Contacts of the strand formed by residues 231 - 237 (chain A) in PDB entry 4RA2
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A THR* 4.9 2.1 - - - +
151A LEU* 3.7 17.6 - - + +
152A CYS 4.2 1.6 - - - -
153A ARG* 2.8 34.4 + - - -
226A ARG* 3.5 18.5 + - - +
227A SER 2.9 34.2 + - - +
228A GLU* 4.7 2.1 - - - +
230A ASP* 1.3 77.2 - - - +
232A GLN* 1.3 61.0 + - - +
291A PHE* 3.4 39.8 - - + +
293A ASN* 4.0 13.3 - - - +
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Residues in contact with GLN 232 (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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152A CYS* 2.9 21.2 + - - +
154A ASN* 4.0 4.7 - - - +
155A ARG* 2.7 46.9 + - - +
230A ASP 3.4 15.0 - - - +
231A ASP* 1.3 73.6 - - - +
233A PHE* 1.3 75.7 + - + +
255A ARG* 4.9 1.7 + - - -
291A PHE* 2.9 25.8 + - - -
293A ASN* 3.2 20.8 + - + +
294A ALA* 3.3 17.2 - - - +
295A PRO* 3.6 21.6 - - - +
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Residues in contact with PHE 233 (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 1.5 - - + +
151A LEU* 3.5 3.6 - - - +
152A CYS* 2.7 61.1 + - + -
232A GLN* 1.3 87.4 - - + +
234A ILE* 1.3 63.3 + - - +
235A ILE* 3.8 27.8 - - + -
251A CYS* 3.8 23.3 - - - -
254A VAL* 3.8 9.9 - - + -
255A ARG* 4.3 6.7 - - + -
258A LEU* 3.8 23.3 - - + -
288A LEU* 3.8 23.6 - - + -
289A ILE 3.2 14.1 - - - +
290A CYS* 4.0 7.2 - - - -
291A PHE* 4.0 3.5 - - - -
295A PRO* 4.0 13.9 - - + -
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Residues in contact with ILE 234 (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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132A VAL* 4.1 15.9 - - + -
134A ILE* 4.0 19.7 - - + -
139A THR* 4.4 9.0 - - + -
141A PHE* 4.1 13.9 - - + -
150A LEU 3.2 10.1 - - - +
151A LEU* 3.8 16.4 - - + -
233A PHE* 1.3 77.2 - - - +
235A ILE* 1.3 64.4 + - - +
236A LEU* 4.0 22.0 - - + -
287A ILE 3.7 0.9 - - - +
288A LEU* 3.5 7.1 - - - +
289A ILE* 2.9 51.7 + - + +
291A PHE* 3.7 25.6 - - + -
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Residues in contact with ILE 235 (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 ARG 4.0 0.3 - - - +
149A GLY* 3.1 5.4 - - - -
150A LEU* 2.9 51.5 + - + +
233A PHE* 3.8 23.6 - - + -
234A ILE* 1.3 76.5 - - - +
236A LEU* 1.3 66.2 + - - +
237A ALA* 4.6 0.7 - - + -
242A TRP* 4.2 9.0 - - + -
250A LEU* 3.9 34.3 - - + +
251A CYS* 4.5 0.4 - - - -
254A VAL* 3.8 28.0 - - + -
286A VAL* 3.9 24.7 - - + -
287A ILE 3.5 3.1 - - - +
288A LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 236 (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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56A PHE* 3.4 47.1 - - + +
57A ALA* 3.8 5.6 - - - +
58A VAL* 3.8 13.3 - - + +
130A VAL* 4.4 7.0 - - + -
131A GLY* 3.8 26.9 - - - +
132A VAL* 4.2 7.6 - - + +
141A PHE* 4.6 1.3 - - + -
148A ARG 3.7 2.7 - - - -
149A GLY* 3.9 13.9 - - - -
234A ILE* 4.0 17.0 - - + -
235A ILE* 1.3 80.0 - - - +
237A ALA* 1.3 62.1 + - - +
286A VAL* 3.2 4.5 - - - +
287A ILE* 2.8 40.3 + - + +
289A ILE* 4.3 4.3 - - + -
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Residues in contact with ALA 237 (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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58A VAL* 4.2 9.1 - - - +
130A VAL* 4.2 1.1 - - - +
147A SER* 3.6 2.1 - - - -
148A ARG 3.0 22.9 + - - -
235A ILE* 4.6 1.1 - - + -
236A LEU* 1.3 77.3 - - - +
238A CYS* 1.3 61.0 + - - +
241A ILE* 3.7 26.5 - - + -
242A TRP* 3.0 29.6 + - + +
285A SER 3.2 14.4 - - - +
286A VAL* 4.2 7.6 - - + -
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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