1 4.7 - - + -
122G ALA* 3.9 11.7 - - + -
127G LEU* 3.6 12.5 - - + +
128G PRO* 3.2 39.3 - - + -
130G PHE* 3.8 20.0 - + - -
163G ALA* 1.3 77.0 - - - +
165G ILE* 1.3 65.2 + - - +
179G ALA* 3.9 20.0 - - + -
180G LEU 3.5 9.2 - - - -
181G LEU* 3.9 15.7 - - + -
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Residues in contact with ILE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G LEU* 4.4 3.1 - - + -
79G LEU* 4.1 28.0 - - + -
83G SER* 6.3 0.2 - - - -
85G ALA* 3.7 14.6 - - + -
90G VAL 3.5 2.7 - - - -
91G GLU* 4.0 6.5 - - + -
127G LEU* 3.9 5.2 - - - -
164G PHE* 1.3 83.0 - - - +
166G GLY* 1.3 59.9 + - - +
167G THR* 3.9 13.2 - - - +
179G ALA* 3.3 5.9 - - - +
180G LEU* 2.8 56.3 + - + +
182G PHE* 4.1 23.8 - - + -
86J LEU* 3.9 36.6 - - + +
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Residues in contact with GLY 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G SER* 3.9 2.8 - - - -
84G SER* 3.5 22.0 + - - -
85G ALA* 3.1 26.9 + - - +
90G VAL* 2.7 26.6 + - - -
127G LEU* 3.8 6.5 - - - +
165G ILE* 1.3 72.1 - - - +
167G THR* 1.3 59.8 + - - -
176G PRO* 4.3 1.8 - - - -
178G LYS 3.7 7.6 - - - -
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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