Contacts of the helix formed by residues 150 - 166 (chain A) in PDB entry 2B4J
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.1 30.2 + - - +
77A VAL* 4.6 11.9 - - + -
79A VAL* 4.0 33.7 - - + +
151A ILE* 1.3 61.4 + - - +
152A GLU* 3.4 3.7 - - - +
153A SER* 3.4 15.1 + - - +
154A MET* 3.0 37.5 + - + +
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Residues in contact with ILE 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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62A GLN* 2.9 54.5 - - + +
63A LEU 3.6 2.9 - - - +
64A ASP* 3.3 39.9 - - + +
75A VAL* 3.4 24.0 - - + +
77A VAL* 3.6 19.1 - - + -
150A VAL* 1.3 74.7 - - - +
152A GLU* 1.3 63.3 + - + +
154A MET* 3.1 5.1 + - - -
155A ASN* 2.6 38.0 + - - +
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Residues in contact with GLU 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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64A ASP* 4.9 2.7 - - - +
150A VAL* 3.4 1.2 - - - +
151A ILE* 1.3 84.7 - - + +
153A SER* 1.3 61.2 + - - +
155A ASN* 3.6 17.8 - - - +
156A LYS* 3.5 19.2 + - - +
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Residues in contact with SER 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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150A VAL* 3.4 17.7 + - - +
151A ILE 3.3 0.4 - - - -
152A GLU* 1.3 78.4 - - - +
154A MET* 1.3 66.2 + - - +
156A LYS* 3.4 7.3 + - - +
157A GLU* 3.1 26.3 + - - +
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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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75A VAL* 5.0 4.0 - - + -
77A VAL* 3.7 32.3 - - + -
82A GLY* 4.0 16.8 - - - +
84A ILE* 3.8 18.8 - - + +
150A VAL* 3.0 25.1 + - + +
151A ILE* 3.1 8.0 + - + +
153A SER* 1.3 81.1 - - - +
155A ASN* 1.3 65.1 + - - +
157A GLU* 3.3 7.4 + - + +
158A LEU* 2.9 26.9 + - - +
183A HIS* 3.6 30.5 - - - +
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Residues in contact with ASN 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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64A ASP* 2.7 42.6 + - - +
65A CYS 4.6 0.4 + - - -
66A THR* 4.0 25.8 - - - +
75A VAL* 3.9 14.9 - - - +
151A ILE* 2.6 24.1 + - - +
152A GLU* 3.6 17.4 - - - +
153A SER 3.4 0.2 - - - -
154A MET* 1.3 71.5 - - - +
156A LYS* 1.3 57.1 + - - +
158A LEU* 3.4 7.3 - - - +
159A LYS* 3.1 36.0 + - + +
301A PO4 4.3 7.7 + - - +
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Residues in contact with LYS 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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152A GLU 3.5 8.9 + - - +
153A SER* 3.4 10.7 + - - +
154A MET 3.1 0.8 - - - -
155A ASN* 1.3 79.1 - - + +
157A GLU* 1.3 69.1 + - + +
159A LYS* 3.5 9.1 + - + +
160A LYS* 3.1 40.4 + - + +
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Residues in contact with GLU 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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153A SER* 3.1 17.1 + - - +
154A MET* 3.3 9.6 + - + +
156A LYS* 1.3 78.7 - - - +
158A LEU* 1.3 57.5 + - - +
160A LYS* 3.2 22.7 + - - +
161A ILE* 3.0 49.4 + - + +
183A HIS* 4.1 26.7 - - + +
186A LYS* 4.4 10.4 + - - -
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Residues in contact with LEU 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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66A THR* 4.9 5.2 - - + -
73A ILE* 4.1 15.3 - - + -
75A VAL* 3.9 31.2 - - + -
84A ILE* 3.9 24.7 - - + -
86A ALA* 4.1 7.2 - - + -
154A MET 2.9 18.5 + - - +
155A ASN* 3.4 5.6 - - - +
157A GLU* 1.3 77.9 - - - +
159A LYS* 1.3 59.0 + - + +
161A ILE* 3.2 9.2 + - + +
162A ILE* 2.8 43.0 + - + +
176A VAL* 4.6 2.9 - - + +
179A ALA* 3.8 23.1 - - + -
180A VAL* 4.3 12.1 - - + +
183A HIS* 6.0 0.8 - - - -
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Residues in contact with LYS 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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66A THR* 2.9 35.3 + - + -
67A HIS 2.8 27.4 + - - -
68A LEU* 4.0 26.0 - - + +
155A ASN* 3.1 18.4 + - + +
156A LYS* 3.9 7.6 - - + +
157A GLU 3.5 0.2 - - - -
158A LEU* 1.3 77.7 - - + +
160A LYS* 1.3 61.4 + - - +
162A ILE* 3.5 12.6 + - + +
163A GLY* 3.1 18.2 + - - -
301A PO4 3.4 14.1 + - - -
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Residues in contact with LYS 160 (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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156A LYS* 3.1 32.2 + - + +
157A GLU* 3.3 30.5 - - - +
158A LEU 3.1 0.2 - - - -
159A LYS* 1.3 75.1 - - - +
161A ILE* 1.3 66.0 + - + +
163A GLY* 3.2 4.5 + - - -
164A GLN* 3.1 49.4 + - + +
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Residues in contact with ILE 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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157A GLU* 3.0 45.4 + - + +
158A LEU* 3.7 6.5 - - - +
160A LYS* 1.3 76.9 - - + +
162A ILE* 1.3 60.9 + - - +
164A GLN* 3.1 27.2 + - - +
165A VAL* 3.1 12.3 + - - +
179A ALA* 3.6 26.2 - - + +
182A ILE* 3.8 29.4 - - + -
183A HIS* 3.9 33.4 - - + +
186A LYS* 4.2 9.4 - - - +
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Residues in contact with ILE 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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68A LEU* 3.6 33.0 - - + -
69A GLU* 5.3 0.2 - - - +
73A ILE* 4.2 5.8 - - + -
158A LEU* 2.8 42.3 + - + +
159A LYS* 3.7 7.0 - - + +
160A LYS 3.3 0.4 - - - -
161A ILE* 1.3 71.1 - - - +
163A GLY* 1.3 58.6 + - - +
165A VAL* 3.3 5.3 + - - +
166A ARG* 2.8 44.3 + - - +
172A LEU* 4.0 14.6 - - + -
175A ALA* 4.2 11.0 - - + +
176A VAL* 3.7 23.6 - - + -
179A ALA* 3.7 17.7 - - + -
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Residues in contact with GLY 163 (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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159A LYS 3.1 13.8 + - - -
160A LYS 3.2 4.4 + - - -
162A ILE* 1.3 76.7 - - - +
164A GLN* 1.3 61.6 + - - +
165A VAL 3.4 0.3 + - - -
166A ARG* 3.6 13.9 + - - +
167A ASP 5.2 0.3 + - - -
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Residues in contact with GLN 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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160A LYS* 3.1 46.7 + - + +
161A ILE* 3.1 27.9 + - - +
163A GLY* 1.3 77.5 - - - +
165A VAL* 1.3 64.3 + - + +
166A ARG 3.6 0.2 - - - -
167A ASP* 4.6 6.0 - - - +
168A GLN* 4.5 6.2 + - - -
182A ILE* 5.5 2.4 - - - +
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Residues in contact with VAL 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 ILE* 3.1 20.4 + - + +
162A ILE* 3.7 6.1 - - - +
164A GLN* 1.3 83.5 - - + +
166A ARG* 1.3 67.7 + - - +
167A ASP* 3.1 3.6 - - - -
168A GLN* 2.9 40.1 + - - +
169A ALA 4.2 1.0 + - - -
175A ALA* 3.9 25.5 - - + +
178A MET* 4.0 19.9 - - + +
179A ALA 4.5 2.9 - - - +
182A ILE* 3.3 32.1 - - + -
132B TRP* 5.1 1.8 - - + -
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Residues in contact with ARG 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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69A GLU* 2.8 40.1 + - - +
162A ILE* 2.8 24.1 + - - +
163A GLY* 3.6 11.8 + - - +
164A GLN 3.6 2.6 - - - -
165A VAL* 1.3 78.4 - - - +
167A ASP* 1.3 56.9 + - - +
168A GLN 3.1 1.7 + - - -
169A ALA* 2.8 55.5 + - - +
170A GLU 3.0 22.2 + - - -
171A HIS 4.0 3.8 + - - -
172A LEU* 3.3 21.7 - - - +
175A ALA* 3.9 17.5 - - - +
404A GOL 3.9 3.8 + - - -
364C LYS* 5.3 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