Contacts of the helix formed by residues 154 - 173 (chain A) in PDB entry 1BO1
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A SER* 1.3 74.2 - - - +
155A GLU* 1.3 71.2 + - - +
157A VAL* 3.6 5.8 + - - +
158A ALA* 3.4 17.5 + - - +
197A TYR* 3.9 34.7 + - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 3.0 14.8 - - - +
154A SER* 1.3 83.9 + - - +
156A ASP* 1.3 59.0 + - - +
158A ALA* 2.8 25.7 + - - +
159A GLU* 2.9 24.0 + - - +
372A THR* 5.4 2.9 - - + +
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Residues in contact with ASP 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 VAL* 3.7 19.7 - - + +
153A SER* 2.8 33.3 + - - +
155A GLU* 1.3 76.8 - - - +
157A VAL* 1.3 53.0 + - - +
159A GLU* 2.8 13.4 + - - +
160A MET* 2.8 34.3 + - - +
186A MET* 4.6 0.2 - - - -
371A LEU* 3.7 21.6 - - + +
372A THR* 3.1 45.3 + - - +
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Residues in contact with VAL 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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98A TYR* 3.5 39.0 - - + +
152A VAL* 3.6 17.9 - - + -
153A SER 3.1 11.4 + - - +
154A SER 3.8 8.5 - - - +
156A ASP* 1.3 75.8 - - - +
158A ALA* 1.3 58.9 + - - +
160A MET* 3.6 3.1 - - - +
161A HIS* 2.9 33.7 + - + +
186A MET* 3.4 19.5 - - + +
197A TYR* 3.1 32.1 - - + -
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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
----------------------------------------------------------
154A SER 3.4 9.5 + - - +
155A GLU* 2.8 14.2 + - - +
157A VAL* 1.3 78.7 - - - +
159A GLU* 1.3 62.4 + - + +
160A MET 3.2 0.2 - - - -
161A HIS* 3.1 9.6 + - - +
162A ASN* 3.1 27.3 + - - +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 2.9 18.6 + - - +
156A ASP* 2.8 16.7 + - - +
158A ALA* 1.3 73.6 - - + +
160A MET* 1.3 66.8 + - - +
162A ASN* 3.1 7.3 + - - +
163A ILE* 3.0 33.3 + - + +
371A LEU* 3.0 46.9 - - + +
372A THR* 2.7 20.3 + - - -
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Residues in contact with MET 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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103A PHE* 3.1 36.1 - - + -
156A ASP 2.8 5.0 + - - +
157A VAL 3.6 4.7 - - - +
159A GLU* 1.3 77.5 - - - +
161A HIS* 1.3 53.8 + - + +
163A ILE* 3.6 11.2 - - - +
164A LEU* 2.7 64.3 + - + +
167A TYR* 5.9 0.4 - - - -
183A PHE* 3.9 35.0 - - + -
186A MET* 3.4 36.6 - - + -
199A VAL* 5.0 3.8 - - + -
371A LEU* 3.9 17.4 - - + +
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Residues in contact with HIS 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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71A PHE* 3.6 27.8 - - - +
72A LYS* 5.3 2.8 - - - -
73A ALA 5.0 2.4 + - - -
98A TYR* 3.6 39.2 - + + +
99A CYS* 3.4 21.8 - - - -
157A VAL* 2.9 25.1 + - + +
158A ALA* 3.1 11.6 + - - +
159A GLU 3.1 0.6 - - - -
160A MET* 1.3 78.8 - - + +
162A ASN* 1.3 67.1 - - - +
163A ILE 3.5 0.2 + - - -
164A LEU* 3.7 14.3 + - + +
165A LYS* 4.6 3.3 + - - +
186A MET* 4.6 4.0 - - - -
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Residues in contact with ASN 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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158A ALA* 3.1 18.1 + - - +
159A GLU* 3.1 11.4 + - - +
161A HIS* 1.3 79.9 - - - +
163A ILE* 1.3 64.3 + - + +
165A LYS* 4.6 4.3 + - - +
166A LYS* 5.0 9.4 + - - +
274A LEU* 5.5 1.0 - - - +
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Residues in contact with ILE 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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159A GLU* 3.0 19.5 + - + +
160A MET* 3.6 15.0 - - - +
162A ASN* 1.3 81.1 - - + +
164A LEU* 1.3 60.4 + - - +
165A LYS 3.2 2.7 - - - -
166A LYS* 2.8 7.3 + - - -
167A TYR* 2.8 41.1 + - + -
183A PHE* 4.9 1.1 - - + -
270A PHE* 5.9 0.4 - - + -
274A LEU* 3.7 36.6 - - + -
276A ILE* 4.4 12.3 - - + -
370A ILE* 4.0 21.3 - - + -
371A LEU* 4.0 26.5 - - + -
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Residues in contact with LEU 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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71A PHE* 3.8 9.5 - - + +
99A CYS* 3.7 33.2 - - + -
102A VAL* 3.9 13.5 - - + -
103A PHE* 3.8 20.4 - - + -
106A LEU* 3.9 26.9 - - + -
160A MET* 2.7 43.0 + - + +
161A HIS* 4.0 12.3 - - + +
162A ASN 3.5 1.2 - - - -
163A ILE* 1.3 73.2 - - - +
165A LYS* 1.3 57.3 + - - +
167A TYR* 4.3 9.2 - - + -
168A HIS* 3.0 29.6 + - - +
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Residues in contact with LYS 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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71A PHE* 3.4 41.0 - - + -
161A HIS 4.6 4.5 + - - +
162A ASN 4.6 3.5 + - - +
163A ILE 2.9 2.2 + - - -
164A LEU* 1.3 72.9 - - - +
166A LYS* 1.3 69.6 + - + +
168A HIS* 3.2 23.2 + - - -
169A GLN* 3.1 38.3 + - - +
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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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162A ASN 5.0 7.8 + - - +
163A ILE 2.8 6.9 + - - +
165A LYS* 1.3 79.7 - - + +
167A TYR* 1.3 58.2 + - - +
169A GLN* 2.8 10.7 + - - +
170A PHE* 2.8 27.4 + - - +
270A PHE* 3.9 11.9 - - + -
273A GLN* 5.2 9.6 + - + +
274A LEU* 3.3 35.3 - - + +
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Residues in contact with TYR 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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106A LEU* 4.0 24.7 - - + -
110A PHE* 3.5 5.9 - + - -
160A MET* 5.9 0.2 - - + -
163A ILE* 2.8 31.2 + - + +
164A LEU* 4.1 10.3 - - + +
166A LYS* 1.3 72.0 - - - +
168A HIS* 1.3 66.3 + - - +
170A PHE* 3.3 3.0 + + - +
171A ILE* 3.0 51.6 + - + +
180A LEU* 4.3 22.7 - - + -
181A PRO 2.5 29.2 + - - -
182A GLN* 3.1 5.5 - - - -
183A PHE* 3.0 42.6 + + - -
270A PHE* 3.4 21.2 - + + -
370A ILE* 4.6 6.1 - - + -
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Residues in contact with HIS 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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66A LEU* 3.4 27.7 - - + +
71A PHE* 4.1 9.0 - + + -
102A VAL* 4.2 4.7 - - + -
105A ASN* 2.8 26.5 + - - -
106A LEU* 3.4 34.8 - - + -
109A ARG* 4.4 3.7 + - - -
164A LEU 3.0 21.4 + - - +
165A LYS* 3.2 22.7 + - - +
166A LYS 3.1 0.2 - - - -
167A TYR* 1.3 84.7 - - + +
169A GLN* 1.3 56.5 + - - +
171A ILE* 3.4 3.3 + - - +
172A VAL* 3.0 51.9 + - + +
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Residues in contact with GLN 169 (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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165A LYS* 3.1 38.3 + - - +
166A LYS* 2.8 11.9 + - - +
168A HIS* 1.3 77.1 + - - +
170A PHE* 1.3 63.2 + - - +
172A VAL* 3.0 38.4 + - - +
173A GLU* 3.2 30.3 + - - +
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Residues in contact with PHE 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 2.8 4.6 + - - -
167A TYR* 3.3 9.9 - + - +
169A GLN* 1.3 76.0 - - - +
171A ILE* 1.3 57.7 + - + +
173A GLU* 2.8 28.6 + - + +
174A CYS* 2.8 46.9 - - - -
178A THR* 3.7 8.7 - - + -
180A LEU* 3.2 36.1 - - + -
266A ARG* 3.6 33.4 - - + -
267A ASP* 3.2 23.3 - - - -
270A PHE* 3.5 39.0 - + + -
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Residues in contact with ILE 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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106A LEU* 4.2 8.5 - - + -
109A ARG* 3.7 24.5 - - + +
110A PHE* 3.4 45.1 - - + -
167A TYR* 3.0 41.2 + - + +
168A HIS 3.6 5.4 - - - +
170A PHE* 1.3 80.8 - - + +
172A VAL* 1.3 63.1 + - - +
174A CYS* 4.0 4.0 - - - -
175A HIS* 3.4 16.1 + - - -
176A GLY* 3.4 7.8 + - - -
178A THR* 4.0 25.1 - - + +
180A LEU* 5.4 0.2 - - + -
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Residues in contact with VAL 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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109A ARG* 2.9 32.8 + - - +
168A HIS* 3.0 47.2 + - + +
169A GLN* 3.1 32.3 - - - +
170A PHE 3.0 0.4 - - - -
171A ILE* 1.3 79.7 - - - +
173A GLU* 1.3 56.3 + - + +
174A CYS 3.5 2.6 + - - -
175A HIS* 3.8 15.8 + - - -
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Residues in contact with GLU 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 GLN* 3.3 32.1 - - - +
170A PHE* 2.8 23.5 + - + +
172A VAL* 1.3 77.6 - - + +
174A CYS* 1.3 54.3 + - - +
175A HIS* 3.7 9.0 - - - -
266A ARG* 3.2 19.6 + - - +
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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