Contacts of the helix formed by residues 155 - 163 (chain A) in PDB entry 1BO6
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 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA 3.9 3.4 - - - -
137A VAL* 3.7 35.2 - - + -
140A TYR* 3.6 46.5 + + + +
154A SER* 1.3 72.4 - - - +
156A SER* 1.3 59.6 + - - +
158A PHE* 3.0 5.6 + + - +
159A VAL* 2.8 52.9 + - + +
267A HIS* 3.6 35.7 - + + +
268A PHE* 3.6 38.6 - + - -
269A PRO* 5.0 0.9 - - + -
272A LEU* 4.2 5.6 - - + -
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Residues in contact with SER 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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154A SER* 3.2 8.4 + - - -
155A PHE* 1.3 79.1 - - - +
157A GLU* 1.3 63.9 + - - +
159A VAL* 3.0 3.3 + - - +
160A GLU* 2.9 30.6 + - - +
269A PRO* 4.5 13.3 - - - +
272A LEU* 3.8 28.2 - - - +
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Residues in contact with GLU 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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152A PRO* 5.3 0.4 - - + -
153A LYS* 3.4 43.5 - - + +
154A SER* 3.1 30.1 + - - +
156A SER* 1.3 80.2 - - - +
158A PHE* 1.3 62.5 + - - +
160A GLU* 3.4 10.3 + - + +
161A LYS* 3.3 30.8 + - - +
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Residues in contact with PHE 158 (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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8A TYR* 5.8 0.2 - - - -
136A ALA* 2.9 33.9 - - + -
139A TYR* 3.3 31.2 - + + -
140A TYR* 3.7 24.2 - + + -
143A LEU* 3.4 33.9 - - + -
152A PRO* 3.7 24.0 - - + +
154A SER 3.1 6.4 + - - +
155A PHE* 3.0 10.7 + + - +
157A GLU* 1.3 75.9 - - - +
159A VAL* 1.3 68.1 + - + +
161A LYS* 3.0 13.9 + - + +
162A PHE* 2.8 36.7 + + + +
167A VAL* 3.9 16.2 - - + -
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Residues in contact with VAL 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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136A ALA* 4.8 3.6 - - + -
155A PHE* 2.8 56.0 + - + +
156A SER 3.0 6.7 + - - +
158A PHE* 1.3 73.5 - - + +
160A GLU* 1.3 66.1 + - - +
162A PHE* 3.1 6.9 + - + +
163A MET* 2.9 34.8 + - + +
268A PHE* 3.9 9.2 - - + -
272A LEU* 3.8 20.0 - - + -
276A PHE* 3.7 29.6 - - + -
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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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156A SER* 2.9 19.1 + - - +
157A GLU* 3.5 12.8 - - + +
159A VAL* 1.3 77.1 - - - +
161A LYS* 1.3 63.6 + - + +
163A MET* 3.5 12.1 + - - +
164A GLN* 3.2 32.7 + - - +
272A LEU* 3.8 9.9 - - - +
275A ARG* 2.5 46.7 + - - -
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Residues in contact with LYS 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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8A TYR* 3.8 42.1 - - + +
9A TYR* 4.7 7.3 + - - +
152A PRO* 6.0 6.5 - - - -
157A GLU* 3.3 21.1 + - - +
158A PHE* 3.0 14.5 + - + +
160A GLU* 1.3 76.7 - - + +
162A PHE* 1.3 62.8 + - - +
164A GLN* 3.1 14.2 + - - +
165A GLY 3.0 3.5 + - - -
166A GLN* 2.8 53.8 + - + +
167A VAL* 4.0 6.3 - - + -
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Residues in contact with PHE 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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46A TYR* 3.9 18.6 + + - -
132A ALA* 4.0 9.4 - - + -
135A VAL* 3.8 25.6 - - + -
136A ALA* 3.9 17.3 - - + -
139A TYR* 4.5 3.4 - + - -
158A PHE* 2.8 32.3 + + + +
159A VAL* 3.1 14.1 + - + +
161A LYS* 1.3 77.4 - - - +
163A MET* 1.3 62.1 + - - +
165A GLY* 3.0 13.4 + - - +
167A VAL* 3.9 12.7 - - + +
170A GLY 5.4 0.2 - - - +
172A TRP* 3.5 39.8 + + + -
173A TYR* 3.9 18.3 - + - -
276A PHE* 3.9 25.8 - + - -
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Residues in contact with MET 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 VAL* 2.9 29.7 + - + +
160A GLU* 3.7 23.3 - - - +
162A PHE* 1.3 76.0 - - - +
164A GLN* 1.3 61.1 + - + +
165A GLY 3.2 0.7 + - - -
171A SER* 5.8 0.2 - - - -
173A TYR* 3.7 19.5 - - - +
272A LEU* 4.4 2.9 - - + -
275A ARG* 3.4 35.0 - - - +
276A PHE* 3.7 42.4 - - + -
279A HIS* 3.2 44.6 + - + +
283A GLN* 5.6 0.2 - - - -
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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