Contacts of the strand formed by residues 236 - 243 (chain D) in PDB entry 3ARE
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 GLN 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D PRO* 3.3 29.3 - - - +
215D VAL 3.8 0.3 - - - +
216D GLN* 3.1 8.6 - - - +
217D PHE* 2.8 40.5 + - + +
232D LYS 4.6 4.9 - - - +
234D VAL* 3.4 26.1 + - + +
235D THR* 1.3 74.9 - - - +
237D ILE* 1.3 64.4 + - - +
238D VAL* 3.7 23.0 - - + +
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Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ARG* 5.9 0.2 - - - +
214D GLN* 3.5 46.9 - - + +
215D VAL 3.5 2.9 - - - -
216D GLN* 3.4 36.6 - - - +
236D GLN* 1.3 78.2 + - - +
238D VAL* 1.3 65.0 + - - +
239D SER* 3.8 10.7 + - - +
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D PRO* 5.0 1.1 - - + -
126D PRO* 3.4 44.6 - - + +
127D GLU* 4.9 1.1 - - - -
128D VAL* 3.5 25.6 - - + +
213D CYS 4.0 0.2 - - - +
215D VAL 3.1 31.1 + - - +
236D GLN* 3.7 25.6 - - + +
237D ILE* 1.3 76.4 - - - +
239D SER* 1.3 65.5 + - - +
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Residues in contact with SER 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D VAL* 4.3 4.8 - - - +
212D ARG* 3.4 27.0 + - - -
213D CYS 3.2 14.5 + - - -
214D GLN* 3.7 14.6 - - - +
237D ILE* 3.8 7.1 + - - +
238D VAL* 1.3 79.8 + - - +
240D ALA* 1.3 59.5 + - - +
241D GLU* 5.9 2.1 - - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LYS* 6.2 4.5 - - + -
128D VAL* 3.4 35.6 - - + +
129D ALA* 3.8 0.7 - - - -
130D VAL* 3.5 28.4 - - + +
212D ARG* 3.5 3.1 - - - +
213D CYS 2.9 30.4 + - - -
239D SER* 1.3 73.4 - - - +
241D GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 3.2 17.8 + - - -
132C LYS* 5.6 2.9 - - - +
130D VAL* 3.9 6.0 - - - +
210D HIS* 3.2 30.8 + - + -
211D PHE 3.2 13.7 - - - +
212D ARG* 4.0 14.4 + - + +
239D SER* 5.9 1.6 - - - +
240D ALA* 1.3 78.8 - - - +
242D ALA* 1.3 59.9 + - - +
243D TRP* 4.0 11.6 + - + +
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 3.7 9.0 - - - +
130D VAL* 3.8 21.0 - - + +
132D GLU* 3.7 25.6 - - + +
146D LEU* 5.0 0.9 - - + -
204D TRP* 4.5 6.7 - - + -
210D HIS* 4.1 1.6 + - - -
211D PHE* 2.9 40.4 + - + +
241D GLU* 1.3 74.9 - - - +
243D TRP* 1.3 68.2 + - - +
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Residues in contact with TRP 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 4.0 7.0 + - - +
204D TRP* 3.2 20.8 - - - -
207D PRO 3.4 22.0 - - - +
208D ARG* 4.4 11.2 - - - -
209D ASN 3.7 12.1 - - - -
210D HIS* 3.3 42.8 + + + -
241D GLU* 4.0 9.4 + - + -
242D ALA* 1.3 79.9 - - - +
244D GLY* 1.3 68.0 + - - +
245D ARG* 4.1 4.5 - - - +
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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