Contacts of the helix formed by residues 232 - 252 (chain A) in PDB entry 5WS3
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 TYR 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A VAL* 5.1 2.1 - - - +
228A PHE* 3.1 36.6 + + + +
230A VAL 3.5 0.2 - - - -
231A THR* 1.3 85.3 + - - +
233A MET* 1.3 69.7 + - - +
234A ALA 3.7 1.1 - - - -
235A PRO* 3.7 3.4 - - - +
236A LEU* 3.1 50.8 + - + +
313A PHE* 4.8 8.6 - + - -
314A ALA* 2.7 39.7 + - - +
317A TYR* 3.8 24.5 - - + -
318A LEU* 3.4 32.8 - - + +
321A SER* 3.6 22.9 - - - +
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.0 42.9 + - + +
229A LEU* 3.4 24.7 + - + -
232A TYR* 1.3 78.5 - - - +
234A ALA* 1.3 61.9 + - - +
236A LEU* 3.2 4.8 + - - +
237A CYS* 2.9 50.1 + - - -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.0 21.3 + - + +
230A VAL* 5.3 1.1 - - - -
233A MET* 1.3 79.7 - - - +
235A PRO* 1.3 68.9 - - + +
237A CYS* 3.2 6.8 + - - +
238A LEU* 3.0 34.2 + - + +
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Residues in contact with PRO 235 (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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142A VAL* 3.7 28.7 - - + +
143A LEU* 5.7 3.8 - - + -
146A SER* 3.6 20.6 + - - +
229A LEU 3.3 13.0 - - - +
230A VAL* 3.3 21.1 - - - +
232A TYR 3.7 7.6 - - - +
233A MET 3.8 0.4 - - - -
234A ALA* 1.3 91.7 - - + +
236A LEU* 1.3 56.5 + - - +
238A LEU* 3.8 10.2 - - + +
239A MET* 2.9 37.3 + - + +
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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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142A VAL* 5.5 0.4 - - - +
232A TYR* 3.1 57.1 + - + +
233A MET* 3.5 4.5 - - - +
234A ALA 3.2 0.2 - - - -
235A PRO* 1.3 76.2 - - - +
237A CYS* 1.3 61.6 + - - +
239A MET* 3.3 7.3 + - + +
240A VAL* 2.9 48.7 + - + +
310A LEU* 4.0 21.5 - - + -
313A PHE* 5.7 3.6 - - + -
314A ALA* 3.8 24.0 - - + -
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Residues in contact with CYS 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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233A MET* 2.9 43.5 + - - +
234A ALA* 3.2 6.5 + - - +
236A LEU* 1.3 79.4 - - - +
238A LEU* 1.3 65.8 + - + +
240A VAL* 3.3 6.5 + - - +
241A LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 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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146A SER* 6.0 0.4 - - - +
234A ALA* 3.0 26.7 + - + +
235A PRO* 3.8 7.9 - - + +
237A CYS* 1.3 79.7 - - + +
239A MET* 1.3 57.4 + - + +
241A LEU* 3.3 15.3 + - + +
242A ALA* 2.9 29.0 + - - +
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Residues in contact with MET 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 4.4 9.6 - - + +
145A LEU* 3.5 43.7 - - + +
146A SER* 3.6 15.7 - - - +
149A ALA* 3.7 20.4 - - + -
235A PRO* 2.9 34.0 + - + +
236A LEU* 3.8 7.9 - - + +
238A LEU* 1.3 74.3 - - + +
240A VAL* 1.3 61.3 + - - +
242A ALA* 3.8 5.7 - - - +
243A TYR* 2.9 38.9 + - + -
310A LEU* 3.7 34.3 - - + -
313A PHE* 5.6 2.5 - - + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 2.9 37.8 + - + +
237A CYS* 3.7 7.0 - - - +
239A MET* 1.3 77.2 - - - +
241A LEU* 1.3 66.1 + - + +
243A TYR* 3.4 3.8 + - - +
244A LEU* 2.9 41.5 + - + +
310A LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 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 CYS* 3.0 24.7 + - + +
238A LEU* 3.7 13.5 - - + +
240A VAL* 1.3 79.5 - - + +
242A ALA* 1.3 62.7 + - - +
244A LEU* 3.2 20.0 + - + +
245A GLN* 3.0 33.1 + - - +
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Residues in contact with ALA 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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149A ALA* 4.5 16.6 - - + +
150A LEU* 5.8 2.7 - - + -
153A TRP* 3.9 29.1 - - + +
238A LEU 2.9 16.7 + - - +
239A MET* 3.8 7.6 - - - +
241A LEU* 1.3 75.5 - - - +
243A TYR* 1.3 58.5 + - - +
245A GLN* 3.2 5.3 + - - +
246A ILE* 2.9 32.9 + - + +
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Residues in contact with TYR 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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145A LEU 4.9 0.6 + - - -
148A ILE* 3.6 19.8 + - - +
149A ALA* 3.6 26.3 + - + -
152A ARG* 4.8 6.3 - - + -
239A MET* 2.9 29.5 + - + +
240A VAL* 4.1 4.0 - - - +
242A ALA* 1.3 73.3 - - - +
244A LEU* 1.3 61.8 + - - +
246A ILE* 3.9 21.5 - - + -
247A PHE* 2.8 30.3 + - - +
303A ALA* 4.6 4.7 - - - -
306A LEU* 3.4 34.2 + - + +
307A MET* 3.7 38.2 - - + +
310A LEU* 3.6 31.2 - - + -
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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
----------------------------------------------------------
240A VAL* 2.9 36.1 + - + +
241A LEU* 3.2 18.6 + - + +
243A TYR* 1.3 76.9 - - - +
245A GLN* 1.3 63.7 + - + +
247A PHE* 3.4 12.6 + - + +
248A ARG* 3.0 25.3 + - - +
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Residues in contact with GLN 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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153A TRP* 2.6 39.5 + - - +
157A CYS* 3.4 18.6 - - - -
241A LEU* 3.0 24.3 + - - +
242A ALA* 3.6 7.0 - - - +
244A LEU* 1.3 76.6 - - + +
246A ILE* 1.3 59.5 + - - +
248A ARG* 3.3 8.5 + - - +
249A LYS* 2.9 30.0 + - - +
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Residues in contact with ILE 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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149A ALA 4.0 6.1 - - - +
152A ARG* 3.6 30.3 - - + +
153A TRP* 3.6 26.2 - - + +
156A ILE* 3.9 15.9 - - + -
157A CYS* 5.1 2.2 - - + -
242A ALA* 2.9 23.2 + - + +
243A TYR* 3.8 21.3 - - + +
244A LEU 3.3 0.2 - - - -
245A GLN* 1.3 72.4 - - - +
247A PHE* 1.3 59.7 + - - +
249A LYS* 3.3 4.9 + - - +
250A LEU* 2.8 51.5 + - + +
303A ALA* 4.3 13.0 - - + -
307A MET* 4.4 4.7 - - + -
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Residues in contact with PHE 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 TYR 2.8 22.0 + - - +
244A LEU* 3.8 13.5 - - + +
246A ILE* 1.3 72.2 - - - +
248A ARG* 1.3 63.6 + - + +
251A TRP* 2.9 81.8 + + + +
252A CYS* 3.9 20.0 - - - -
307A MET* 4.2 12.3 - - + +
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Residues in contact with ARG 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 3.0 17.7 + - - +
245A GLN* 3.7 7.9 - - - +
246A ILE 3.3 0.2 - - - -
247A PHE* 1.3 83.5 - - + +
249A LYS* 1.3 59.0 + - + +
252A CYS* 3.2 29.9 + - - +
253A ARG* 3.0 77.0 + - - +
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Residues in contact with LYS 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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156A ILE* 3.1 39.6 + - + +
157A CYS* 3.5 29.8 + - + +
158A HIS 5.4 1.6 - - - -
159A PRO* 5.4 4.2 - - - +
245A GLN 2.9 17.9 + - - +
246A ILE* 3.8 3.8 - - - +
248A ARG* 1.3 80.8 - - + +
250A LEU* 1.3 57.6 + - - +
253A ARG* 3.5 18.0 + - - +
254A GLN* 3.1 41.4 + - - +
1123A PRO* 5.4 5.1 - - - +
1124A PHE* 3.4 37.3 - - + -
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Residues in contact with LEU 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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156A ILE* 3.7 37.2 - - + -
246A ILE* 2.8 30.1 + - + +
249A LYS* 1.3 74.8 - - - +
251A TRP* 1.3 71.8 + - + +
254A GLN* 3.5 27.3 - - - +
296A ILE* 4.5 12.1 - - + +
299A ARG* 3.7 44.6 - - + +
300A ARG* 2.9 29.6 + - + +
303A ALA* 3.9 8.1 - - + -
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Residues in contact with TRP 251 (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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247A PHE* 2.9 60.1 + + + +
250A LEU* 1.3 111.8 - - + +
252A CYS* 1.3 62.4 + - - +
253A ARG 3.7 0.2 - - - -
254A GLN 3.7 9.9 - - - +
300A ARG* 3.3 68.9 + - + +
303A ALA* 4.2 10.3 - - + -
304A ARG* 4.4 15.7 - - + -
307A MET* 4.3 7.9 - - + -
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Residues in contact with CYS 252 (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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247A PHE* 3.9 28.5 - - - -
248A ARG* 3.2 39.2 + - - +
251A TRP* 1.3 81.4 - - - +
253A ARG* 1.3 62.8 + - - +
254A GLN 3.6 1.6 - - - +
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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
------------------------------------------------------------
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