Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 2BAP
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 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B SER* 1.3 75.1 - - - +
137B MET* 1.3 55.9 + - - +
138B MET 3.0 3.4 - - - -
139B TYR* 2.7 36.5 + - - +
140B ILE* 3.5 5.2 + - - +
170B TRP* 3.5 48.9 - - + +
173B THR* 4.5 6.9 - - - +
174B PHE* 4.3 22.7 - - + +
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Residues in contact with MET 137 (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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135B SER 3.4 15.4 - - - +
136B ALA* 1.3 78.3 - - - +
138B MET* 1.3 61.7 + - - +
140B ILE* 3.4 29.0 + - + +
141B GLN* 3.1 31.1 + - + +
173B THR* 4.5 22.4 - - + +
177B GLU* 6.0 0.4 - - - +
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Residues in contact with MET 138 (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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150A MET* 4.2 25.1 - - + +
151A HIS* 4.0 53.2 - - + +
154A SER* 4.5 11.9 - - - +
135B SER 4.0 14.1 + - - +
136B ALA 3.0 0.6 - - - -
137B MET* 1.3 79.2 - - - +
139B TYR* 1.3 80.6 + - + +
141B GLN* 3.6 6.3 + - - +
142B GLU* 3.0 59.9 + - + +
155B CYS* 5.7 0.2 - - - -
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Residues in contact with TYR 139 (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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154A SER* 3.5 20.7 + - - -
157A GLU* 3.5 2.6 + - - -
135B SER 5.2 1.3 - - - -
136B ALA* 2.7 17.8 + - - +
138B MET* 1.3 84.3 - - + +
140B ILE* 1.3 65.6 + - - +
142B GLU* 3.1 12.0 + - - +
143B LEU* 3.2 24.5 + - + +
155B CYS* 3.8 33.7 - - - -
158B SER* 2.6 24.8 + - - -
159B LEU* 3.6 25.1 - - + -
162B SER* 2.9 16.7 + - - -
170B TRP* 3.8 34.8 - + - -
174B PHE* 3.8 16.6 - - + -
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Residues in contact with ILE 140 (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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136B ALA 3.5 2.2 + - - +
137B MET* 3.4 32.3 + - + +
139B TYR* 1.3 79.0 - - - +
141B GLN* 1.3 68.2 + - + +
142B GLU 3.2 0.2 + - - -
143B LEU* 3.5 5.2 + - - +
144B ARG* 3.2 58.3 + - - +
173B THR 3.5 24.5 - - - +
174B PHE* 3.7 26.9 - - + -
177B GLU* 3.8 17.9 - - + +
178B GLY* 4.2 8.3 - - - +
181B SER* 4.6 1.3 + - - -
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Residues in contact with GLN 141 (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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137B MET* 3.1 19.4 + - + +
138B MET* 3.7 6.5 - - - +
140B ILE* 1.3 84.5 - - + +
142B GLU* 1.3 57.5 + - - +
144B ARG* 3.8 11.3 - - - +
145B SER* 2.8 41.1 + - - +
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Residues in contact with GLU 142 (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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151A HIS* 4.6 11.2 + - - -
138B MET* 3.0 41.5 + - + +
139B TYR* 3.1 15.8 + - - +
141B GLN* 1.3 77.3 - - - +
143B LEU* 1.3 63.2 + - - +
145B SER* 3.3 16.3 + - - -
146B GLY 3.8 0.2 + - - -
147B LEU* 3.0 33.3 - - + +
155B CYS* 3.7 27.8 - - + -
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Residues in contact with LEU 143 (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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139B TYR* 3.2 20.6 + - + +
140B ILE* 4.3 2.2 - - - +
142B GLU* 1.3 74.7 - - + +
144B ARG* 1.3 61.4 + - - +
146B GLY* 3.4 12.5 + - - -
147B LEU* 4.3 6.4 + - - -
152B LEU* 4.8 4.3 - - + -
155B CYS* 4.4 15.9 - - - -
156B LEU* 3.8 28.9 - - + -
159B LEU* 4.4 6.7 - - + -
174B PHE* 3.9 27.1 - - + -
178B GLY 4.4 2.2 - - - +
181B SER* 4.1 24.2 - - - -
182B LEU* 4.5 8.3 - - + -
185B ILE* 3.8 33.5 - - + +
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Residues in contact with ARG 144 (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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140B ILE* 3.2 37.5 + - - +
141B GLN* 3.8 13.5 - - - +
143B LEU* 1.3 75.4 - - - +
145B SER* 1.3 54.0 + - - +
146B GLY* 2.7 18.0 + - - -
177B GLU* 2.8 46.3 + - - +
180B ALA* 4.9 3.2 - - - +
181B SER* 2.9 19.1 + - - +
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Residues in contact with SER 145 (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 GLN* 2.8 30.2 + - - +
142B GLU* 3.3 8.4 + - - -
144B ARG* 1.3 73.5 - - - +
146B GLY* 1.3 65.0 + - - +
147B LEU* 3.8 1.1 - - - +
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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