Contacts of the helix formed by residues 152 - 161 (chain B) in PDB entry 3BRW
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 ASN 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE 3.6 2.2 + - - -
151B PRO* 1.3 74.1 - - - +
153B VAL* 1.3 65.5 + - - +
154B VAL* 3.1 13.8 + - - +
155B GLN* 2.8 74.5 + - - +
156B MET* 2.9 11.1 + - - +
407C SER 3.4 17.1 + - - +
408C MET* 3.2 21.1 - - - +
409C MET 4.4 7.5 + - - +
410C GLY* 5.0 5.7 - - - -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.5 50.0 - - + +
114B PHE* 3.6 16.8 - - + -
116B LEU* 4.3 1.3 - - + -
152B ASN* 1.3 69.2 - - - +
154B VAL* 1.3 62.3 + - + +
156B MET* 3.3 17.3 + - + +
157B ALA* 3.0 24.9 + - - +
169B PHE* 3.7 33.2 - - + +
408C MET* 2.9 25.0 + - + +
409C MET* 4.6 8.5 - - - +
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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
----------------------------------------------------------
152B ASN* 3.1 9.5 + - - +
153B VAL* 1.3 76.2 - - + +
155B GLN* 1.3 68.2 + - + +
157B ALA* 3.3 3.8 + - - +
158B LYS* 3.1 39.1 + - + +
164B VAL* 5.5 1.3 - - + +
166B VAL* 3.4 21.8 - - + +
167B ASP* 3.6 24.5 - - - +
168B ARG* 3.6 16.6 - - - -
169B PHE* 3.9 18.3 - - + +
409C MET 4.6 4.5 - - - +
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Residues in contact with GLN 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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151B PRO* 3.3 17.7 - - + +
152B ASN* 2.8 55.2 + - - +
154B VAL* 1.3 74.7 - - + +
156B MET* 1.3 60.9 + - - +
158B LYS* 3.3 9.0 + - - +
159B LEU* 3.1 26.7 + - - +
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Residues in contact with MET 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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102B TYR* 5.9 0.2 - - + -
114B PHE* 3.8 10.1 - - + -
116B LEU* 3.7 28.9 - - + -
127B LEU* 3.7 34.3 - - + -
129B LEU* 3.3 18.9 - - + +
150B PHE* 5.4 4.7 - - + -
151B PRO* 3.3 39.7 - - + +
152B ASN 2.9 5.2 + - - +
153B VAL* 3.5 24.5 - - + +
155B GLN* 1.3 74.6 - - - +
157B ALA* 1.3 64.3 + - - +
159B LEU* 3.2 24.0 + - + +
160B VAL* 3.6 0.3 + - - +
175C PRO* 5.9 0.7 - - + -
408C MET* 3.9 14.6 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.6 20.1 - - + -
131B LEU* 4.3 9.0 - - + +
153B VAL 3.0 11.3 + - - +
154B VAL 3.3 7.8 + - - +
156B MET* 1.3 75.2 - - - +
158B LYS* 1.3 58.3 + - - +
160B VAL* 3.1 9.1 + - - +
161B CYS* 2.8 29.0 + - - +
164B VAL* 4.7 7.6 - - + -
169B PHE* 3.7 31.0 - - + -
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Residues in contact with LYS 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 VAL* 3.1 32.0 + - + +
155B GLN* 3.6 11.7 - - - +
156B MET 3.3 0.2 - - - -
157B ALA* 1.3 75.1 - - - +
159B LEU* 1.3 61.2 + - - +
160B VAL 3.3 0.2 - - - -
161B CYS 3.4 9.9 - - - +
162B GLU* 3.5 32.3 + - + +
164B VAL* 3.2 31.9 + - + +
165B ASN* 3.8 19.9 + - - +
166B VAL 5.2 0.9 - - - +
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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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127B LEU* 4.9 4.3 - - + -
129B LEU* 4.1 3.6 - - + -
140B ASP* 4.8 6.1 - - - +
142B ILE* 3.6 36.0 - - + +
151B PRO* 4.6 12.6 - - + -
155B GLN 3.1 14.1 + - - +
156B MET* 3.2 32.3 - - + +
158B LYS* 1.3 78.5 - - - +
160B VAL* 1.3 59.6 + - - +
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Residues in contact with VAL 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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114B PHE* 4.4 10.3 - - + -
129B LEU* 4.0 16.8 - - + -
131B LEU* 3.8 31.6 - - + +
138B TYR* 3.9 24.7 - - + +
139B HIS* 3.8 17.5 - - - +
140B ASP* 3.7 30.3 - - + +
156B MET 3.6 0.6 + - - -
157B ALA* 3.1 15.9 + - - +
159B LEU* 1.3 78.6 - - - +
161B CYS* 1.3 60.0 + - - +
162B GLU* 5.2 0.6 - - - +
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Residues in contact with CYS 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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109B LEU* 4.7 5.4 - - - -
131B LEU* 3.7 22.2 - - + -
138B TYR* 4.1 30.5 - - + -
157B ALA 2.8 6.9 + - - +
158B LYS* 3.4 17.2 + - - -
159B LEU 3.4 1.4 - - - -
160B VAL* 1.3 80.8 - - - +
162B GLU* 1.3 66.3 + - - +
163B ASP* 3.7 25.8 - - - -
164B VAL* 3.3 23.5 + - - +
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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