Contacts of the helix formed by residues 157 - 168 (chain A) in PDB entry 3BGD
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 ASP 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A PHE* 3.6 27.5 - - + -
153A ILE* 3.6 20.0 - - + -
154A ASN* 2.8 33.9 + - - +
156A GLY* 1.3 75.3 - - - +
158A HIS* 1.3 56.2 + - - -
159A ASP 3.3 2.7 - - - -
160A ARG* 3.3 29.2 + - - +
161A TYR* 2.8 28.8 + - - +
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Residues in contact with HIS 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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150A LEU* 4.1 18.6 + - + -
153A ILE* 4.0 17.0 + - + -
154A ASN 3.6 9.0 - - - -
155A PRO* 3.2 36.6 + - + +
156A GLY 3.4 0.8 - - - -
157A ASP* 1.3 76.3 - - - +
159A ASP* 1.3 57.7 + - - +
161A TYR* 3.6 6.0 - - - +
162A ALA* 2.9 31.4 + - - +
192A PHE* 5.4 1.6 - - + +
193A TYR 5.1 4.3 - - - -
194A VAL* 4.0 21.5 - - + +
198A GLU* 2.8 43.0 + - + +
201A ARG* 4.3 3.6 - - - +
202A LEU* 3.7 14.6 - - + +
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Residues in contact with ASP 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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156A GLY 4.9 3.1 + - - +
157A ASP 3.3 0.8 - - - -
158A HIS* 1.3 79.3 - - - +
160A ARG* 1.3 58.2 + - + +
162A ALA* 3.8 2.2 - - - +
163A ASP* 3.0 38.2 + - - +
201A ARG* 2.9 33.2 + - - -
202A LEU* 3.3 15.7 - - - +
201B ARG* 6.3 2.9 - - - +
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Residues in contact with ARG 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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131A PHE* 3.5 47.0 + - + +
156A GLY 5.4 2.7 + - - +
157A ASP* 3.3 35.7 + - - +
159A ASP* 1.3 75.1 - - + +
161A TYR* 1.3 65.3 + - - +
163A ASP* 3.4 7.2 + - - +
164A ILE* 3.1 25.6 + - - +
159B ASP* 3.7 44.4 - - - +
160B ARG* 4.7 3.4 - - - +
163B ASP* 3.6 24.5 + - - -
201B ARG* 4.8 7.8 - - - +
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Residues in contact with TYR 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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63A PRO* 3.5 17.0 - - + +
64A LEU* 4.5 2.9 - - + -
130A ILE* 3.6 33.2 - - + -
131A PHE* 3.8 10.9 - - + -
146A ASP* 2.6 33.4 + - - -
150A LEU* 3.5 39.0 + - + -
153A ILE* 3.5 34.1 - - + -
157A ASP 2.8 20.6 + - - +
158A HIS* 3.6 3.6 - - - +
160A ARG* 1.3 72.6 - - - +
162A ALA* 1.3 66.2 + - - +
164A ILE* 2.9 17.7 + - - +
165A ILE* 3.0 31.2 + - + +
175A TYR* 4.3 3.4 - - - -
203A PHE* 4.8 2.0 - + - -
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Residues in contact with ALA 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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158A HIS 2.9 20.8 + - - +
159A ASP* 3.8 4.5 - - - +
161A TYR* 1.3 75.5 - - + +
163A ASP* 1.3 61.6 + - - +
165A ILE* 3.9 1.4 - - - +
166A LEU* 3.0 32.3 + - + +
202A LEU* 3.8 29.8 - - + +
203A PHE* 3.8 28.3 - - + -
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Residues in contact with ASP 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 ASP* 3.0 25.8 + - - +
160A ARG* 3.9 6.4 + - - +
161A TYR 3.3 0.4 - - - -
162A ALA* 1.3 74.0 - - - +
164A ILE* 1.3 67.5 + - + +
166A LEU* 3.5 14.6 + - - +
167A SER* 3.0 24.9 + - - -
201B ARG* 6.1 0.7 - - - -
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Residues in contact with ILE 164 (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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130A ILE* 4.1 33.2 - - + +
131A PHE* 4.5 13.9 - - + +
133A LEU* 5.6 0.9 - - + -
134A PRO* 3.3 34.3 - - + -
160A ARG 3.1 17.0 + - - +
161A TYR* 2.9 11.9 + - - +
163A ASP* 1.3 75.9 - - + +
165A ILE* 1.3 57.8 + - + +
167A SER* 2.8 33.9 + - - +
168A LEU* 3.2 27.1 + - + +
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Residues in contact with ILE 165 (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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61A PHE* 4.2 23.8 - - + -
63A PRO* 4.3 7.2 - - + -
130A ILE* 4.6 4.3 - - + -
144A ILE* 3.8 20.4 - - + +
161A TYR* 3.0 53.3 + - + +
162A ALA 3.9 5.8 - - - +
164A ILE* 1.3 78.0 - - - +
166A LEU* 1.3 64.4 + - - +
168A LEU* 3.1 17.8 + - + +
169A LEU* 3.4 17.9 - - + +
175A TYR* 3.8 30.5 - - + +
203A PHE* 4.0 7.9 - - + -
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Residues in contact with LEU 166 (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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162A ALA* 3.0 29.5 + - + +
163A ASP* 3.9 14.1 - - - +
165A ILE* 1.3 76.9 - - - +
167A SER* 1.3 61.4 + - - +
168A LEU 3.1 0.9 + - - -
169A LEU* 3.5 28.0 + - + +
173A PHE* 5.7 0.4 - - + -
202A LEU 4.1 18.4 - - - +
203A PHE* 3.7 21.5 - - + -
206A LYS* 3.9 36.6 - - + +
207A CYS* 3.9 21.3 - - - -
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Residues in contact with SER 167 (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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134A PRO* 5.5 4.0 - - - +
139A GLY 5.2 0.2 - - - +
140A LYS* 3.2 28.8 + - - +
163A ASP 3.0 13.0 + - - -
164A ILE* 2.8 22.3 + - - +
166A LEU* 1.3 76.9 - - - +
168A LEU* 1.3 61.3 - - - +
169A LEU 3.3 1.8 - - - -
15B LYS* 5.9 5.2 - - - -
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Residues in contact with LEU 168 (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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61A PHE* 3.5 41.3 - - + -
133A LEU* 4.6 4.3 - - + -
134A PRO* 6.0 8.1 - - + -
138A ILE* 4.1 19.7 - - + -
139A GLY 3.9 19.3 - - - +
140A LYS* 3.3 3.4 - - - -
141A PHE* 2.8 37.2 + - + +
144A ILE* 4.8 5.2 - - + -
164A ILE* 3.2 32.4 + - + +
165A ILE* 3.1 12.0 + - - +
167A SER* 1.3 83.5 - - - +
169A LEU* 1.3 59.9 + - - +
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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