Contacts of the helix formed by residues 235 - 250 (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 SER 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A VAL* 3.8 2.4 + - - -
234A THR* 1.3 75.6 - - - +
236A LEU* 1.3 59.7 + - - +
237A TYR* 3.4 8.3 + - - +
238A GLU* 2.8 43.1 + - - +
239A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 236 (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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157A PRO* 3.6 33.2 - - + +
234A THR 3.9 0.2 + - - -
235A SER* 1.3 72.8 - - - +
237A TYR* 1.3 61.9 + - - +
239A ALA* 3.8 2.6 - - + +
240A ARG* 3.0 32.1 + - + +
293A THR* 4.0 22.4 - - + -
294A VAL* 3.4 37.2 - - + +
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Residues in contact with TYR 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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235A SER* 3.2 8.4 + - - +
236A LEU* 1.3 78.6 - - - +
238A GLU* 1.3 65.5 + - + +
240A ARG* 3.8 5.0 - - + +
241A ASN* 3.1 31.3 + - + +
1D NAG 3.7 28.0 + - - -
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Residues in contact with GLU 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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233A VAL 4.5 2.4 - - - +
234A THR* 3.6 15.3 - - + +
235A SER* 2.8 42.9 + - - +
237A TYR* 1.3 78.4 - - + +
239A ALA* 1.3 56.9 + - - +
241A ASN* 3.3 6.0 + - - +
242A ARG* 2.9 64.0 + - - +
1D NAG 5.6 9.4 - - + +
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Residues in contact with ALA 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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155A ALA* 4.1 20.4 - - + +
157A PRO* 5.3 1.6 - - + -
234A THR* 3.7 7.6 - - + +
235A SER 2.9 17.3 + - - +
236A LEU* 3.8 7.4 - - + +
238A GLU* 1.3 75.8 - - - +
240A ARG* 1.3 53.6 + - - +
242A ARG* 3.1 6.5 + - - +
243A THR* 2.8 38.1 + - - -
290A PHE* 5.6 1.1 - - - -
293A THR* 3.9 22.7 - - + -
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Residues in contact with ARG 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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155A ALA 4.3 4.9 + - - -
156A LEU* 4.3 8.7 - - - +
157A PRO* 3.9 28.7 - - + -
236A LEU* 3.0 21.7 + - + +
237A TYR* 3.8 5.4 - - + +
239A ALA* 1.3 75.3 - - - +
241A ASN* 1.3 61.8 + - - +
243A THR* 3.4 2.3 + - - -
244A LEU* 2.9 54.6 + - + +
257A GLU* 2.3 37.3 + - - -
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Residues in contact with ASN 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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237A TYR* 3.1 25.0 + - + +
238A GLU* 3.3 6.9 + - - +
240A ARG* 1.3 78.6 - - - +
242A ARG* 1.3 58.9 + - + +
244A LEU* 3.4 9.6 + - - +
245A ASN* 2.8 42.7 + - - +
279A VAL 5.1 0.6 + - - -
1D NAG 1.5 69.0 + - - +
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Residues in contact with ARG 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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234A THR* 3.9 13.3 + - - +
238A GLU* 2.9 59.4 + - - +
239A ALA* 3.7 4.3 - - - +
241A ASN* 1.3 77.5 - - + +
243A THR* 1.3 60.8 + - - +
246A LEU* 2.9 29.5 + - - +
279A VAL* 3.6 38.3 - - + +
280A VAL* 3.3 25.0 - - + +
288A VAL 3.1 18.2 + - - -
289A ASN* 3.0 31.4 + - - +
290A PHE* 4.2 11.4 - - + -
1D NAG 6.2 2.6 - - - +
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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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154A LEU* 3.8 31.0 - - + +
155A ALA 2.7 33.5 + - - +
156A LEU* 3.5 33.4 - - + -
239A ALA 2.8 17.7 + - - -
240A ARG 3.8 3.6 - - - -
242A ARG* 1.3 73.0 - - - +
244A LEU* 1.3 59.1 + - + +
246A LEU* 3.3 4.2 + - - +
247A ALA* 3.0 26.3 + - - +
260A ILE* 5.1 5.6 - - + -
261A ILE* 4.7 3.1 - - + -
264A LEU* 5.1 2.6 - - + +
290A PHE* 4.5 2.5 - - - -
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Residues in contact with LEU 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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156A LEU* 4.8 12.6 - - + -
240A ARG* 2.9 47.7 + - - +
241A ASN* 3.8 9.2 - - - +
243A THR* 1.3 77.8 - - + +
245A ASN* 1.3 60.1 + - - +
247A ALA* 3.3 6.5 + - + +
248A LYS* 2.9 28.6 + - - +
253A SER* 4.6 1.4 + - - -
257A GLU* 5.0 3.4 - - - +
260A ILE* 4.0 26.9 - - + -
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Residues in contact with ASN 245 (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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241A ASN* 2.8 33.2 + - - +
242A ARG 3.7 5.2 - - - +
244A LEU* 1.3 72.0 - - - +
246A LEU* 1.3 59.7 + - - +
248A LYS* 3.3 4.5 + - - +
249A LEU* 2.9 35.8 + - - +
279A VAL* 2.8 34.1 + - - +
280A VAL* 5.0 0.4 - - - +
281A PRO* 5.6 0.2 - - - +
1D NAG 3.0 35.2 + - - +
3D FUC 3.4 27.8 - - + +
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Residues in contact with LEU 246 (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* 5.6 1.6 - - + -
150A ALA* 3.9 18.6 - - + -
154A LEU* 3.7 25.1 - - + -
242A ARG 2.9 18.5 + - - +
243A THR* 3.5 5.8 - - - +
245A ASN* 1.3 75.1 - - - +
247A ALA* 1.3 63.4 + - - +
249A LEU* 3.3 3.2 + - - +
250A THR* 3.0 35.0 + - + +
264A LEU* 4.5 18.6 - - + -
272A ILE* 4.1 20.6 - - + +
275A ASN* 3.8 30.7 - - + -
276A GLU* 4.3 3.4 - - + +
279A VAL* 3.8 17.4 - - + +
290A PHE* 4.3 3.1 - - + -
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Residues in contact with ALA 247 (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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243A THR 3.0 13.8 + - - +
244A LEU* 3.3 13.7 - - + +
245A ASN 3.2 0.2 - - - -
246A LEU* 1.3 75.4 - - - +
248A LYS* 1.3 61.4 + - - +
250A THR* 3.2 6.6 + - - -
251A GLY 3.2 3.6 + - - -
252A CYS* 2.7 40.7 + - - -
253A SER* 3.7 8.1 - - - +
260A ILE* 3.6 30.3 - - + -
264A LEU* 4.6 3.7 - - - +
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Residues in contact with LYS 248 (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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244A LEU 2.9 13.7 + - - +
245A ASN* 3.6 8.7 - - - +
247A ALA* 1.3 75.2 - - - +
249A LEU* 1.3 63.4 + - - +
250A THR 3.2 1.0 + - - -
251A GLY* 3.3 10.4 + - - -
253A SER* 3.2 19.2 + - - +
2D NAG 5.2 12.2 - - - +
3D FUC 3.9 23.1 - - + +
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Residues in contact with LEU 249 (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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245A ASN 2.9 24.5 + - - +
246A LEU* 3.7 4.7 - - - +
248A LYS* 1.3 76.8 - - + +
250A THR* 1.3 59.4 + - - +
251A GLY 3.5 0.2 - - - -
275A ASN* 3.5 54.9 + - + +
278A PHE* 3.8 29.8 - - + +
279A VAL* 4.2 3.4 - - + +
3D FUC 3.7 26.7 - - + +
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Residues in contact with THR 250 (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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246A LEU* 3.0 26.8 + - + +
247A ALA 3.2 5.4 + - - -
249A LEU* 1.3 79.7 - - - +
251A GLY* 1.3 61.2 + - - +
252A CYS* 3.5 5.7 + - - +
264A LEU* 3.4 22.1 - - + +
267A LYS* 3.1 42.0 + - + +
271A GLU* 4.3 15.0 - - + +
272A ILE* 5.0 2.5 - - - -
275A ASN* 3.9 23.3 - - + +
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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