Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 3V56
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 CYS 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN 3.5 15.0 - - - -
145A ASP* 1.3 74.5 - - - +
147A LEU* 1.3 62.2 + - - +
172A PHE* 3.5 30.0 - - + -
173A LYS* 3.7 1.0 - - - +
174A ARG* 2.8 48.3 + - - +
178A LEU* 4.0 5.7 - - - +
281A ALA 3.3 14.6 - - - +
282A LEU* 3.9 17.9 - - + -
192C TYR* 4.8 0.7 - - - -
250C ILE* 4.3 7.9 - - + -
284C LEU* 4.3 13.2 - - - -
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Residues in contact with LEU 147 (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* 1.3 76.2 - - - +
148A GLN* 1.3 62.4 + - - +
149A LEU* 3.8 24.5 - - + -
170A LEU* 3.9 20.4 - - + -
172A PHE* 3.5 6.3 - - - +
173A LYS* 4.0 10.8 - - + -
178A LEU* 3.8 24.4 - - + +
179A GLU* 3.6 36.3 - - - +
180A GLU* 3.7 4.5 - - + +
185A ILE* 3.8 31.0 - - + -
196A TYR* 4.3 1.1 + - - -
280A GLY* 3.2 2.8 - - - -
281A ALA 3.0 31.5 + - - +
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Residues in contact with GLN 148 (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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147A LEU* 1.3 75.8 - - - +
149A LEU* 1.3 67.5 + - - +
150A ILE* 4.3 7.9 - - + +
170A LEU* 3.8 4.9 - - - +
171A SER* 2.8 53.5 + - - -
172A PHE* 3.0 31.7 + - + +
196A TYR* 2.6 34.9 + - + +
278A PHE* 5.0 4.7 - - + -
279A PHE 3.6 7.0 - - - +
230C PHE* 4.6 9.6 - - - -
249C GLY* 4.1 1.9 - - - -
250C ILE* 3.2 35.7 + - - -
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Residues in contact with LEU 149 (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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147A LEU* 3.8 16.2 - - + -
148A GLN* 1.3 75.2 - - - +
150A ILE* 1.3 62.0 + - - +
168A TRP* 3.8 42.8 - - + -
169A LEU 3.4 13.0 - - - +
170A LEU* 4.0 11.2 - - + -
180A GLU* 3.8 28.3 - - + -
183A ASN 5.1 0.7 - - - +
184A LYS 4.9 8.1 - - - -
185A ILE* 3.7 24.9 - - + -
278A PHE* 3.3 6.9 - - - +
279A PHE* 2.6 47.8 + - + +
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Residues in contact with ILE 150 (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 GLN* 4.3 7.2 - - - +
149A LEU* 1.3 78.1 - - - +
151A ALA* 1.3 66.4 + - - +
168A TRP* 3.5 4.7 - - - -
169A LEU* 2.9 46.4 + - + +
170A LEU 4.9 1.3 - - - +
171A SER* 3.8 28.3 - - - +
274A GLY* 3.5 34.5 - - - +
277A THR 3.8 3.6 - - - -
278A PHE* 3.9 7.0 - - + -
230C PHE* 6.5 0.4 - - + -
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Residues in contact with ALA 151 (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 ILE* 1.3 77.0 - - - +
152A ASP* 1.3 60.0 + - - +
153A SER* 3.4 2.4 + - - -
166A VAL* 3.8 7.9 - - + -
167A PRO 3.7 6.3 - - - -
168A TRP* 3.6 5.2 - - - -
169A LEU* 4.7 1.0 - - - +
272A LEU* 3.4 39.9 - - + +
273A ASP 4.3 1.1 - - - +
274A GLY* 4.1 9.3 + - - -
277A THR* 3.0 36.3 + - + +
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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