Contacts of the helix formed by residues 258 - 269 (chain X) in PDB entry 2W6C
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 SER 258 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256X LEU 3.4 2.7 + - - -
257X ASN* 1.3 78.5 + - - +
259X ASP* 1.3 66.3 + - - +
260X GLU* 3.4 15.7 + - - +
261X GLU* 2.8 36.2 + - - +
262X LEU* 2.9 23.0 + - - +
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Residues in contact with ASP 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X LEU* 3.8 17.4 - - - +
159X HIS 4.5 0.3 - - - +
160X GLY 5.3 0.2 - - - -
161X SER* 4.2 14.5 + - - -
242X ARG* 2.9 45.1 + - - -
258X SER* 1.3 71.4 - - - +
260X GLU* 1.3 73.2 + - - +
262X LEU* 3.3 8.7 + - - +
263X ILE* 3.0 40.5 + - + +
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Residues in contact with GLU 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X GLU* 6.3 3.4 - - + -
258X SER* 3.1 12.3 - - - +
259X ASP* 1.3 92.7 - - + +
261X GLU* 1.3 63.8 + - + +
263X ILE* 4.0 6.1 - - + +
264X HIS* 3.0 25.8 + - - +
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Residues in contact with GLU 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X ASN* 3.1 49.3 + - - +
257X ASN* 4.9 2.8 - - + +
258X SER* 2.8 34.8 + - - +
260X GLU* 1.3 79.5 - - + +
262X LEU* 1.3 61.1 + - - +
264X HIS* 3.5 6.5 + - - +
265X CYS* 3.1 22.3 + - - +
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Residues in contact with LEU 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X LEU* 4.5 18.4 - - + -
245X ALA 4.3 2.2 - - - +
246X VAL* 3.9 38.4 - - + +
249X GLY* 3.7 25.4 - - - +
254X CYS* 4.2 8.3 - - + -
255X ASN 3.6 11.8 + - - +
256X LEU* 4.4 12.1 - - + -
258X SER 2.9 16.0 + - - +
259X ASP* 3.7 6.3 - - - +
261X GLU* 1.3 75.3 - - - +
263X ILE* 1.3 60.5 + - - +
265X CYS* 3.2 5.2 + - - +
266X LEU* 2.9 47.5 + - + +
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Residues in contact with ILE 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X PHE* 4.4 8.5 - - + -
156X LEU* 5.3 1.6 - - + -
158X LEU* 3.7 26.7 - - + -
161X SER* 3.7 25.8 - - - +
163X GLU* 3.8 14.8 - - + +
164X ALA* 4.1 10.8 - - + -
259X ASP* 3.0 25.9 + - + +
260X GLU* 4.1 5.6 - - + +
262X LEU* 1.3 71.4 - - - +
264X HIS* 1.3 61.5 + - - +
266X LEU* 3.2 8.8 + - - +
267X ARG* 2.8 68.5 + - + +
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Residues in contact with HIS 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260X GLU 3.0 19.6 + - - +
261X GLU* 3.6 7.6 + - - +
263X ILE* 1.3 78.1 - - - +
265X CYS* 1.3 64.8 + - - +
267X ARG* 3.1 11.6 + - + +
268X GLU* 3.1 45.5 + - + +
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Residues in contact with CYS 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253X ASN 4.8 0.4 - - - -
254X CYS* 2.1 58.3 - - + -
255X ASN* 4.6 4.0 - - + +
261X GLU 3.1 13.3 + - - +
262X LEU 3.2 5.1 + - - +
264X HIS* 1.3 78.9 + - - +
266X LEU* 1.3 63.0 + - - +
268X GLU* 3.0 16.1 + - - +
269X LYS* 3.2 34.8 + - - +
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Residues in contact with LEU 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ARG* 2.7 21.0 + - - -
45X PHE* 3.5 20.6 - - + -
156X LEU* 4.0 35.4 - - + -
158X LEU* 5.6 0.7 - - + -
245X ALA 4.8 2.7 - - - +
248X LEU* 4.2 14.6 - - + -
249X GLY* 4.3 6.3 - - - -
252X LEU* 4.0 26.7 - - + -
254X CYS* 4.1 11.7 - - - -
262X LEU* 2.9 39.2 + - + +
263X ILE* 3.2 5.6 + - + +
265X CYS* 1.3 75.2 - - - +
267X ARG* 1.3 59.7 + - - +
269X LYS* 3.4 12.4 + - - +
274X LEU* 4.2 5.6 - - + +
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Residues in contact with ARG 267 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X GLY* 4.1 19.8 - - - +
42X ASN* 3.3 26.6 + - - +
44X ARG* 3.0 41.2 + - + +
45X PHE* 3.9 13.2 - - + -
46X ARG* 3.6 6.5 - - - +
163X GLU* 2.9 58.4 + - - +
263X ILE* 2.8 36.2 + - - +
264X HIS* 3.1 9.5 + - + +
266X LEU* 1.3 77.2 - - - +
268X GLU* 1.3 66.5 + - - +
269X LYS 4.2 0.5 - - - +
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Residues in contact with GLU 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264X HIS* 3.1 35.6 + - + +
265X CYS* 3.0 11.5 + - - +
267X ARG* 1.3 81.7 - - - +
269X LYS* 1.3 63.4 + - + +
270X LYS* 3.8 2.1 + - - +
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Residues in contact with LYS 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ARG* 2.9 24.1 + - - -
252X LEU* 2.7 47.9 + - + +
253X ASN* 5.4 0.6 - - - +
265X CYS* 3.2 37.2 - - - +
266X LEU* 3.7 5.4 - - - +
267X ARG 3.3 2.1 - - - +
268X GLU* 1.3 81.1 - - + +
270X LYS* 1.3 65.8 + - - +
273X GLU* 3.9 22.0 + - + +
274X LEU* 3.3 27.4 - - + -
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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