Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 2BV1
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 PHE 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 4.1 14.1 - + + -
105A CYS* 3.6 23.6 - - + -
108A TYR* 3.8 33.8 - + + -
120A ALA* 3.6 39.7 - - + -
123A ILE* 3.7 26.0 - - + -
124A TYR 4.6 1.3 - - - -
128A VAL* 4.6 6.3 - - + -
146A THR* 3.8 19.3 - - + -
150A ILE* 3.7 24.7 - - + -
155A PRO 5.2 0.2 + - - -
156A THR 3.3 0.4 - - - -
157A CYS* 1.3 82.8 - - - +
159A ASP* 1.3 54.1 + - - +
160A GLU 3.3 2.9 - - - -
161A ALA* 3.3 6.1 + - + +
162A GLN* 2.7 37.2 + - - +
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Residues in contact with ASP 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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109A LYS* 4.2 22.0 + - - +
149A LYS* 6.1 0.4 - - - +
155A PRO 4.3 0.9 - - - +
156A THR* 3.2 42.5 + - - +
157A CYS 3.4 0.2 - - - -
158A PHE* 1.3 76.7 - - - +
160A GLU* 1.3 58.8 + - + +
162A GLN* 3.8 11.4 - - - +
163A LYS* 3.0 29.5 + - - +
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Residues in contact with GLU 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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142A THR* 4.1 18.1 + - + +
145A SER* 3.5 20.8 + - - -
146A THR* 5.2 3.1 - - - +
149A LYS* 4.0 23.9 + - - +
156A THR 4.9 0.2 + - - -
157A CYS 4.8 2.9 + - - +
158A PHE 3.3 0.4 - - - -
159A ASP* 1.3 77.1 - - + +
161A ALA* 1.3 67.1 + - - +
163A LYS* 3.3 7.1 + - - +
164A VAL* 3.1 25.5 + - - +
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Residues in contact with ALA 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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101A PHE* 3.8 22.4 - - + -
128A VAL* 5.4 0.2 - - + -
136A ILE* 4.6 0.2 - - + -
138A ILE* 4.0 23.0 - - + +
142A THR* 3.9 9.3 - - + +
146A THR* 3.9 24.3 + - + +
158A PHE 3.3 6.7 + - - +
160A GLU* 1.3 78.1 - - - +
162A GLN* 1.3 62.6 + - - +
164A VAL* 3.4 3.3 + - - +
165A ILE* 3.0 27.4 + - - +
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Residues in contact with GLN 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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101A PHE* 3.9 10.1 - - - -
102A TRP* 3.2 48.1 + - + +
105A CYS* 3.6 20.8 - - + +
106A GLU* 2.7 25.0 + - - -
109A LYS* 2.9 25.2 + - - -
158A PHE 2.7 21.8 + - - +
159A ASP* 3.8 11.4 - - - +
161A ALA* 1.3 75.4 - - - +
163A LYS* 1.3 56.6 + - - +
165A ILE* 3.3 2.5 + - - +
166A TYR* 2.8 29.0 + - + +
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Residues in contact with LYS 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 ASP 3.0 18.0 + - - +
160A GLU* 3.6 6.5 - - - +
162A GLN* 1.3 74.8 - - - +
164A VAL* 1.3 65.8 + - + +
166A TYR* 3.3 8.2 + - + +
167A THR* 3.0 31.9 + - - +
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Residues in contact with VAL 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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137A ASN 4.2 7.0 - - - +
138A ILE* 3.8 27.1 - - + -
139A ASP* 4.4 17.0 - - - +
142A THR* 4.4 13.2 - - + +
160A GLU 3.1 14.7 + - - +
161A ALA 3.6 6.5 - - - +
163A LYS* 1.3 75.2 - - + +
165A ILE* 1.3 59.6 + - - +
167A THR* 3.2 8.1 + - - -
168A LEU* 2.9 33.6 + - + +
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Residues in contact with ILE 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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98A ASN* 3.3 56.1 - - + +
101A PHE* 3.7 21.8 - - + -
102A TRP* 4.9 2.7 - - + -
136A ILE* 3.7 23.3 - - + -
137A ASN 4.1 7.2 - - - +
138A ILE* 3.8 13.9 - - + -
161A ALA 3.0 21.8 + - - +
162A GLN* 3.8 3.4 - - - +
164A VAL* 1.3 71.9 - - - +
166A TYR* 1.3 67.5 + - - +
168A LEU* 3.2 15.4 + - + +
169A MET* 3.1 26.5 + - + +
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Residues in contact with TYR 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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73A LEU* 3.7 20.4 - - + +
74A GLU* 3.1 38.9 + - - +
77A LEU* 3.9 15.5 - - + -
102A TRP* 3.5 29.6 - + - +
162A GLN* 2.8 21.2 + - + +
163A LYS* 3.6 9.0 - - + +
165A ILE* 1.3 73.6 - - - +
167A THR* 1.3 59.9 + - - +
169A MET* 3.3 9.7 + - + +
170A GLU* 2.8 54.8 + - - +
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Residues in contact with THR 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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163A LYS* 3.0 20.2 + - - +
164A VAL* 3.5 9.6 - - - -
166A TYR* 1.3 79.2 - - - +
168A LEU* 1.3 68.0 + - + +
170A GLU* 4.2 9.7 + - - +
171A LYS* 2.9 42.8 + - + +
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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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98A ASN* 4.6 16.6 - - - +
137A ASN* 3.4 42.4 - - + +
164A VAL* 2.9 21.3 + - + +
165A ILE* 3.2 20.4 + - + +
167A THR* 1.3 77.5 - - + +
169A MET* 1.3 57.7 + - - +
171A LYS* 5.2 1.3 - - - -
172A ASP* 3.1 37.2 + - + +
173A SER* 3.9 0.5 + - - -
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Residues in contact with MET 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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73A LEU* 3.8 8.3 - - + -
77A LEU* 4.5 16.6 - - + -
86A PHE* 4.0 22.0 - - + -
90A LEU* 4.4 2.2 - - + -
98A ASN* 3.8 19.3 - - + +
99A ILE* 3.9 28.7 - - + -
102A TRP* 4.0 31.9 - - + -
165A ILE* 3.1 19.7 + - + +
166A TYR* 3.5 13.9 - - - +
168A LEU* 1.3 76.1 - - - +
170A GLU* 1.3 65.3 + - - +
171A LYS 3.1 1.0 + - - -
172A ASP 3.4 3.6 + - - -
173A SER* 3.6 16.4 - - - +
174A TYR* 2.9 26.5 + - - +
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Residues in contact with GLU 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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72A SER* 5.3 5.0 - - - -
73A LEU* 3.6 25.2 + - + +
166A TYR* 2.8 47.8 + - - +
167A THR* 3.1 10.7 + - - +
169A MET* 1.3 72.3 - - - +
171A LYS* 1.3 82.9 + - + +
174A TYR* 3.8 11.8 - - + -
175A PRO* 3.1 21.1 - - - +
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Residues in contact with LYS 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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167A THR* 2.9 34.0 + - + +
168A LEU* 4.6 2.0 - - - +
170A GLU* 1.3 105.8 + - + +
172A ASP* 1.3 61.0 + - + +
175A PRO* 3.8 12.0 - - - +
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Residues in contact with ASP 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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168A LEU* 3.1 20.4 + - + +
169A MET 3.4 0.4 + - - -
171A LYS* 1.3 80.8 - - + +
173A SER* 1.3 68.0 + - - +
174A TYR 3.5 0.9 - - - -
175A PRO* 3.5 10.0 - - - +
176A ARG* 2.8 54.0 + - - +
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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