Contacts of the strand formed by residues 236 - 241 (chain A) in PDB entry 1R6J
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 HIS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 5.0 7.0 + - + -
217A LYS* 3.5 1.8 - - - +
218A ILE* 2.9 29.8 + - + +
233A LEU* 3.5 42.0 - - + +
234A THR 2.8 22.4 + - - -
235A GLU* 1.3 85.7 + - + +
237A ASN* 1.3 65.6 + - - +
269A ILE* 4.0 28.7 - - + -
270A MET* 3.2 9.6 - - - +
271A PRO* 3.5 36.2 - - + +
272A ALA 4.7 0.7 - - - +
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Residues in contact with ASN 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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215A ASN 4.5 8.5 + - - -
216A GLY* 3.2 11.7 + - - +
217A LYS* 2.8 37.5 + - - +
236A HIS* 1.3 72.5 - - - +
238A ILE* 1.3 66.3 + - - +
239A CYS* 3.6 9.4 + - - -
247A ILE* 6.3 1.3 - - + -
269A ILE* 3.2 9.7 - - - -
270A MET* 2.8 34.9 + - + +
272A ALA* 3.5 20.5 - - + +
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Residues in contact with ILE 238 (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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211A PHE* 4.1 17.5 - - + -
213A PHE* 3.9 39.0 - - + -
216A GLY* 2.8 19.5 + - - +
218A ILE* 4.0 18.8 - - + -
237A ASN* 1.3 73.8 - - - +
239A CYS* 1.3 62.5 + - - +
241A ILE* 4.0 15.7 - - + -
246A VAL* 3.8 26.1 - - + +
247A ILE* 4.3 7.3 - - - +
254A ILE* 4.3 17.1 - - + +
258A LEU* 5.3 0.4 - - + -
267A ILE* 3.8 22.0 - - + -
268A THR 3.9 3.4 - - - -
269A ILE* 4.6 0.2 - - - -
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Residues in contact with CYS 239 (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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237A ASN* 3.7 19.5 - - - -
238A ILE* 1.3 75.6 - - - +
240A GLU* 1.3 62.4 + - + +
245A ASN* 3.3 11.3 - - - +
246A VAL* 3.1 23.1 + - - -
247A ILE* 3.6 24.6 + - + +
268A THR* 2.9 23.6 + - + +
270A MET* 4.1 27.6 - - - -
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Residues in contact with GLU 240 (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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238A ILE 3.8 0.2 - - - -
239A CYS* 1.3 80.0 - - + +
241A ILE* 1.3 65.9 + - - +
243A GLY* 3.4 30.1 + - - +
244A GLN 3.2 26.2 - - - +
245A ASN* 4.0 3.4 + - - +
246A VAL* 3.8 1.5 - - - +
266A THR* 3.7 1.8 - - - +
267A ILE* 3.2 7.8 - - - +
268A THR* 3.0 48.1 + - + +
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Residues in contact with ILE 241 (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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238A ILE* 4.0 16.6 - - + -
240A GLU* 1.3 79.9 - - - +
242A ASN* 1.3 86.8 + - - +
243A GLY 3.1 0.9 - - - -
244A GLN* 2.9 25.9 + - - +
246A VAL* 4.2 13.4 - - + +
254A ILE* 3.9 29.2 - - + +
257A ILE* 3.9 29.7 - - + +
258A LEU* 3.9 19.7 - - + +
261A SER* 5.8 0.2 - - - -
265A VAL* 4.3 15.3 - - + -
266A THR 3.3 5.6 - - - +
267A ILE* 4.3 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