Contacts of the helix formed by residues 149 - 163 (chain B) in PDB entry 2BP1
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 PRO 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B GLY 4.2 4.9 - - - +
148B THR* 1.3 87.0 - - + +
150B VAL* 1.3 67.4 + - - +
151B GLU* 4.5 5.8 - - + +
152B GLU* 3.0 44.6 + - + +
153B THR 3.6 2.6 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 5.6 1.3 - - + -
148B THR 3.3 5.5 + - - +
149B PRO* 1.3 72.3 - - - +
151B GLU* 1.3 59.9 + - - +
153B THR* 3.3 11.6 + - - +
154B LEU* 2.9 38.2 + - + +
174B TYR* 4.6 12.6 - - + +
181B GLU* 4.1 20.6 - - - +
182B ILE* 3.7 34.8 - - + -
185B LEU* 3.8 24.0 - - + -
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Residues in contact with GLU 151 (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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149B PRO* 3.1 6.0 - - + +
150B VAL* 1.3 80.2 - - + +
152B GLU* 1.3 59.4 + - - +
154B LEU* 4.5 7.0 - - - -
155B HIS* 3.0 28.8 + - - +
185B LEU* 4.4 24.8 - - + +
189B ASN* 3.1 24.8 + - - +
191B TRP* 3.6 19.6 - - + -
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Residues in contact with GLU 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 LYS* 4.9 3.3 - - - +
117B PRO* 3.9 26.3 - - + +
148B THR* 4.0 14.8 - - + +
149B PRO* 3.0 34.0 + - + +
151B GLU* 1.3 74.8 - - - +
153B THR* 1.3 66.8 + - - +
155B HIS* 3.3 7.0 + - - +
156B ALA* 3.2 19.2 + - - +
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Residues in contact with THR 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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115B LEU* 2.9 42.5 + - + +
117B PRO* 5.1 0.2 - - - -
120B VAL* 4.0 5.4 - - + -
141B LEU* 3.8 39.0 - - + -
145B ASP* 5.4 0.9 - - - +
148B THR* 3.7 13.5 + - - +
149B PRO 3.9 2.8 + - - -
150B VAL* 3.3 15.1 + - - +
152B GLU* 1.3 77.0 - - - +
154B LEU* 1.3 61.6 + - - +
156B ALA* 3.1 11.3 + - - +
157B CYS* 3.1 20.5 + - - -
174B TYR* 5.3 0.7 - - - +
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Residues in contact with LEU 154 (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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141B LEU* 4.4 20.9 - - + -
150B VAL* 2.9 30.8 + - + +
151B GLU* 4.6 1.1 - - - -
153B THR* 1.3 72.0 - - - +
155B HIS* 1.3 60.8 + - - +
157B CYS* 3.2 6.5 + - - +
158B GLN* 2.9 29.1 + - - +
169B LEU* 4.5 16.4 - - + -
171B LEU* 5.3 0.2 - - + -
182B ILE* 3.8 49.8 - - + +
185B LEU* 4.6 9.9 - - + -
186B CYS* 4.0 17.7 - - - -
191B TRP* 3.6 20.1 - - + +
192B ILE* 5.9 0.2 - - - +
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Residues in contact with HIS 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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117B PRO* 6.3 0.2 - - + -
151B GLU 3.0 18.6 + - - +
152B GLU* 3.7 6.3 - - - +
154B LEU* 1.3 75.6 - - - +
156B ALA* 1.3 58.4 + - - +
158B GLN* 3.3 6.0 + - + +
159B ARG* 3.0 36.3 + - + +
191B TRP* 3.4 38.2 - + + -
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Residues in contact with ALA 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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117B PRO* 3.7 39.4 - - + +
120B VAL* 4.5 11.2 - - + -
152B GLU 3.2 5.7 + - - +
153B THR* 3.1 11.5 + - - +
155B HIS* 1.3 79.1 + - - +
157B CYS* 1.3 57.1 + - - +
159B ARG* 3.4 17.4 + - - +
160B LEU* 2.9 35.4 + - + +
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Residues in contact with CYS 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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120B VAL* 4.5 4.7 - - - -
139B PHE* 4.3 11.2 - - - -
141B LEU* 4.0 26.0 - - - -
153B THR 3.1 19.8 + - - -
154B LEU* 3.2 10.0 + - + +
156B ALA* 1.3 73.1 - - - +
158B GLN* 1.3 60.7 + - - +
160B LEU* 3.4 2.6 + - - -
161B HIS* 2.9 24.8 + - - +
166B PHE* 3.2 19.0 - - + -
169B LEU* 3.8 37.9 - - + -
192B ILE* 4.8 2.9 - - + -
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Residues in contact with GLN 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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154B LEU 2.9 13.9 + - - +
155B HIS* 3.3 11.6 + - + +
157B CYS* 1.3 75.4 - - - +
159B ARG* 1.3 58.9 + - - +
161B HIS* 3.2 8.5 + - - +
162B GLN* 2.9 54.6 + - + +
190B GLY 3.7 8.3 + - - -
191B TRP* 3.5 47.9 - - + +
192B ILE* 3.0 31.6 + - + +
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Residues in contact with ARG 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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117B PRO* 3.6 36.8 + - - +
118B ASP* 5.6 0.4 - - - +
121B ARG* 3.3 32.8 - - - +
155B HIS* 3.0 23.7 + - + +
156B ALA* 3.6 17.4 + - - +
158B GLN* 1.3 76.4 - - - +
160B LEU* 1.3 58.1 + - - +
162B GLN* 3.1 11.9 + - + +
163B GLU* 3.0 45.5 + - + +
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Residues in contact with LEU 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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120B VAL* 3.7 29.2 - - + -
121B ARG* 3.4 60.8 - - + +
124B LEU* 4.2 15.3 - - + -
125B GLU* 5.6 0.7 - - + -
139B PHE* 4.8 2.0 - - + -
156B ALA* 2.9 24.1 + - + +
157B CYS* 4.7 1.3 - - - -
159B ARG* 1.3 73.6 - - - +
161B HIS* 1.3 62.9 + - - +
163B GLU* 3.5 8.2 + - - +
164B GLY 3.4 3.3 + - - -
165B LYS* 3.0 43.1 + - + +
166B PHE* 3.7 17.9 - - + -
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Residues in contact with HIS 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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157B CYS 2.9 18.3 + - - +
158B GLN* 3.5 7.6 - - - +
160B LEU* 1.3 74.1 - - - +
162B GLN* 1.3 73.6 + - - +
164B GLY* 2.8 22.3 + - - -
166B PHE* 3.0 38.3 + - + -
167B VAL* 3.2 26.8 + - + -
192B ILE* 3.7 30.9 - - + +
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Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 2.9 42.6 + - + +
159B ARG* 3.1 11.4 + - + +
161B HIS* 1.3 87.6 - - - +
163B GLU* 1.3 61.1 + - + +
164B GLY 3.2 0.9 + - - -
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Residues in contact with GLU 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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121B ARG* 2.9 45.0 + - - -
159B ARG* 3.0 25.6 + - + +
160B LEU* 3.6 10.9 - - - +
161B HIS 3.1 0.4 - - - -
162B GLN* 1.3 77.6 - - + +
164B GLY* 1.3 59.8 + - - +
165B LYS* 3.4 25.1 + - + +
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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