Contacts of the strand formed by residues 236 - 244 (chain A) in PDB entry 2V9R
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 GLY 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A LYS* 4.2 0.7 - - - -
207A ASP* 3.5 13.5 - - - -
234A ASP 3.3 2.4 + - - -
235A ALA* 1.3 74.8 - - - +
237A LYS* 1.3 60.8 + - - -
238A TYR* 3.3 10.6 - - - -
254A ALA 3.3 2.4 - - - +
255A GLU* 3.6 14.4 + - - +
256A LEU 3.0 32.7 + - - -
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Residues in contact with LYS 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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205A LYS 3.4 1.6 - - - +
206A LYS* 3.2 5.2 - - - +
207A ASP* 2.9 47.2 + - - +
236A GLY* 1.3 70.5 - - - -
238A TYR* 1.3 61.8 + - - +
239A VAL* 4.1 2.6 + - + +
253A VAL* 3.4 27.6 - - + -
254A ALA 3.3 4.9 - - - -
255A GLU* 3.1 31.9 - - - +
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Residues in contact with TYR 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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176A PRO* 4.7 2.2 - - - +
189A MET* 3.6 26.9 - - + -
204A TRP* 4.9 6.1 - + + -
205A LYS 3.3 3.1 - - - -
206A LYS* 3.6 25.6 - - + +
211A LEU* 4.2 20.9 - - + -
225A LEU* 4.0 25.4 - - + -
227A ILE* 4.0 10.5 - - + +
234A ASP* 2.5 38.5 + - - +
236A GLY 3.3 22.2 - - - -
237A LYS* 1.3 71.5 - - - +
239A VAL* 1.3 64.4 + - - +
252A GLU 4.0 0.9 - - - +
253A VAL* 3.3 1.6 - - - -
254A ALA* 2.5 46.8 + - - +
256A LEU* 3.6 25.2 - - + +
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 4.8 0.7 - - - -
204A TRP* 3.5 8.5 - - - -
205A LYS* 2.9 53.3 + - + +
237A LYS* 5.0 2.5 - - + +
238A TYR* 1.3 79.9 - - - +
240A CYS* 1.3 60.3 + - - +
241A VAL* 3.9 16.2 - - + -
250A GLU* 4.2 20.9 - - + +
251A SER* 3.5 21.5 - - - +
253A VAL* 3.6 28.7 - - + +
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Residues in contact with CYS 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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172A PHE* 3.3 12.3 - - + -
176A PRO* 3.9 9.1 - - + +
191A CYS* 2.0 53.6 - - + -
202A ILE* 3.5 23.3 - - - -
203A SER 3.6 3.8 - - - -
204A TRP* 3.9 13.7 - - + -
239A VAL* 1.3 72.4 - - - +
241A VAL* 1.3 62.6 + - - +
251A SER* 2.9 32.0 + - - +
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Residues in contact with VAL 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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172A PHE* 3.7 3.3 - - - -
201A THR 3.7 0.3 - - - +
202A ILE* 3.5 10.9 - - - +
203A SER* 2.7 55.4 + - - +
204A TRP 5.0 0.4 - - - -
205A LYS* 4.5 18.4 - - + -
239A VAL* 3.9 14.1 - - + +
240A CYS* 1.3 77.3 - - - +
242A GLY* 1.3 63.5 + - - +
243A THR* 3.8 13.4 + - - +
248A GLU* 4.0 22.4 - - + +
249A ARG 3.5 8.7 - - - +
250A GLU* 3.9 23.6 - - + -
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Residues in contact with GLY 242 (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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168A LEU* 4.4 4.2 - - - +
172A PHE* 3.3 15.5 - - - -
193A PRO* 4.5 10.8 - - - -
194A PRO* 5.4 0.9 - - - -
200A PRO* 4.6 3.6 - - - -
201A THR 3.7 4.5 - - - -
241A VAL* 1.3 73.0 - - - +
243A THR* 1.3 64.6 + - - -
247A GLY 3.6 1.4 - - - +
248A GLU* 3.4 2.9 - - - -
249A ARG* 2.8 44.4 + - - +
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Residues in contact with THR 243 (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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199A GLU 4.2 0.3 - - - +
200A PRO* 3.3 7.6 - - - +
201A THR* 3.0 48.7 + - - +
202A ILE 6.3 0.2 - - - -
203A SER* 4.7 4.4 + - - -
241A VAL* 3.8 14.9 - - - +
242A GLY* 1.3 79.2 + - - -
244A ASN* 1.3 69.7 + - - +
247A GLY 3.5 7.4 - - - +
248A GLU* 4.3 9.9 - - + +
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Residues in contact with ASN 244 (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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167A ILE 3.1 26.1 + - - -
168A LEU* 3.1 24.2 - - - +
196A GLY* 4.2 2.4 - - - -
197A HIS 3.6 9.9 + - - +
198A PRO* 2.9 36.4 + - + +
199A GLU 4.4 1.8 - - - +
200A PRO* 4.3 4.8 - - + +
243A THR* 1.3 83.4 - - - +
245A MET* 1.3 61.8 + - - +
246A VAL* 2.8 22.8 + - - +
247A GLY* 3.1 15.5 + - - +
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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