Contacts of the helix formed by residues 256 - 265 (chain A) in PDB entry 2WSL
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 ASN 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ARG* 3.5 4.5 - - - +
255A GLU* 1.3 89.1 + - + +
257A GLU* 1.3 58.8 + - - +
258A THR* 3.1 12.8 + - - -
259A GLU* 3.1 29.7 + - + +
260A ILE* 3.0 22.2 + - - +
1537A NAG 1.4 66.3 + - - +
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Residues in contact with GLU 257 (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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156A LEU* 3.8 29.2 - - + +
159A ASN* 4.4 11.0 + - - +
240A ARG* 2.3 39.9 + - - -
244A LEU* 5.0 3.6 - - - +
255A GLU 4.7 6.3 - - - +
256A ASN* 1.3 69.9 + - - +
258A THR* 1.3 65.6 + - - +
260A ILE* 3.1 29.1 + - + +
261A ILE* 3.2 17.0 + - - +
1537A NAG 4.6 10.4 - - + +
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Residues in contact with THR 258 (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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159A ASN* 3.5 16.9 + - - +
161A GLU* 4.1 20.9 - - + +
256A ASN* 3.1 11.6 + - - -
257A GLU* 1.3 78.2 - - - +
259A GLU* 1.3 59.2 + - - +
261A ILE* 3.5 5.9 + - - +
262A LYS* 3.1 25.8 + - + +
265A ARG* 5.0 3.2 + - - +
1537A NAG 3.2 40.0 + - - +
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Residues in contact with GLU 259 (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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254A ARG* 3.6 21.3 + - + +
255A GLU* 4.6 4.5 - - - +
256A ASN* 3.1 34.8 + - + +
258A THR* 1.3 78.5 - - - +
260A ILE* 1.3 63.3 + - - +
262A LYS* 3.4 29.0 + - - +
263A CYS* 3.0 23.6 + - - +
1537A NAG 4.5 19.6 + - - +
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Residues in contact with ILE 260 (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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156A LEU* 4.8 5.8 - - + -
243A THR* 5.1 4.5 - - + -
244A LEU* 4.0 25.6 - - + -
247A ALA* 3.6 27.4 - - + -
252A CYS* 3.8 13.6 - - - +
253A SER* 5.4 0.4 - - - -
254A ARG* 3.6 34.9 - - + +
255A GLU 5.5 0.4 - - - +
256A ASN 3.0 9.3 + - - +
257A GLU* 3.3 28.5 - - + +
259A GLU* 1.3 75.5 - - - +
261A ILE* 1.3 63.0 + - + +
263A CYS* 3.2 5.9 + - - +
264A LEU* 2.9 39.4 + - + +
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Residues in contact with ILE 261 (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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43A PHE* 4.1 11.7 - - + -
154A LEU* 3.8 17.3 - - + -
156A LEU* 3.7 22.7 - - + -
159A ASN* 4.8 2.9 - - - +
161A GLU* 3.6 39.5 - - + +
162A ALA* 3.6 23.3 - - + -
243A THR* 4.7 1.1 - - + -
257A GLU 3.2 13.3 + - - +
258A THR* 3.9 7.2 - - - +
259A GLU 3.2 0.2 - - - -
260A ILE* 1.3 74.2 - - + +
262A LYS* 1.3 65.9 + - - +
264A LEU* 3.1 13.5 + - + +
265A ARG* 2.9 35.0 + - - +
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Residues in contact with LYS 262 (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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258A THR* 3.1 16.9 + - + +
259A GLU* 3.6 30.2 + - - +
261A ILE* 1.3 76.3 - - - +
263A CYS* 1.3 64.5 + - - +
265A ARG* 3.2 36.4 + - - +
266A ASN* 3.3 33.1 + - - +
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Residues in contact with CYS 263 (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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250A THR 5.2 0.2 - - - -
251A GLY 4.0 3.1 - - - -
252A CYS* 2.1 54.9 - - + +
254A ARG* 3.6 25.6 - - - +
259A GLU 3.0 13.8 + - - +
260A ILE 3.4 8.3 - - - +
262A LYS* 1.3 77.4 - - - +
264A LEU* 1.3 61.5 + - - +
266A ASN* 3.0 26.3 + - - +
267A LYS* 3.5 10.2 + - - +
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Residues in contact with LEU 264 (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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42A ARG* 2.9 19.2 + - - -
43A PHE* 3.7 15.0 - - + -
154A LEU* 4.2 32.5 - - + -
243A THR* 5.1 3.1 - - + +
246A LEU* 4.5 21.1 - - + +
247A ALA* 4.6 4.7 - - - +
250A THR* 3.4 30.1 - - + +
252A CYS* 4.0 9.4 - - + -
260A ILE* 2.9 31.2 + - + +
261A ILE* 3.1 11.4 + - + +
263A CYS* 1.3 76.2 - - - +
265A ARG* 1.3 58.6 + - - +
266A ASN 3.1 0.2 - - - -
267A LYS* 3.2 18.1 + - + +
272A ILE* 3.7 9.2 - - + +
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Residues in contact with ARG 265 (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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39A GLY* 3.4 32.1 - - - +
40A ARG* 3.7 24.2 + - - +
42A ARG* 3.5 40.7 + - + +
43A PHE* 4.0 9.0 - - + -
44A LYS* 5.4 0.6 - - - +
161A GLU* 2.8 43.6 + - - +
258A THR* 5.0 4.4 + - - +
261A ILE* 2.9 20.7 + - - +
262A LYS* 3.2 46.1 + - - +
264A LEU* 1.3 76.4 - - - +
266A ASN* 1.3 63.0 + - - +
267A LYS 3.4 0.2 - - - -
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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