Contacts of the helix formed by residues 237 - 252 (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 237 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236X VAL* 1.3 79.2 - - - +
238X VAL* 1.3 64.6 + - - +
239X ALA* 3.6 8.8 + - - +
240X GLU* 3.1 23.4 + - - +
241X GLY 3.0 18.9 + - - -
295X VAL* 3.7 4.1 - - - +
296X ILE* 4.8 9.0 - - - +
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Residues in contact with VAL 238 (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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157X ALA* 4.9 1.4 - - - +
159X HIS* 3.8 43.3 - - + +
237X SER* 1.3 75.4 - - - +
239X ALA* 1.3 63.6 + - + +
241X GLY* 3.9 0.2 - - - -
242X ARG* 2.9 33.4 + - - +
295X VAL* 4.2 11.7 - - + -
296X ILE 3.2 24.9 + - - +
297X ASP* 4.1 9.0 - - + -
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Residues in contact with ALA 239 (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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237X SER* 3.2 8.4 + - - +
238X VAL* 1.3 85.1 - - + +
240X GLU* 1.3 58.4 + - - +
242X ARG* 3.2 8.6 + - - +
243X ARG* 2.8 31.4 + - - +
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Residues in contact with GLU 240 (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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236X VAL* 4.1 14.6 - - + -
237X SER* 3.1 19.1 + - - +
239X ALA* 1.3 77.9 - - - +
241X GLY* 1.3 58.1 + - - +
243X ARG* 2.6 46.3 + - - -
244X ARG* 2.8 61.5 + - - +
283X PRO* 3.4 17.6 - - - +
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Residues in contact with GLY 241 (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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157X ALA* 3.4 19.9 + - - +
236X VAL* 4.1 12.5 - - - +
237X SER 3.0 14.0 + - - -
238X VAL 3.9 2.2 - - - -
240X GLU* 1.3 73.8 - - - +
242X ARG* 1.3 60.1 + - - +
244X ARG* 3.3 6.7 + - - +
245X ALA* 2.9 26.2 + - - +
292X PHE* 5.6 1.6 - - - -
295X VAL* 4.6 7.6 - - - -
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Residues in contact with ARG 242 (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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157X ALA 3.4 12.3 + - - +
158X LEU* 3.5 23.0 - - + +
159X HIS* 2.6 34.6 + - + +
238X VAL* 2.9 19.0 + - - +
239X ALA* 3.5 6.7 - - - +
241X GLY* 1.3 74.8 - - - +
243X ARG* 1.3 64.3 + - - +
245X ALA* 3.1 3.8 + - - +
246X VAL* 3.0 36.5 + - + +
259X ASP* 2.9 41.4 + - - -
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Residues in contact with ARG 243 (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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239X ALA 2.8 20.5 + - - +
240X GLU* 2.6 48.4 + - - +
242X ARG* 1.3 75.9 - - - +
244X ARG* 1.3 65.4 + - - +
246X VAL* 3.6 6.3 + - - +
247X GLU* 3.0 47.6 + - - +
281X VAL* 3.1 29.5 + - - +
282X LEU 4.4 0.4 + - - -
283X PRO* 3.5 22.3 - - - +
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Residues in contact with ARG 244 (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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236X VAL* 3.9 27.7 - - - +
240X GLU* 2.8 45.7 + - - +
241X GLY* 4.0 5.4 - - - +
242X ARG 3.2 0.2 - - - -
243X ARG* 1.3 90.3 - - - +
245X ALA* 1.3 61.7 + - - +
247X GLU* 4.3 5.4 - - - -
248X LEU* 2.8 27.7 + - - +
281X VAL* 3.8 25.1 - - + +
282X LEU* 3.9 6.2 - - - +
283X PRO* 3.6 18.7 - - - +
289X ARG* 5.8 3.6 - - - +
290X PHE 2.6 23.2 + - - -
291X SER* 2.5 41.9 + - - +
292X PHE* 4.3 10.6 - - + -
293X VAL* 4.8 0.8 - - - +
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Residues in contact with ALA 245 (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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156X LEU* 4.1 28.0 - - + +
157X ALA 4.1 3.6 - - - +
158X LEU* 3.7 29.6 - - + -
241X GLY 2.9 13.8 + - - +
242X ARG 3.4 8.5 - - - +
244X ARG* 1.3 76.5 - - - +
246X VAL* 1.3 62.7 + - - +
248X LEU* 3.0 5.5 + - - +
249X GLY* 3.0 19.4 + - - -
262X LEU* 4.3 7.5 - - + +
266X LEU* 4.8 0.4 - - + +
292X PHE* 4.5 1.9 - - - -
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Residues in contact with VAL 246 (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* 4.7 4.5 - - + -
242X ARG* 3.0 28.1 + - + +
243X ARG* 3.7 9.0 - - - +
245X ALA* 1.3 76.1 - - - +
247X GLU* 1.3 62.7 + - - +
249X GLY* 3.0 3.6 + - - -
250X ARG* 2.7 32.0 + - - +
256X LEU* 4.0 27.9 - - + +
262X LEU* 3.9 20.8 - - + +
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Residues in contact with GLU 247 (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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243X ARG* 3.0 32.5 + - - +
244X ARG* 3.8 6.1 - - - +
246X VAL* 1.3 76.3 - - - +
248X LEU* 1.3 58.8 + - - +
250X ARG* 3.2 29.7 + - - +
251X ASN* 2.7 43.8 + - - +
280X ASN 4.5 5.6 - - - +
281X VAL* 3.8 24.5 - - + -
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Residues in contact with LEU 248 (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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152X ALA* 4.1 10.8 - - + -
156X LEU* 3.6 25.8 - - + -
244X ARG 2.8 15.8 + - - +
245X ALA* 3.0 12.1 - - - +
247X GLU* 1.3 72.7 - - - +
249X GLY* 1.3 60.7 + - - +
251X ASN* 2.8 27.2 + - - +
252X LEU* 3.4 9.4 + - + +
266X LEU* 4.2 17.5 - - + -
274X LEU* 4.5 19.5 - - + +
277X VAL* 3.7 25.4 - - + -
278X GLU* 4.6 6.3 - - - -
281X VAL* 3.7 11.8 - - + +
292X PHE* 3.9 19.7 - - + -
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Residues in contact with GLY 249 (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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245X ALA 3.0 7.1 + - - -
246X VAL 3.0 3.8 + - - -
248X LEU* 1.3 79.7 - - - +
250X ARG* 1.3 61.4 + - - +
252X LEU* 2.9 13.7 + - - -
254X CYS* 3.1 26.5 + - - +
256X LEU* 3.9 7.6 - - - -
262X LEU* 3.7 24.8 - - - +
266X LEU* 4.3 4.0 - - - +
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Residues in contact with ARG 250 (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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246X VAL* 2.7 21.1 + - - +
247X GLU* 3.5 34.0 + - - +
249X GLY* 1.3 71.6 - - - +
251X ASN* 1.3 61.0 + - - +
252X LEU 3.4 0.5 + - - -
253X ASN* 3.5 13.6 + - - +
254X CYS 4.9 0.9 - - - +
256X LEU* 3.8 28.8 - - + +
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Residues in contact with ASN 251 (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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247X GLU* 2.7 47.9 + - - +
248X LEU* 2.8 17.4 + - - +
250X ARG* 1.3 73.2 - - - +
252X LEU* 1.3 63.2 + - - +
253X ASN* 3.5 7.5 + - - -
277X VAL* 3.7 24.9 - - + +
280X ASN* 2.9 40.8 + - - +
281X VAL* 4.4 2.6 - - - +
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Residues in contact with LEU 252 (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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248X LEU* 3.4 15.5 + - + +
249X GLY 2.9 6.1 + - - +
251X ASN* 1.3 79.7 - - - +
253X ASN* 1.3 76.5 + - - +
254X CYS* 3.2 4.8 + - - -
266X LEU* 4.0 22.7 - - + -
269X LYS* 2.7 46.1 + - + +
273X GLU* 3.7 32.3 - - + +
274X LEU* 4.2 20.9 - - + -
277X VAL* 3.9 20.6 - - + -
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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