Contacts of the helix formed by residues 235 - 250 (chain H) in PDB entry 2W3S
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 GLY 235 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H GLN* 3.5 10.8 + - - -
181H ALA* 5.3 1.4 - - - +
194H CYS* 6.1 0.2 - - - +
195H SER 5.6 2.7 - - - -
196H SER* 5.4 7.9 - - - -
202H ILE* 3.8 12.9 - - - +
230H GLY 5.0 0.6 + - - -
231H LYS* 5.0 4.5 - - - +
233H SER 2.8 6.9 + - - +
234H GLN* 1.3 75.0 - - - +
236H ASN* 1.3 66.6 + - - +
237H HIS 3.5 1.8 - - - -
238H LEU* 3.4 8.7 + - - +
239H ALA* 3.3 23.4 + - - +
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Residues in contact with ASN 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA* 3.2 34.5 - - + +
77H SER 4.8 2.1 - - - -
198H HIS* 6.2 0.4 - - - +
201H GLU* 3.9 24.1 - - - +
202H ILE* 3.7 23.6 - - - +
205H LYS* 3.5 28.0 - - + +
233H SER* 3.0 20.2 + - - +
234H GLN 3.4 0.2 - - - -
235H GLY* 1.3 76.8 - - - +
237H HIS* 1.3 64.3 + - - +
238H LEU 3.3 0.3 + - - -
239H ALA* 3.5 1.7 + - - +
240H ILE* 3.0 30.2 + - + +
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Residues in contact with HIS 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.8 9.8 - - + -
76H ALA* 4.0 19.3 - - + +
83H GLU* 3.5 25.7 + - - -
84H PRO 4.0 9.6 + - - -
85H VAL* 3.8 42.8 - - + +
97H PRO* 4.5 11.8 - - + +
233H SER 5.5 0.4 - - - -
234H GLN* 4.6 17.3 + - - -
235H GLY 3.5 0.4 - - - -
236H ASN* 1.3 77.3 + - + +
238H LEU* 1.3 59.4 + - + +
241H ALA* 3.0 30.0 + - - +
257H TYR* 4.0 17.2 + - - +
265H ILE* 5.8 5.6 - - + +
299H TRP* 5.5 2.6 - - - -
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Residues in contact with LEU 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H GLN* 3.6 17.9 - - + +
180H ALA* 3.5 21.8 - - - +
181H ALA* 3.9 12.6 - - + -
234H GLN 3.5 22.2 - - - +
235H GLY* 3.9 7.4 - - - +
236H ASN 3.2 0.6 - - - -
237H HIS* 1.3 78.3 - - - +
239H ALA* 1.3 53.4 + - - +
241H ALA* 3.2 6.8 + - - +
242H CYS* 2.7 38.6 + - - +
255H MET* 3.3 39.7 - - + +
256H ARG* 4.3 1.6 - - - -
257H TYR* 3.4 38.8 - - + +
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Residues in contact with ALA 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H ALA* 3.9 12.0 - - + +
192H ILE* 4.3 12.6 - - + +
194H CYS* 5.3 0.2 - - + -
202H ILE* 3.7 33.2 - - + -
206H VAL* 3.8 10.9 - - + +
235H GLY 3.3 13.5 + - - +
236H ASN* 4.1 2.7 - - - +
238H LEU* 1.3 75.2 - - - +
240H ILE* 1.3 60.9 + - - +
242H CYS* 3.7 3.7 - - - +
243H ALA* 2.8 32.2 + - - +
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Residues in contact with ILE 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LEU* 4.6 7.0 - - + -
73H ASP 5.6 0.4 - - - +
75H ASP 3.4 25.6 - - - +
76H ALA* 3.6 17.0 - - + -
85H VAL* 3.9 22.4 - - + -
205H LYS* 3.8 27.4 - - + +
206H VAL* 4.4 3.1 - - + +
209H ALA* 3.9 21.1 - - + -
236H ASN 3.0 21.6 + - - +
237H HIS 4.0 2.7 - - - +
239H ALA* 1.3 74.1 - - - +
241H ALA* 1.3 57.7 + - - +
243H ALA* 3.1 4.8 + - - +
244H VAL* 2.7 53.6 + - + +
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Residues in contact with ALA 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.3 7.9 - - + +
37H PHE* 3.8 11.4 - - + -
85H VAL* 5.4 1.6 - - + -
100H LEU* 3.7 35.8 - - + +
237H HIS 3.0 20.7 + - - +
238H LEU 3.4 4.7 - - - +
240H ILE* 1.3 79.0 - - - +
242H CYS* 1.3 61.5 + - - +
244H VAL* 4.7 2.5 - - - -
245H ALA* 3.2 26.2 + - - +
255H MET* 4.0 3.4 - - - -
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Residues in contact with CYS 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.7 6.7 - - - -
181H ALA 3.6 14.8 - - - -
182H LEU 4.6 1.1 - - - -
183H ALA* 3.5 19.9 - - + +
192H ILE* 5.7 0.2 - - + -
238H LEU 2.7 19.2 + - - +
239H ALA* 3.7 6.7 - - - +
240H ILE 3.1 0.2 - - - -
241H ALA* 1.3 78.4 - - - +
243H ALA* 1.3 58.4 + - - +
245H ALA* 3.8 1.7 - - - +
246H ALA* 2.9 30.1 + - - +
253H CYS* 3.4 23.3 - - - +
254H LYS 3.7 2.9 - - - -
255H MET* 3.6 30.7 - - - -
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Residues in contact with ALA 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H ALA* 3.7 8.5 - - - +
190H VAL* 5.1 3.8 - - + +
192H ILE* 4.4 6.1 - - + -
206H VAL* 3.5 30.7 - - + +
209H ALA* 5.8 0.4 - - + -
210H LEU* 3.8 16.5 - - + +
239H ALA 2.8 18.7 + - - +
240H ILE* 3.7 3.1 - - - +
242H CYS* 1.3 74.0 - - - +
244H VAL* 1.3 67.9 + - + +
246H ALA* 3.1 3.5 + - - +
247H ARG* 2.9 24.6 + - - +
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Residues in contact with VAL 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H PHE* 4.7 20.0 - - + -
69H ASP 5.0 0.9 - - - +
70H LEU* 3.9 30.3 - - + -
71H PRO* 4.2 21.3 - - + -
100H LEU* 5.6 2.7 - - + -
209H ALA* 4.3 20.6 - - + +
210H LEU* 4.1 8.3 - - + -
240H ILE* 2.7 33.0 + - + +
241H ALA* 4.2 4.5 - - - +
243H ALA* 1.3 72.4 - - - +
245H ALA* 1.3 58.6 + - - +
247H ARG* 3.1 9.0 - - - +
248H ALA* 3.0 25.2 + - + +
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Residues in contact with ALA 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.9 12.6 - - + -
65H PHE* 3.9 30.3 - - + -
100H LEU* 4.5 1.8 - - + -
102H ALA* 4.7 2.5 - - + -
241H ALA 3.2 18.0 + - - +
242H CYS 3.8 0.2 - - - +
244H VAL* 1.3 76.5 - - - +
246H ALA* 1.3 54.5 - - - +
249H THR* 2.7 43.6 + - + +
253H CYS* 3.8 17.0 - - - -
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Residues in contact with ALA 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H ALA* 4.2 12.6 - - + +
184H LEU 5.5 0.2 - - - -
185H PRO* 3.9 23.7 - - + +
190H VAL* 5.6 4.7 - - + -
242H CYS 2.9 19.0 + - - +
243H ALA* 3.5 4.5 - - - +
245H ALA* 1.3 72.4 - - - +
247H ARG* 1.3 62.4 + - - +
250H GLY* 2.8 35.3 + - - -
251H ARG 3.3 23.2 + - - +
253H CYS* 3.7 2.6 - - - -
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Residues in contact with ARG 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H PRO* 3.5 41.2 - - - +
72H HIS* 4.0 12.5 - - - -
210H LEU* 3.6 33.5 + - + -
243H ALA 2.9 11.8 + - - +
244H VAL* 3.1 12.6 - - - +
246H ALA* 1.3 77.8 - - - +
248H ALA* 1.3 63.8 + - - +
250H GLY* 4.1 3.8 + - - -
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Residues in contact with ALA 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H PHE* 3.6 32.5 - - + -
244H VAL* 3.0 11.3 + - + +
245H ALA 3.1 4.2 + - - +
247H ARG* 1.3 82.7 - - - +
249H THR* 1.3 65.2 + - + +
250H GLY 3.3 0.9 + - - -
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Residues in contact with THR 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 3.6 29.2 - - + -
62H ILE* 4.5 7.2 - - + -
63H ALA* 4.3 24.0 - - + -
65H PHE* 4.8 2.5 - - + -
102H ALA* 4.7 5.4 - - + -
245H ALA 2.7 30.5 + - - +
248H ALA* 1.3 71.4 - - + +
250H GLY* 1.3 59.7 + - - +
251H ARG* 3.2 29.5 + - - +
253H CYS* 4.0 3.3 - - - -
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Residues in contact with GLY 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ASN* 5.2 2.1 + - - -
185H PRO* 4.5 11.5 - - - +
246H ALA 2.8 17.2 + - - -
247H ARG 4.1 2.9 + - - -
248H ALA 3.2 4.1 + - - -
249H THR* 1.3 73.1 - - - +
251H ARG* 1.3 60.1 + - - +
252H PRO* 4.8 0.5 - - - +
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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