Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 3BX7
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 ALA 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLN* 4.8 6.5 + - - +
144A LEU* 1.3 77.5 - - - +
146A SER* 1.3 65.9 + - - +
147A GLU* 4.3 7.9 - - + +
148A LEU* 3.1 32.8 + - + +
149A LYS* 3.3 9.4 + - - +
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Residues in contact with SER 146 (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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144A LEU 3.5 1.6 + - - -
145A ALA* 1.3 71.2 - - - +
147A GLU* 1.3 58.7 + - - +
149A LYS* 3.1 18.0 + - - +
150A GLU* 2.9 48.6 + - - +
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Residues in contact with GLU 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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145A ALA* 3.2 5.9 - - + +
146A SER* 1.3 78.8 - - - +
148A LEU* 1.3 66.3 + - + +
150A GLU* 3.2 8.7 + - + +
151A ASN* 3.0 45.4 + - - +
154A ARG* 5.3 4.7 + - - +
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Residues in contact with LEU 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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117A GLN* 3.3 35.4 - - - +
118A TYR* 4.0 39.7 - - + -
137A ILE* 3.8 16.8 - - + +
144A LEU* 4.2 14.6 - - + -
145A ALA* 3.1 21.7 + - + +
147A GLU* 1.3 80.8 - - + +
149A LYS* 1.3 62.6 + - - +
151A ASN* 3.4 13.2 + - + +
152A PHE* 3.1 21.5 + - - +
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Residues in contact with LYS 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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34A VAL* 4.0 26.9 - - + +
137A ILE* 4.8 3.6 - - + -
143A GLU* 6.1 0.8 - - - +
144A LEU* 3.4 30.7 + - + +
145A ALA 3.3 7.6 + - - +
146A SER* 3.1 16.6 + - - +
148A LEU* 1.3 74.2 - - - +
150A GLU* 1.3 70.2 + - - +
152A PHE* 3.2 10.3 + - - +
153A ILE* 3.0 28.2 + - + +
168A PHE* 4.0 26.2 - - + -
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Residues in contact with GLU 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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146A SER* 2.9 40.5 + - - +
147A GLU* 3.2 9.6 + - - +
149A LYS* 1.3 81.9 - - - +
151A ASN* 1.3 60.9 + - - +
153A ILE* 3.2 22.1 + - - +
154A ARG* 3.0 39.7 + - - +
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Residues in contact with ASN 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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147A GLU* 3.0 39.4 + - - +
148A LEU* 3.7 14.3 - - + +
150A GLU* 1.3 76.0 - - - +
152A PHE* 1.3 56.0 - - - +
154A ARG* 2.6 43.6 + - - +
155A PHE* 2.8 32.0 + - - +
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Residues in contact with PHE 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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35A GLY* 3.9 15.0 - - - -
36A LEU 3.8 15.0 - - - -
37A ALA* 4.0 5.4 - - + -
120A VAL* 4.6 10.1 - - + -
135A ILE* 3.2 50.3 - - + -
136A THR 3.8 10.8 - - - -
137A ILE* 3.8 26.2 - - + -
148A LEU 3.1 13.7 + - - +
149A LYS* 3.3 11.0 - - - +
150A GLU 3.2 0.2 - - - -
151A ASN* 1.3 78.2 - - - +
153A ILE* 1.3 57.7 + - - +
155A PHE* 3.3 6.8 + + - +
156A SER* 2.8 41.7 + - - -
166A ILE* 4.0 18.8 - - + -
168A PHE* 4.2 16.4 - + - -
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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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43A ARG* 5.6 1.3 - - - +
149A LYS* 3.0 17.3 + - + +
150A GLU* 3.2 26.0 + - - +
152A PHE* 1.3 76.4 - - - +
154A ARG* 1.3 59.5 + - + +
156A SER* 3.2 2.8 + - - -
157A LYS* 2.9 55.1 + - + +
163A GLU* 4.5 17.3 - - - +
166A ILE* 4.0 20.2 - - + -
168A PHE* 3.8 30.7 - - + -
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Residues in contact with ARG 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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147A GLU* 4.9 4.9 + - - +
150A GLU* 3.0 22.9 + - - +
151A ASN* 2.6 46.4 + - - +
153A ILE* 1.3 79.9 - - + +
155A PHE* 1.3 57.5 + - - +
157A LYS* 3.3 9.5 + - + +
158A SER* 2.9 29.3 + - - -
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Residues in contact with PHE 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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15A LYS 3.7 20.2 - - - -
16A VAL* 4.4 5.2 - - + -
17A PRO* 3.8 22.2 - - + -
111A VAL* 4.0 16.6 - - + -
120A VAL* 4.1 16.8 - - + -
135A ILE* 3.9 37.5 - - + -
151A ASN 2.8 18.5 + - - +
152A PHE* 3.6 7.6 - + - +
154A ARG* 1.3 77.4 - - - +
156A SER* 1.3 61.3 + - - +
158A SER* 2.7 28.0 + - - -
159A LEU* 3.2 31.9 + - + +
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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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37A ALA* 3.5 22.8 - - - +
135A ILE* 4.7 3.8 - - - +
152A PHE* 2.8 33.6 + - - -
153A ILE 3.2 6.0 + - - -
155A PHE* 1.3 77.9 - - - +
157A LYS* 1.3 57.8 + - - +
159A LEU* 3.0 25.1 + - - +
161A LEU* 3.2 24.9 + - - +
166A ILE* 3.5 23.5 - - - +
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Residues in contact with LYS 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 ILE* 2.9 34.4 + - + +
154A ARG* 3.7 8.5 - - + +
156A SER* 1.3 71.3 - - - +
158A SER* 1.3 58.6 + - - +
159A LEU 2.9 4.7 - - - -
160A GLY* 2.8 22.2 + - - -
161A LEU 3.3 20.8 + - - +
162A PRO* 5.1 0.7 - - + -
163A GLU* 2.8 45.2 + - - +
166A ILE* 4.9 2.0 - - + -
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Residues in contact with SER 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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15A LYS* 4.2 22.5 + - - +
154A ARG 2.9 15.6 + - - -
155A PHE* 2.7 30.9 + - - -
157A LYS* 1.3 77.2 - - - +
159A LEU* 1.3 66.0 + - - +
160A GLY 3.2 1.2 + - - -
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Residues in contact with LEU 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 ILE* 4.9 0.5 - - - +
9A PRO 4.7 3.1 - - - +
11A PRO* 3.8 43.2 - - + +
15A LYS* 3.8 27.4 - - + +
16A VAL* 4.2 4.0 - - + -
122A PHE* 4.4 5.8 - - + -
133A PHE* 4.0 19.3 - - + -
135A ILE* 3.6 38.1 - - + -
155A PHE* 3.2 28.0 - - + +
156A SER* 3.0 9.3 + - - +
157A LYS 2.9 1.4 - - - -
158A SER* 1.3 88.3 - - - +
160A GLY* 1.3 61.4 + - - +
161A LEU* 3.5 2.0 - - + -
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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