Contacts of the helix formed by residues 146 - 163 (chain A) in PDB entry 1J1U
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 VAL 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PRO 4.3 0.4 + - - -
145A LYS* 1.3 72.1 - - - +
147A ALA* 1.3 64.1 + - - +
148A GLU 2.9 1.2 + - - -
149A VAL* 3.0 28.8 + - + +
150A ILE* 3.3 26.4 + - + +
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Residues in contact with ALA 147 (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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73A LEU* 3.4 49.5 - - + +
75A GLN* 6.3 0.4 - - - +
145A LYS* 3.0 12.2 - - + +
146A VAL* 1.3 79.6 - - - +
148A GLU* 1.3 60.8 + - - +
150A ILE* 3.3 8.4 + - - +
151A TYR* 3.1 24.1 + - - +
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Residues in contact with GLU 148 (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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73A LEU 5.3 2.2 - - - -
74A ASN* 6.2 1.6 - - - +
131A ARG* 3.7 37.5 + - - +
134A MET* 3.4 24.8 - - + +
138A ALA* 3.7 30.7 - - + +
139A ARG 5.3 1.4 - - - +
141A ASP* 5.8 2.1 - - - +
144A PRO* 3.9 22.0 - - - +
145A LYS* 3.0 18.5 + - + +
146A VAL 2.9 0.2 + - - -
147A ALA* 1.3 81.9 - - - +
149A VAL* 1.3 60.7 + - + +
150A ILE 3.4 0.2 - - - -
151A TYR* 4.1 0.7 - - - -
152A PRO* 3.0 18.7 - - - +
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Residues in contact with VAL 149 (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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127A LEU* 4.0 28.3 - - + -
130A ALA* 3.8 20.9 - - + +
131A ARG* 3.7 32.3 - - + +
145A LYS 5.1 2.0 - - - +
146A VAL* 3.0 30.1 + - + +
148A GLU* 1.3 79.9 - - + +
150A ILE* 1.3 67.0 + - + +
151A TYR 3.4 0.4 - - - -
152A PRO* 3.5 17.5 - - - +
153A ILE* 3.9 12.4 - - - +
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Residues in contact with ILE 150 (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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73A LEU* 4.0 12.8 - - + -
118A VAL* 4.8 9.6 - - + -
146A VAL* 3.3 30.0 + - + +
147A ALA* 3.3 12.7 + - - +
149A VAL* 1.3 78.0 - - + +
151A TYR* 1.3 67.1 + - - +
153A ILE* 3.1 16.2 + - + +
154A MET* 3.1 45.9 + - + +
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Residues in contact with TYR 151 (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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36A GLU* 2.4 34.2 + - - +
70A HIS* 3.2 56.8 + + + -
73A LEU* 4.2 13.7 - - + +
74A ASN* 3.7 13.9 - - + -
134A MET* 3.4 21.5 - - + -
137A ILE* 3.5 17.1 - - + +
147A ALA 3.1 15.9 + - - +
148A GLU* 3.8 4.0 - - - +
150A ILE* 1.3 77.7 - - - +
152A PRO* 1.3 71.7 - - + +
154A MET* 3.2 0.6 + - - -
155A GLN* 3.1 37.5 + - - +
176A ILE* 4.3 2.0 - - + -
401A TYR* 2.9 23.1 + - - +
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Residues in contact with PRO 152 (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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130A ALA* 4.0 14.4 - - + +
133A SER* 3.4 21.5 - - - +
134A MET* 3.6 15.7 - - + -
148A GLU 3.0 26.2 - - - +
149A VAL 3.5 12.8 - - - +
151A TYR* 1.3 89.8 - - + +
153A ILE* 1.3 60.5 + - + +
155A GLN* 3.3 2.8 + - + +
156A VAL* 2.9 32.6 + - - +
176A ILE* 3.9 19.6 - - + +
179A LEU* 4.8 7.4 - - + -
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Residues in contact with ILE 153 (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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118A VAL* 3.7 24.0 - - + +
121A LEU* 3.7 15.9 - - + +
122A ALA* 3.6 34.8 - - + -
125A THR* 3.6 37.5 - - + +
130A ALA* 5.4 0.2 - - + -
149A VAL 3.9 15.0 - - - +
150A ILE* 3.1 20.6 + - + +
152A PRO* 1.3 81.3 - - + +
154A MET* 1.3 59.6 + - - +
156A VAL* 3.4 8.3 + - - +
157A ASN* 2.9 26.7 + - - +
179A LEU* 5.0 4.3 - - + -
183A LEU* 5.4 1.3 - - + -
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Residues in contact with MET 154 (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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69A LEU* 4.4 16.6 - - + -
70A HIS* 3.5 15.9 - - + +
73A LEU* 3.5 26.7 - - + -
109A GLN* 4.1 31.9 - - + +
114A TYR* 2.9 34.3 + - + +
118A VAL* 3.9 20.2 - - + -
150A ILE* 3.1 27.4 + - + +
151A TYR 3.8 2.2 - - - +
152A PRO 3.2 0.2 - - - -
153A ILE* 1.3 77.1 - - - +
155A GLN* 1.3 60.8 + - - +
157A ASN* 3.1 2.9 + - - -
158A ASP* 2.8 26.9 + - - -
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Residues in contact with GLN 155 (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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32A TYR* 4.2 2.2 - - - +
70A HIS* 3.2 12.5 + - - +
151A TYR* 3.1 15.3 + - - +
152A PRO* 3.7 7.2 - - + +
154A MET* 1.3 75.5 - - - +
156A VAL* 1.3 65.2 + - - +
158A ASP* 3.1 18.2 + - - +
159A ILE* 3.3 16.8 + - + +
173A GLN* 3.0 23.6 + - - +
176A ILE* 3.4 32.8 - - + +
177A HIS* 4.2 16.0 + - - -
401A TYR* 2.8 52.1 + - + +
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Residues in contact with VAL 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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121A LEU* 4.1 14.8 - - + -
152A PRO 2.9 19.3 + - - +
153A ILE* 3.5 11.0 - - - +
155A GLN* 1.3 77.6 - - - +
157A ASN* 1.3 63.4 + - - +
158A ASP 3.2 0.7 + - - -
159A ILE* 3.2 14.5 + - - +
160A HIS 3.3 8.5 + - - -
176A ILE* 3.9 23.8 - - + +
179A LEU* 4.2 15.9 - - + -
180A ALA* 3.9 23.8 - - - +
183A LEU* 4.5 7.9 - - + -
184A LEU* 3.6 31.6 - - + +
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Residues in contact with ASN 157 (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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114A TYR* 2.9 55.3 + - + +
117A ASN* 2.8 28.3 + - - +
118A VAL* 3.4 12.2 - - + +
121A LEU* 3.7 13.0 - - + -
153A ILE 2.9 17.9 + - - +
154A MET* 3.1 7.4 + - - +
156A VAL* 1.3 77.4 - - - +
158A ASP* 1.3 58.4 + - - +
160A HIS* 3.3 8.1 + - - +
161A TYR* 2.8 32.4 + - - +
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Residues in contact with ASP 158 (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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32A TYR* 4.1 1.8 - - - +
65A LEU* 3.4 9.7 - - + +
70A HIS* 3.4 2.9 - - - -
108A PHE* 3.5 7.5 - - - -
109A GLN* 3.0 22.8 - - - +
114A TYR* 2.7 31.7 + - - -
154A MET 2.8 16.0 + - - +
155A GLN 3.4 2.7 - - - +
156A VAL 3.1 0.2 - - - -
157A ASN* 1.3 75.8 - - - +
159A ILE* 1.3 67.2 + - - +
161A TYR* 4.4 2.0 - - - -
162A LEU* 2.9 35.5 + - + +
401A TYR* 2.6 41.4 + - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.3 28.0 - - + +
155A GLN* 3.7 13.9 - - + +
156A VAL* 3.4 7.9 - - - +
158A ASP* 1.3 77.4 - - - +
160A HIS* 1.3 64.9 + - - +
163A GLY* 3.3 13.7 + - - -
164A VAL* 3.8 16.1 + - + +
167A ALA* 4.3 6.5 - - + -
176A ILE* 5.4 0.9 - - + +
177A HIS* 3.9 25.1 - - + -
180A ALA* 3.7 23.1 - - + -
184A LEU* 3.8 13.2 - - + -
186A LYS 5.6 1.8 - - - +
188A VAL* 3.6 35.9 - - + +
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Residues in contact with HIS 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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117A ASN* 3.7 18.4 + - + -
156A VAL 3.3 3.6 + - - +
157A ASN* 3.5 12.1 - - - +
158A ASP 3.1 0.4 - - - -
159A ILE* 1.3 82.0 - - - +
161A TYR* 1.3 69.9 + + + +
163A GLY* 3.3 12.6 + - - -
184A LEU* 3.7 33.3 - - + +
185A PRO* 4.4 20.5 - - + +
503A MG 2.2 31.5 - - - -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.5 38.3 - + + +
111A ASP* 3.0 20.2 + - - -
113A ASP* 3.7 29.1 + - - -
114A TYR* 3.8 33.2 - + + -
157A ASN* 2.8 21.9 + - - +
158A ASP* 3.9 3.1 - - - +
160A HIS* 1.3 84.0 - + + +
162A LEU* 1.3 66.8 + - + +
163A GLY* 3.2 1.1 + - - -
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Residues in contact with LEU 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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30A SER* 5.2 0.9 + - - -
32A TYR* 3.8 35.9 - - + -
63A ILE* 4.6 29.8 - - + +
65A LEU* 4.7 4.5 - - + -
101A LYS* 5.3 7.2 - - - +
103A VAL* 5.7 4.0 - - + -
108A PHE* 4.0 35.7 - - + -
158A ASP* 2.9 21.4 + - + +
159A ILE 4.3 0.9 - - - +
161A TYR* 1.3 82.5 - - + +
163A GLY* 1.3 62.4 + - - +
164A VAL* 3.3 18.0 + - + +
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Residues in contact with GLY 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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30A SER* 3.8 6.3 + - - -
159A ILE 3.3 3.6 + - - -
160A HIS 3.3 12.3 + - - -
161A TYR 3.2 4.4 - - - -
162A LEU* 1.3 78.1 - - - +
164A VAL* 1.3 66.1 + - - +
165A ASP* 3.7 1.4 + - - +
186A LYS* 4.1 12.9 + - - -
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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