Contacts of the strand formed by residues 156 - 164 (chain A) in PDB entry 3RAW
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 TYR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASP 3.9 0.5 - - - +
151A TRP* 3.1 6.6 - - - +
152A LEU* 2.8 42.2 + - + +
153A GLN* 4.6 1.8 - - + -
155A ARG* 1.3 112.7 + - + +
157A GLU* 1.3 59.2 + - - +
158A ILE 4.2 0.2 + - - -
173A CYS* 4.2 14.8 - - + -
174A LEU 3.4 2.0 - - - -
175A ASP* 3.6 31.3 + - - -
183A VAL* 3.9 26.9 - - + -
185A LEU* 4.3 9.9 - - + -
223A SER* 5.3 0.3 + - - -
224A ASP* 3.0 30.7 + - - +
226A PHE* 3.3 38.6 - + - -
235A ALA* 4.1 9.4 - - + +
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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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149A GLY* 4.2 14.3 - - - +
150A ASP 3.5 7.2 - - - +
151A TRP* 3.8 26.4 - - + +
155A ARG 3.8 0.6 + - - -
156A TYR* 1.3 73.0 - - - +
158A ILE* 1.3 64.2 + - - +
159A VAL* 3.5 21.1 + - - +
173A CYS* 3.2 5.5 - - - -
174A LEU* 2.9 38.2 + - + +
176A HIS* 2.8 43.6 + - + +
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Residues in contact with ILE 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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146A CYS* 4.0 30.5 - - + +
147A ARG 3.9 24.7 - - - +
148A ILE* 3.6 9.2 - - + +
149A GLY* 2.7 29.3 + - - -
150A ASP* 2.9 22.8 + - + +
152A LEU* 3.7 28.7 - - + -
157A GLU* 1.3 70.1 - - - +
159A VAL* 1.3 65.8 + - - +
160A GLY 4.1 17.3 - - - +
171A VAL* 4.1 19.3 - - + -
172A GLU 3.7 4.5 - - - -
173A CYS* 3.9 10.3 - - - -
187A ILE* 4.9 0.4 - - + -
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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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148A ILE* 4.0 19.8 - - + +
157A GLU* 3.6 25.8 - - - +
158A ILE* 1.3 78.6 - - - +
160A GLY* 1.3 59.4 + - - +
172A GLU* 3.0 40.8 + - + +
173A CYS* 4.1 0.4 - - - -
174A LEU* 3.9 33.9 - - + -
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Residues in contact with GLY 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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148A ILE* 4.0 14.3 - - - +
158A ILE* 3.8 5.6 - - - +
159A VAL* 1.3 81.1 - - - +
161A ASN* 1.3 59.4 + - - -
162A LEU* 5.2 0.4 - - - -
171A VAL* 3.5 10.4 - - - +
172A GLU* 3.0 34.7 + - - +
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Residues in contact with ASN 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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148A ILE* 5.1 3.3 - - + +
160A GLY* 1.3 72.1 - - - -
162A LEU* 1.3 73.0 + - - +
163A GLY* 3.2 9.4 + - - +
164A GLU* 2.8 29.8 + - - +
169A LYS* 4.2 12.1 + - - +
170A VAL 3.2 12.2 - - - +
171A VAL* 4.4 5.3 - - + +
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Residues in contact with LEU 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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1A 3RA 3.9 29.2 - - + +
160A GLY 5.7 0.2 - - - -
161A ASN* 1.3 81.2 + - - +
163A GLY* 1.3 58.4 + - - +
170A VAL* 2.9 21.0 + - + +
171A VAL 3.9 1.6 - - - -
172A GLU* 3.7 34.1 - - + +
184A ALA* 3.9 16.2 - - + -
238A LEU* 3.6 31.0 - - + -
239A LEU 5.6 1.3 - - - +
240A GLY 6.5 0.2 - - - -
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Residues in contact with GLY 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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1A 3RA 4.0 15.5 - - - -
161A ASN* 3.2 7.7 + - - +
162A LEU* 1.3 80.1 - - - +
164A GLU* 1.3 70.0 + - - +
169A LYS* 3.6 0.9 - - - -
170A VAL 2.7 30.6 + - - +
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Residues in contact with GLU 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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1A 3RA 4.1 11.1 - - - -
143A HIS* 5.1 3.8 - - + -
161A ASN* 2.8 30.9 + - - -
163A GLY* 1.3 85.4 - - - +
165A GLY* 1.3 62.3 + - - +
167A PHE* 4.6 2.5 - - - -
168A GLY 3.3 14.1 - - - +
169A LYS* 3.7 24.2 + - + +
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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