Contacts of the helix formed by residues 155 - 175 (chain A) in PDB entry 5J2N
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 GLY 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PHE* 3.5 33.3 - - - -
153A TRP* 3.4 18.6 - - - -
154A LYS* 1.3 78.4 - - - +
156A SER* 1.3 63.4 + - - +
157A PRO 3.5 0.4 - - - -
158A ALA* 3.5 4.5 + - - +
159A ILE* 3.0 29.3 + - - +
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Residues in contact with SER 156 (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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115A TYR* 3.7 17.7 - - - -
149A LEU* 3.9 12.4 - - - +
150A PRO* 2.7 34.4 + - - +
152A GLY 5.4 0.2 - - - -
153A TRP* 3.2 28.3 - - - +
154A LYS 3.3 0.4 - - - -
155A GLY* 1.3 77.6 - - - +
157A PRO* 1.3 70.8 - - - +
160A PHE* 3.0 27.0 + - - +
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Residues in contact with PRO 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 5.0 0.9 - - - +
115A TYR* 3.2 21.8 - - + +
153A TRP 3.7 7.0 - - - +
154A LYS 3.4 14.6 - - - +
155A GLY 3.7 0.2 - - - -
156A SER* 1.3 94.1 - - - +
158A ALA* 1.3 60.8 + - - +
160A PHE* 4.0 0.5 - - - +
161A GLN* 3.0 45.3 + - - +
184A MET* 5.1 1.6 - - - -
822P 6FM 5.1 1.1 - - - -
706T T 4.1 14.6 - - + +
707T G 3.3 39.3 - - + +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.7 9.2 - - + -
88A TRP 4.5 4.5 - - - +
89A GLU* 3.6 27.7 + - - +
90A VAL* 4.0 5.7 - - - +
154A LYS 4.9 0.4 + - - +
155A GLY* 3.5 8.2 + - - +
156A SER 3.4 0.6 - - - -
157A PRO* 1.3 80.1 - - - +
159A ILE* 1.3 57.4 + - - +
161A GLN* 3.9 8.4 - - - -
162A SER* 3.0 31.2 + - - -
52B PRO* 3.6 24.2 - - + +
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Residues in contact with ILE 159 (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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8A VAL* 3.9 36.1 - - + +
10A VAL* 3.8 17.5 - - + -
87A PHE* 4.2 8.3 - - + -
118A VAL* 4.7 4.3 - - + -
119A PRO 5.3 2.2 - - - +
120A LEU* 5.3 1.8 - - + -
149A LEU* 4.0 21.1 - - + -
153A TRP* 3.7 29.6 - - + -
155A GLY 3.0 22.6 + - - +
156A SER 4.1 1.8 - - - +
158A ALA* 1.3 74.8 - - - +
160A PHE* 1.3 61.5 + - - +
162A SER* 3.5 1.8 + - - -
163A SER* 2.8 39.1 + - - +
52B PRO* 4.2 11.0 - - + -
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Residues in contact with PHE 160 (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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111A VAL* 5.4 2.0 - - + -
114A ALA* 3.5 44.2 - - + -
115A TYR* 3.8 22.7 - + + -
118A VAL* 3.6 22.7 - - + -
149A LEU* 3.9 9.4 - - + +
156A SER 3.0 18.5 + - - +
157A PRO 4.0 1.3 - - - +
159A ILE* 1.3 78.0 - - - +
161A GLN* 1.3 56.1 + - + +
163A SER* 3.2 4.9 + - - -
164A MET* 2.7 53.8 + - + +
184A MET* 3.2 43.7 - - + -
185A ASP* 3.7 9.4 - - + -
214A LEU* 5.1 6.3 - - + -
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Residues in contact with GLN 161 (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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89A GLU* 5.0 2.4 - - - +
90A VAL* 3.8 19.9 + - + +
91A GLN* 3.6 41.3 + - - +
157A PRO* 3.0 33.1 + - - +
158A ALA* 4.0 2.1 - - - -
160A PHE* 1.3 80.6 - - + +
162A SER* 1.3 60.1 + - - +
164A MET* 4.3 3.8 - - - -
165A THR* 2.9 27.0 + - - -
182A GLN* 3.4 6.4 + - - +
183A TYR* 6.1 0.4 - - - -
184A MET* 3.1 42.1 - - - +
140B PRO* 4.1 9.4 - - + +
707T G 5.3 8.5 + - - +
708T G 5.6 1.0 + - - -
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Residues in contact with SER 162 (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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8A VAL* 5.5 3.7 - - - +
90A VAL* 4.2 12.7 - - - +
158A ALA 3.0 19.7 + - - -
159A ILE* 3.8 3.1 - - - -
161A GLN* 1.3 75.0 - - - +
163A SER* 1.3 65.4 + - - +
165A THR* 3.1 16.6 + - - -
166A LYS* 3.1 30.5 + - - +
50B ILE 5.1 0.2 + - - -
51B GLY* 4.1 3.3 - - - -
52B PRO* 3.5 27.3 - - - +
140B PRO* 5.9 0.2 - - - -
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Residues in contact with SER 163 (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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5A ILE* 3.8 24.4 - - - +
6A GLU 5.1 2.3 + - - -
8A VAL* 4.5 9.2 - - - +
118A VAL* 4.1 25.3 - - - +
159A ILE* 2.8 27.8 + - - +
160A PHE* 3.8 3.4 - - - -
162A SER* 1.3 75.4 + - - +
164A MET* 1.3 62.2 + - - +
166A LYS* 3.3 5.8 + - - +
167A ILE* 3.0 33.0 + - - +
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Residues in contact with MET 164 (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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111A VAL* 3.9 17.0 - - + -
160A PHE* 2.7 38.4 + - + +
161A GLN* 3.7 3.4 - - - +
162A SER 3.2 0.4 - - - -
163A SER* 1.3 72.8 - - - +
165A THR* 1.3 61.1 + - - +
167A ILE* 3.5 5.9 + - - +
168A LEU* 3.1 32.6 + - + +
182A GLN* 3.3 24.0 - - - +
184A MET 3.8 17.3 - - - +
185A ASP* 4.8 1.1 - - - +
187A LEU* 3.8 39.0 - - + -
209A LEU* 4.4 9.4 - - + -
214A LEU* 3.7 22.2 - - - -
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Residues in contact with THR 165 (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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161A GLN 2.9 15.1 + - - -
162A SER* 3.1 10.5 + - - -
164A MET* 1.3 75.0 - - - +
166A LYS* 1.3 65.4 + - + +
168A LEU* 3.4 1.7 + - - +
169A GLU* 3.1 25.1 + - + +
172A ARG* 4.2 6.4 + - - +
182A GLN* 3.1 16.7 + - - +
139B THR* 3.9 22.7 - - + -
140B PRO* 3.8 13.1 - - - +
141B GLY 6.0 0.7 - - - +
142B ILE* 4.1 22.0 - - + -
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Residues in contact with LYS 166 (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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5A ILE* 4.3 19.5 - - + -
162A SER* 3.1 28.2 + - - +
163A SER* 3.3 9.6 + - - +
165A THR* 1.3 75.7 - - - +
167A ILE* 1.3 63.1 + - - +
169A GLU* 3.5 7.6 + - - +
170A PRO* 3.4 18.0 - - - +
212A TRP* 6.2 0.2 - - - -
49B LYS* 5.0 18.3 - - + +
50B ILE* 4.4 19.8 + - - +
51B GLY* 4.6 3.0 - - - +
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Residues in contact with ILE 167 (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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3A SER* 3.9 21.5 - - - +
5A ILE* 4.1 15.0 - - + -
118A VAL* 6.0 3.1 - - + -
163A SER* 3.0 22.5 + - - +
164A MET* 3.9 5.8 - - - +
165A THR 3.2 0.2 - - - -
166A LYS* 1.3 78.2 - - - +
168A LEU* 1.3 55.8 + - - +
169A GLU 3.2 0.2 - - - -
170A PRO* 3.3 7.2 - - - +
208A HIS* 2.6 32.1 + - - +
209A LEU* 3.8 26.5 - - + -
212A TRP* 3.7 41.6 - - + +
214A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 168 (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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164A MET* 3.1 25.9 + - + +
165A THR 3.4 1.1 + - - +
167A ILE* 1.3 74.6 - - - +
169A GLU* 1.3 63.6 + - - +
170A PRO 3.5 0.4 - - - -
171A PHE* 3.4 5.8 + - + +
172A ARG* 3.0 51.1 + - + +
180A ILE* 4.2 9.9 - - + -
182A GLN* 3.4 27.4 - - + +
187A LEU* 3.9 26.0 - - + -
205A LEU* 3.8 28.3 - - + -
208A HIS* 4.5 2.2 - - + -
209A LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 169 (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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165A THR* 3.1 18.0 + - + +
166A LYS* 3.6 9.0 - - - +
167A ILE 3.2 0.2 - - - -
168A LEU* 1.3 77.6 - - - +
170A PRO* 1.3 79.8 - - + +
172A ARG* 3.3 7.7 + - - +
173A LYS* 3.0 50.5 + - + +
49B LYS* 5.1 19.5 + - - -
142B ILE* 6.3 3.6 - - + -
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Residues in contact with PRO 170 (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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166A LYS 3.4 11.2 - - - +
167A ILE* 3.3 14.4 - - - +
169A GLU* 1.3 101.1 - - + +
171A PHE* 1.3 58.8 + - - +
173A LYS* 3.5 5.3 + - + +
174A GLN* 3.1 25.7 + - - +
208A HIS* 3.8 18.6 - - + -
212A TRP* 5.2 8.5 - - + +
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Residues in contact with PHE 171 (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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168A LEU* 3.4 9.5 + - + +
169A GLU 3.3 0.6 - - - -
170A PRO* 1.3 76.1 - - - +
172A ARG* 1.3 61.4 + - - +
174A GLN* 4.7 3.8 - - - -
175A ASN* 2.8 57.9 + - + +
178A ILE* 4.3 12.1 - - + -
180A ILE* 3.5 32.1 - - + -
189A VAL* 5.9 0.4 - - + -
201A LYS* 3.9 16.8 - - + -
204A GLU* 3.8 20.0 - - + -
205A LEU* 3.6 48.2 - - + -
208A HIS* 4.0 26.7 + + + -
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Residues in contact with ARG 172 (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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165A THR* 4.2 9.9 + - - +
168A LEU* 3.0 38.9 + - - +
169A GLU* 3.8 5.8 - - + +
171A PHE* 1.3 75.2 - - - +
173A LYS* 1.3 67.1 + - + +
175A ASN 3.2 23.8 - - - +
176A PRO* 3.2 10.1 - - + +
178A ILE 5.1 5.6 - - - +
180A ILE* 3.0 48.0 + - + +
182A GLN* 3.0 38.9 + - - +
138B GLU* 4.9 4.7 + - - -
139B THR* 3.5 30.6 + - - +
142B ILE* 6.1 0.2 - - - +
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Residues in contact with LYS 173 (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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169A GLU* 3.0 39.8 + - + +
170A PRO* 3.8 7.2 - - + +
172A ARG* 1.3 77.6 - - + +
174A GLN* 1.3 61.1 + - - +
176A PRO* 4.1 9.4 - - - +
39B THR* 5.0 19.2 - - - +
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Residues in contact with GLN 174 (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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170A PRO 3.1 18.3 + - - +
171A PHE* 3.9 5.0 - - - +
173A LYS* 1.3 78.9 - - - +
175A ASN* 1.3 69.6 + - - +
176A PRO* 3.2 8.7 - - - +
201A LYS* 5.4 1.6 - - - +
204A GLU* 2.9 28.8 + - - +
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Residues in contact with ASN 175 (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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171A PHE* 2.8 49.3 + - + +
172A ARG* 3.2 10.1 - - - +
174A GLN* 1.3 92.2 + - - +
176A PRO* 1.3 66.1 - - - +
177A ASP 3.2 3.4 + - - -
178A ILE* 3.4 35.6 + - + +
201A LYS* 3.3 31.3 - - - +
204A GLU* 3.4 9.1 + - - +
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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