Contacts of the strand formed by residues 138 - 144 (chain A) in PDB entry 3R6O
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 ILE 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLU* 1.3 70.9 - - - +
139A GLU* 1.3 63.4 + - - +
165A LEU* 4.2 17.0 - - + -
166A ALA 3.7 10.8 - - - +
167A ASN* 3.7 4.9 - - - +
219A PHE* 3.7 31.7 - - + -
220A GLU 3.2 34.3 - - - +
221A LEU* 3.8 11.9 - - + +
229A GLN* 3.0 42.7 + - + +
262A GLY 3.7 0.2 - - - +
263A THR* 2.8 25.1 + - - -
264A PRO* 3.7 3.8 - - + +
285A ALA* 3.7 21.3 - - + -
286A HIS 4.4 0.9 - - - +
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Residues in contact with GLU 139 (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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88A LEU 3.9 0.9 + - - +
137A GLU* 3.3 10.3 - - - +
138A ILE* 1.3 83.7 - - - +
140A ILE* 1.3 68.3 + - - +
141A ALA 4.0 0.2 - - - -
165A LEU* 3.8 2.4 - - - +
166A ALA* 2.9 33.8 + - - +
168A ASP* 3.2 18.5 - - - +
219A PHE* 4.9 2.9 - - - -
260A LEU* 3.3 29.0 - - + +
262A GLY* 2.8 46.3 + - - +
263A THR* 3.6 10.0 - - - -
400A MG 2.3 29.2 - - - -
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Residues in contact with ILE 140 (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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92A TYR* 5.1 1.5 + - - +
139A GLU* 1.3 74.6 - - - +
141A ALA* 1.3 66.1 + - - +
163A TYR* 4.5 5.8 - - + -
164A MET 3.8 1.3 - - - -
165A LEU* 3.7 27.8 - - + -
217A PHE* 4.3 10.3 - - + -
219A PHE* 3.8 37.6 - - + -
233A THR* 3.9 13.7 - - + -
240A PHE* 3.7 26.2 - - + -
261A THR* 2.6 44.8 + - - +
262A GLY 4.3 1.6 + - - -
287A SER* 4.8 0.4 - - - +
290A LEU* 3.7 25.6 - - + -
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Residues in contact with ALA 141 (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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139A GLU 3.9 1.0 + - - -
140A ILE* 1.3 74.7 - - - +
142A VAL* 1.3 62.5 + - - +
163A TYR* 3.3 8.0 - - - +
164A MET* 2.8 49.2 + - + +
166A ALA* 4.1 9.6 - - + -
258A ILE* 3.8 22.9 - - + -
259A ILE 3.0 12.3 - - - +
260A LEU* 4.1 11.0 - - + +
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Residues in contact with VAL 142 (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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140A ILE 4.2 0.6 + - - -
141A ALA* 1.3 74.5 - - - +
143A VAL* 1.3 63.4 + - - +
144A ILE* 4.9 2.6 - - + +
160A VAL* 4.0 25.4 - - + -
162A GLY 3.4 7.4 - - - +
163A TYR* 3.8 22.0 - - + -
214A PHE* 4.7 2.2 - - + -
240A PHE* 3.6 30.1 - - + +
243A VAL* 5.5 1.1 - - + -
244A VAL* 4.6 7.0 - - + -
258A ILE* 3.4 3.8 - - - +
259A ILE* 2.7 62.8 + - + +
261A THR* 4.5 6.0 - - + +
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Residues in contact with VAL 143 (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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46A ILE* 4.6 7.4 - - + -
79A ILE* 4.1 24.9 - - + -
142A VAL* 1.3 78.9 - - - +
144A ILE* 1.3 71.2 + - - +
160A VAL* 3.5 5.2 - - - -
161A ALA* 2.8 28.1 + - + -
162A GLY 3.0 7.3 + - - +
164A MET* 3.8 32.1 - - + -
205A LEU* 3.7 29.8 - - + -
256A GLY* 4.5 8.1 - - - +
257A ASP 3.4 9.2 - - - +
258A ILE* 4.3 4.0 - - + -
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Residues in contact with ILE 144 (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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46A ILE* 3.5 7.7 - - - +
142A VAL* 4.9 2.0 - - + -
143A VAL* 1.3 75.7 - - - +
145A GLY* 1.3 61.2 + - - +
146A LYS 3.4 21.3 - - - +
159A HIS* 3.3 12.8 - - + +
160A VAL* 4.5 12.6 - - + -
161A ALA 4.1 0.2 - - - -
244A VAL* 4.8 6.7 - - + -
253A LEU* 3.7 34.8 - - + -
254A ARG 3.5 26.5 - - - +
255A ALA* 3.4 0.4 - - - -
256A GLY 3.0 24.3 + - - -
257A ASP* 2.9 28.7 + - + +
259A ILE* 4.1 18.2 - - + -
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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