Contacts of the helix formed by residues 151 - 164 (chain B) in PDB entry 1BQ4
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 LEU 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ARG* 5.1 4.4 - - - +
115B SER 4.4 5.7 + - - +
116B PHE* 3.4 24.9 + - + +
150B SER* 1.3 72.3 - - - +
152B ALA* 1.3 65.8 + - - +
154B VAL* 3.0 7.1 + - + +
155B ILE* 2.9 34.2 + - + +
183B ASN* 3.3 38.1 + - + +
186B ARG* 4.1 20.4 - - - +
187B GLY* 3.9 14.6 - - - +
200B ILE* 3.4 45.1 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 2.8 43.8 + - + +
117B ASP* 3.9 15.7 - - + -
150B SER* 3.6 7.9 - - - +
151B LEU* 1.3 77.1 - - - +
153B LEU* 1.3 65.5 + - + +
155B ILE* 3.4 5.8 + - - +
156B ASP* 3.0 30.9 + - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PRO* 5.0 11.0 - - + -
148B THR* 5.0 3.8 - - + +
149B GLU* 3.7 28.0 - - + -
150B SER* 3.1 21.2 + - - +
152B ALA* 1.3 81.7 - - + +
154B VAL* 1.3 61.6 + - - +
155B ILE 3.0 1.3 - - - -
156B ASP* 2.7 42.5 + - + +
157B ARG* 3.0 15.5 + - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN 4.6 0.2 - - - +
87B ARG* 3.6 25.4 - - + -
149B GLU* 3.3 24.7 - - - +
150B SER 2.8 16.7 + - - +
151B LEU* 3.4 12.8 - - + +
153B LEU* 1.3 74.0 - - - +
155B ILE* 1.3 60.9 + - + +
157B ARG* 3.0 36.8 + - - +
158B LEU* 2.9 26.9 + - + +
183B ASN* 4.5 4.3 - - + +
184B SER* 3.9 25.8 - - - +
187B GLY* 5.7 0.7 - - - -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.9 26.7 - - + -
151B LEU* 2.9 25.5 + - + +
152B ALA 3.5 5.6 - - - +
154B VAL* 1.3 73.1 - - + +
156B ASP* 1.3 68.9 + - - +
157B ARG 2.9 3.3 + - - -
158B LEU* 4.3 6.7 - - + +
159B LEU* 3.1 51.2 + - + +
187B GLY* 3.8 41.5 - - - +
190B LYS* 4.3 13.9 - - + +
191B HIS* 5.2 4.3 - - + +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 3.0 16.4 + - - +
153B LEU* 2.7 33.9 + - + +
155B ILE* 1.3 74.0 - - - +
157B ARG* 1.3 54.0 + - - +
159B LEU* 4.5 4.8 - - - +
160B PRO* 3.4 19.2 - - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 3.6 17.4 - - - -
82B TRP* 3.3 42.4 + - + -
83B ARG* 2.7 67.4 + - - +
84B LEU 3.9 0.8 - - - -
85B ASN 2.4 26.3 + - - -
86B GLU 3.4 12.7 + - - -
144B VAL* 6.0 1.1 - - + -
149B GLU* 3.3 29.4 + - - +
153B LEU* 3.0 13.3 + - + +
154B VAL* 3.0 38.7 + - - +
155B ILE 2.9 0.8 + - - -
156B ASP* 1.3 76.4 - - + +
158B LEU* 1.3 58.4 + - - +
159B LEU 3.5 0.4 - - - -
160B PRO* 3.7 0.7 - - - -
184B SER* 3.9 1.6 - - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 3.3 26.7 - - - +
84B LEU* 4.0 21.8 - - + -
154B VAL* 2.9 18.1 + - + +
155B ILE* 3.1 6.2 + - - +
157B ARG* 1.3 76.6 - - - +
159B LEU* 1.3 85.0 + - + +
161B TYR* 3.1 19.3 + - + +
162B TRP* 3.3 13.4 + - + -
184B SER* 3.4 34.8 - - - +
185B LEU* 6.4 0.7 - - + -
187B GLY* 5.0 2.7 - - - -
188B LEU* 4.3 31.9 - - + +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 3.1 33.2 + - + +
156B ASP* 4.5 3.8 - - - +
158B LEU* 1.3 91.0 - - + +
160B PRO* 1.4 58.0 - - + +
162B TRP* 3.1 11.2 + - + +
163B GLN* 2.7 55.0 + - - +
188B LEU* 5.8 0.4 - - + -
191B HIS* 3.4 54.3 - - + +
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 3.7 16.6 - - - +
156B ASP 3.4 18.2 - - - +
157B ARG 3.6 5.2 - - - +
158B LEU 3.4 4.3 - - - -
159B LEU* 1.4 92.1 - - + +
161B TYR* 1.3 59.4 + - - +
162B TRP 3.3 0.2 - - - -
163B GLN* 3.4 15.5 - - - +
164B ASP* 3.4 26.2 + - - +
165B VAL* 4.9 0.3 - - - +
83D ARG* 3.5 11.3 + - - +
160D PRO* 3.4 38.4 - - + -
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 3.2 36.3 - + - -
79B ASN* 3.5 14.9 - - - +
80B ARG 3.9 9.3 + - - -
81B SER* 3.5 34.1 - - - -
83B ARG* 3.7 21.0 - - + +
84B LEU* 4.3 16.8 - - + -
158B LEU 3.1 9.4 + - - +
160B PRO* 1.3 77.2 - - - +
162B TRP* 1.3 61.8 + - - +
165B VAL* 3.1 42.1 + - + +
166B ILE* 3.0 39.1 + - + -
164D ASP* 4.9 5.8 - - - -
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Residues in contact with TRP 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 4.0 29.6 - - + -
158B LEU* 3.3 16.4 + - + +
159B LEU* 3.1 28.6 + - + +
161B TYR* 1.3 82.0 - - - +
163B GLN* 1.3 67.5 + - + +
166B ILE* 3.6 43.7 - - + +
167B ALA* 3.1 28.2 + - - +
170B LEU* 4.1 9.0 - - + -
188B LEU* 4.0 23.6 - - + -
191B HIS* 3.8 12.1 - + - -
192B LEU* 4.2 20.6 - - + -
215B LEU* 4.3 13.2 - - + -
219B LEU* 4.0 25.4 - - + -
141D ASP* 3.6 23.1 + - - -
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 2.7 39.3 + - + +
160B PRO* 3.4 14.4 - - - +
162B TRP* 1.3 84.0 - - + +
164B ASP* 1.3 58.0 + - - +
167B ALA* 3.5 5.7 - - - +
191B HIS* 5.3 4.2 - - - +
83D ARG* 3.2 29.1 + - - +
140D VAL* 3.5 4.9 - - - -
141D ASP* 2.9 48.5 + - + +
144D VAL* 3.1 42.3 - - + +
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Residues in contact with ASP 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO 3.4 10.4 + - - +
163B GLN* 1.3 79.2 - - - +
165B VAL* 1.3 72.9 + - + +
167B ALA 4.5 2.9 - - - -
168B LYS* 4.2 9.9 - - - +
81D SER* 4.7 2.1 + - - -
82D TRP* 3.2 18.4 + - - -
83D ARG* 2.7 48.2 + - - +
139D TYR 4.1 12.5 - - - +
140D VAL* 3.9 4.4 - - - +
161D TYR* 4.7 9.9 - - - -
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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