Contacts of the helix formed by residues 220 - 242 (chain C) in PDB entry 2WMZ
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 ASN 220 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA 2.8 18.2 + - - +
219C ARG* 1.3 75.3 + - - +
221C LEU* 1.3 60.1 + - - +
222C SER* 3.6 16.8 + - - -
223C LEU* 3.0 26.5 + - + +
224C LEU* 3.0 24.8 + - - +
319C ALA 4.9 1.2 + - - -
323C VAL* 3.1 38.2 - - + +
402C SER 4.1 7.4 - - - +
403C ALA* 3.5 15.9 - - - +
404C LEU 3.0 12.6 + - - -
405C GLY* 4.0 0.2 - - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 3.3 16.6 - - + +
99C GLN* 3.5 37.2 - - + +
100C THR* 3.1 48.7 + - + +
103C GLN* 4.0 23.6 - - + +
219C ARG 2.9 13.3 + - - +
220C ASN* 1.3 73.6 + - - +
222C SER* 1.3 61.0 + - - +
224C LEU* 3.5 18.6 - - + +
225C GLN* 3.3 17.2 + - - +
405C GLY* 4.3 11.5 - - - +
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C THR* 5.1 10.0 - - - +
220C ASN* 3.1 16.4 + - - -
221C LEU* 1.3 74.0 - - - +
223C LEU* 1.3 67.1 + - - +
224C LEU 3.0 1.3 + - - -
225C GLN* 3.2 15.7 + - - +
226C ALA* 3.2 12.5 + - - +
319C ALA* 4.4 7.5 - - - +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ALA 4.5 0.4 - - - +
217C GLU* 3.7 23.6 - - - +
220C ASN* 3.0 28.2 + - + +
222C SER* 1.3 76.1 - - - +
224C LEU* 1.3 62.1 + - - +
226C ALA* 3.4 1.7 + - - +
227C ARG* 3.1 54.7 + - - +
316C LEU* 3.9 12.3 - - + -
319C ALA* 3.7 11.4 - - + -
320C HIS* 3.5 53.2 - - + +
323C VAL* 4.2 6.3 - - + -
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 3.4 32.8 - - + -
99C GLN* 5.4 3.1 - - - +
219C ARG 5.2 2.9 - - - +
220C ASN 3.0 12.8 + - - +
221C LEU* 3.5 23.6 - - + +
222C SER 3.0 0.2 - - - -
223C LEU* 1.3 78.0 - - - +
225C GLN* 1.3 56.7 + - - +
227C ARG* 3.1 22.6 + - + +
228C LEU* 2.9 36.8 + - + +
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Residues in contact with GLN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.9 22.9 - - + +
96C VAL* 3.1 27.4 + - + +
97C THR* 2.8 46.3 + - - +
100C THR* 4.3 6.9 + - - +
221C LEU 3.3 4.2 + - - +
222C SER* 3.2 10.3 + - - +
224C LEU* 1.3 75.3 - - - +
226C ALA* 1.3 57.3 + - - +
227C ARG 3.0 2.0 - - - -
228C LEU* 4.2 4.7 - - - -
229C SER* 2.7 42.3 + - - +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C SER 3.2 6.1 + - - +
223C LEU 3.6 4.0 - - - +
225C GLN* 1.3 78.2 - - - +
227C ARG* 1.3 57.5 + - - +
229C SER* 3.9 5.3 - - - -
230C GLN* 3.0 27.5 + - - +
312C ALA 4.6 2.5 - - - +
315C GLN* 4.2 4.0 - - + +
316C LEU* 3.3 34.3 - - + +
319C ALA* 3.4 27.1 - - + -
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Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU* 3.3 27.1 + - - +
218C LYS* 5.8 2.0 - - - +
223C LEU* 3.1 37.6 + - - +
224C LEU* 3.2 22.8 - - + +
225C GLN 3.0 0.2 - - - -
226C ALA* 1.3 76.3 - - - +
228C LEU* 1.3 69.0 + - + +
230C GLN* 3.0 17.7 + - - +
231C ASP* 3.1 13.4 + - - +
316C LEU* 4.0 22.7 - - + +
320C HIS* 5.3 2.6 - - - -
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LYS* 5.1 1.7 - - - +
92C GLY* 3.8 6.1 - - - +
93C ILE* 3.5 37.9 - - + +
96C VAL* 3.5 30.7 - - + -
224C LEU* 2.9 28.0 + - + +
225C GLN* 3.7 6.5 - - - +
227C ARG* 1.3 78.4 - - + +
229C SER* 1.3 58.2 + - - +
231C ASP* 3.1 12.7 + - + +
232C LEU* 2.9 25.6 + - - +
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.3 27.7 - - - +
225C GLN* 2.7 27.3 + - - +
226C ALA* 4.1 5.4 - - - -
228C LEU* 1.3 70.8 - - - +
230C GLN* 1.3 63.4 + - - +
232C LEU* 3.4 5.9 + - - +
233C ALA* 3.1 20.1 + - - +
312C ALA* 4.1 5.7 - - - +
315C GLN* 5.9 2.5 - - - -
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Residues in contact with GLN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ALA 3.0 18.7 + - - +
227C ARG* 3.0 7.6 + - - +
229C SER* 1.3 73.6 - - - +
231C ASP* 1.3 65.8 + - - +
233C ALA* 3.2 4.7 + - - +
234C ARG* 3.2 30.4 + - - +
309C PHE* 3.3 19.9 - - + -
312C ALA* 3.8 19.3 + - + +
313C SER* 2.7 34.9 + - - +
316C LEU* 3.5 22.5 - - + +
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Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LYS* 2.8 45.4 + - - +
227C ARG 3.1 10.5 + - - +
228C LEU* 3.1 14.4 + - + +
230C GLN* 1.3 76.9 + - - +
232C LEU* 1.3 59.8 + - - +
234C ARG* 2.8 31.0 + - - +
235C GLU* 2.8 26.0 + - - +
238C ARG* 5.6 2.9 + - - -
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 3.4 37.2 - - + +
89C LYS* 3.8 22.4 - - + -
90C ALA* 4.8 9.4 - - + +
93C ILE* 4.1 18.6 - - + -
228C LEU 2.9 12.7 + - - +
229C SER* 3.5 12.6 - - - +
231C ASP* 1.3 80.3 + - - +
233C ALA* 1.3 56.5 + - - +
235C GLU* 3.1 4.3 + - - +
236C GLN* 2.9 49.8 + - + +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER 3.1 6.9 + - - +
230C GLN 3.3 9.9 - - - +
231C ASP 3.1 0.2 - - - -
232C LEU* 1.3 75.2 - - - +
234C ARG* 1.3 61.8 + - - +
236C GLN* 3.4 16.9 + - - +
237C ILE* 3.2 23.4 + - - +
305C ALA 4.1 3.6 - - - +
308C ASN* 3.7 13.6 - - - +
309C PHE* 3.6 13.7 - - + -
312C ALA* 3.4 29.4 - - + -
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C GLN* 3.2 17.6 + - - -
231C ASP* 2.8 41.0 + - - +
233C ALA* 1.3 78.1 - - - +
235C GLU* 1.3 58.1 + - - +
237C ILE* 2.8 37.8 + - + +
238C ARG* 3.2 38.8 + - + +
309C PHE* 3.5 37.1 - - + -
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 2.9 30.8 + - - -
85C THR* 3.3 24.5 + - + +
86C LEU* 3.2 28.3 - - + -
89C LYS* 3.5 25.2 - - + -
231C ASP* 2.8 12.3 + - - +
232C LEU 3.1 5.8 + - - +
234C ARG* 1.3 75.8 - - - +
236C GLN* 1.3 56.8 + - - +
238C ARG* 2.5 39.2 + - - +
239C GLN* 3.1 23.7 + - - +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.0 14.5 - - + +
232C LEU* 2.9 35.4 + - + +
233C ALA* 3.5 12.6 + - - +
234C ARG 3.1 0.2 - - - -
235C GLU* 1.3 75.0 - - - +
237C ILE* 1.3 64.3 + - - +
239C GLN* 3.3 20.4 + - - +
240C ALA* 3.1 21.8 + - - +
305C ALA* 3.9 5.0 - - + +
308C ASN* 3.5 10.6 - - - +
1430C PGE 3.3 47.4 + - - +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ALA 3.2 14.6 + - - +
234C ARG* 2.8 17.9 + - + +
236C GLN* 1.3 75.0 - - - +
238C ARG* 1.3 66.6 + - + +
240C ALA* 3.1 13.9 + - - +
241C GLN* 3.2 28.8 + - - +
302C VAL* 4.5 5.4 - - + -
305C ALA* 3.4 21.3 - - + +
306C GLN* 3.8 32.8 - - + +
309C PHE* 3.6 33.0 - - + -
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.1 31.8 - - - +
89C LYS* 5.6 0.4 - - - +
231C ASP* 5.6 3.8 + - - -
234C ARG* 3.2 39.9 + - + +
235C GLU* 2.5 35.9 + - - +
237C ILE* 1.3 80.5 - - + +
239C GLN* 1.3 64.0 - - - +
241C GLN* 2.8 30.9 + - - +
242C ASP* 3.0 16.8 + - - +
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C SER* 5.7 5.1 + - - -
82C ARG* 3.3 28.5 - - + +
83C ALA* 5.0 7.1 - - - +
86C LEU* 3.2 27.1 - - + +
235C GLU 3.1 7.7 + - - +
236C GLN* 3.3 22.6 + - - +
238C ARG* 1.3 78.7 - - - +
240C ALA* 1.3 64.0 + - - +
242C ASP* 3.1 21.4 + - + +
243C GLY 4.0 1.6 + - - -
1430C PGE 5.5 5.5 - - - +
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLN 3.1 11.2 + - - +
237C ILE 3.1 11.2 + - - +
239C GLN* 1.3 76.2 - - - +
241C GLN* 1.3 62.5 + - - +
243C GLY* 3.2 12.1 + - - -
298C VAL* 3.5 14.7 - - - +
301C GLN* 3.9 21.3 + - + +
302C VAL* 3.6 32.5 - - + +
305C ALA* 3.9 5.2 - - + -
1430C PGE 4.9 4.9 - - - -
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 3.3 21.0 - - - +
238C ARG* 2.8 31.8 + - - +
240C ALA* 1.3 71.4 - - - +
242C ASP* 1.3 62.1 + - - +
243C GLY 2.9 6.8 + - - -
244C HIS* 3.1 27.7 + - - +
245C LEU* 4.3 3.7 + - - +
302C VAL* 3.6 31.2 - - + +
306C GLN* 5.5 2.6 - - - +
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Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C MET* 4.0 22.5 - - + +
79C SER* 4.0 13.6 + - - +
82C ARG* 2.8 51.9 + - - +
238C ARG* 3.0 14.7 + - - +
239C GLN 3.1 10.7 + - - +
241C GLN* 1.3 76.7 - - - +
243C GLY* 1.3 56.6 + - - +
244C HIS 3.0 6.3 + - - -
245C LEU* 3.0 35.2 + - - +
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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
------------------------------------------------------------
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