Contacts of the helix formed by residues 152 - 161 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B SER 3.5 17.6 + - - +
408B MET* 3.3 23.8 - - - +
409B MET* 5.0 0.9 - - - -
410B GLY* 4.5 13.8 - - - +
150C PHE 3.2 5.7 + - - -
151C PRO* 1.3 73.7 - - - +
153C VAL* 1.3 67.5 + - - +
154C VAL* 3.4 12.6 + - - +
155C GLN* 3.0 59.6 + - - +
156C MET* 2.9 19.3 + - - +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET* 3.1 24.5 + - + +
409B MET* 4.7 12.1 - - - -
102C TYR* 3.7 43.5 - - + -
114C PHE* 3.9 12.5 - - + -
116C LEU* 4.2 2.2 - - + -
152C ASN* 1.3 71.0 - - - +
154C VAL* 1.3 74.8 + - + +
156C MET* 3.2 13.5 + - - +
157C ALA* 2.9 21.7 + - - +
168C ARG* 5.4 0.2 - - - -
169C PHE* 3.7 36.8 - - + +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B MET* 6.5 1.1 - - - -
152C ASN* 3.2 10.4 + - - +
153C VAL* 1.3 77.5 - - + +
155C GLN* 1.3 66.3 + - + +
157C ALA* 3.0 14.7 + - - +
158C LYS* 3.1 31.3 + - + +
164C VAL* 5.7 2.2 - - + +
166C VAL* 3.7 20.0 - - + +
167C ASP 3.5 23.1 - - - +
168C ARG* 3.7 17.5 - - + -
169C PHE* 4.0 18.6 - - + +
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Residues in contact with GLN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C PRO* 3.2 27.3 - - + +
152C ASN* 3.0 41.8 + - - +
154C VAL* 1.3 77.8 - - + +
156C MET* 1.3 62.3 + - - +
158C LYS* 3.5 15.8 + - - +
159C LEU* 3.3 21.1 + - - +
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Residues in contact with MET 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PRO* 6.1 1.1 - - + -
408B MET* 5.2 6.3 - - - +
114C PHE* 4.4 3.6 - - + -
116C LEU* 3.6 39.9 - - + -
127C LEU* 3.5 37.9 - - + -
129C LEU* 3.1 34.9 - - + +
150C PHE* 5.2 6.3 - - + -
151C PRO* 3.3 39.3 - - + +
152C ASN 2.9 9.3 + - - +
153C VAL* 3.4 9.0 - - - +
155C GLN* 1.3 73.9 - - - +
157C ALA* 1.3 66.3 + - - +
159C LEU* 2.9 19.3 + - + +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 3.7 16.9 - - + -
131C LEU* 3.9 9.6 - - + +
153C VAL 2.9 8.2 + - - +
154C VAL 3.4 9.0 - - - +
156C MET* 1.3 75.9 - - - +
158C LYS* 1.3 57.1 + - - +
160C VAL* 3.3 8.1 - - - +
161C CYS* 2.9 32.2 + - - +
164C VAL* 4.3 7.4 - - + -
169C PHE* 3.5 35.9 - - + -
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C VAL* 3.1 26.8 + - + +
155C GLN* 3.6 12.8 - - - +
156C MET 3.1 1.0 - - - -
157C ALA* 1.3 76.7 - - - +
159C LEU* 1.3 57.8 + - + +
160C VAL 3.4 0.2 + - - -
161C CYS 3.3 11.9 - - - +
162C GLU* 3.1 39.5 + - - +
164C VAL* 3.3 28.8 + - + +
165C ASN* 4.2 17.1 - - - +
166C VAL 5.7 0.4 - - - +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C LEU* 5.2 1.6 - - + -
140C ASP* 4.4 9.7 - - - +
142C ILE* 3.5 37.2 - - + +
151C PRO* 4.5 13.5 - - + -
155C GLN 3.3 18.2 - - - +
156C MET* 2.9 23.8 + - + +
158C LYS* 1.3 77.1 - - + +
160C VAL* 1.3 57.8 + - - +
162C GLU* 3.8 5.6 - - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.3 2.7 - - + -
129C LEU* 3.8 29.4 - - + -
131C LEU* 4.0 25.6 - - + +
138C TYR* 3.7 40.0 - - + +
139C HIS 3.7 3.6 - - - +
140C ASP* 3.7 29.2 - - + +
156C MET 3.6 0.8 + - - -
157C ALA 3.3 11.7 - - - +
159C LEU* 1.3 78.5 - - - +
161C CYS* 1.3 63.4 + - + +
162C GLU* 3.4 9.1 - - - +
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Residues in contact with CYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 4.8 9.2 - - - -
131C LEU* 4.3 8.5 - - + -
138C TYR* 3.4 44.2 - - + -
157C ALA 2.9 19.9 + - - +
158C LYS* 3.3 8.8 - - - -
160C VAL* 1.3 85.7 - - + +
162C GLU* 1.3 65.9 + - - +
163C ASP* 4.4 7.0 - - - -
164C VAL* 3.5 31.1 + - + +
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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