Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 5SY1
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A THR* 3.9 17.7 - - - +
220A LEU* 2.8 12.6 + - - -
221A SER* 1.3 79.7 + - - +
223A SER* 1.3 63.3 + - - +
224A TYR* 3.0 25.5 + - - +
225A TYR* 3.6 8.1 + - - -
226A ARG* 3.7 20.9 + - - +
270A ARG* 5.9 1.3 - - - -
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Residues in contact with SER 223 (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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222A SER* 1.3 76.0 - - - +
224A TYR* 1.3 59.4 + - - +
226A ARG* 4.0 23.5 - - - +
227A ASP* 2.9 46.3 + - - +
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Residues in contact with TYR 224 (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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83A HIS* 4.5 8.4 - - + +
84A THR* 3.7 13.5 - - + -
222A SER* 3.0 11.4 + - - +
223A SER* 1.3 79.0 + - - +
225A TYR* 1.3 95.6 + + - +
227A ASP* 5.0 0.2 - - - -
228A TYR* 3.0 36.3 + - + +
268A VAL* 3.6 24.0 + - + +
269A PHE* 3.4 26.4 - - - -
270A ARG* 2.7 66.9 + - + +
375A TYR* 5.7 0.2 + - - -
558A PRO* 5.0 15.6 - - + +
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Residues in contact with TYR 225 (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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82A ASP* 3.6 4.5 + - - -
83A HIS* 4.0 12.3 + + + +
84A THR* 3.5 22.7 - - + +
218A GLU 4.9 3.1 - - - -
219A ASP* 5.1 3.6 - - - -
220A LEU 4.5 15.9 - - - -
221A SER* 4.9 8.1 - - - +
222A SER* 3.6 12.7 + - - +
223A SER 3.5 0.2 - - - -
224A TYR* 1.3 103.9 - + - +
226A ARG* 1.3 62.1 + - - +
228A TYR* 3.6 4.0 + - - +
229A VAL* 3.5 14.9 + - - +
558A PRO* 4.5 19.5 - - + +
561A LYS* 3.2 60.8 + - + +
562A ALA* 3.4 33.7 - - + +
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Residues in contact with ARG 226 (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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221A SER* 5.0 8.8 + - - +
222A SER 3.7 14.8 + - - +
223A SER* 3.6 26.2 + - - +
224A TYR 3.2 0.6 - - - -
225A TYR* 1.3 78.4 - - - +
227A ASP* 1.3 69.7 + - - +
229A VAL* 3.5 4.2 + - - +
230A LYS* 3.0 38.3 + - - +
562A ALA* 5.2 0.2 - - - -
76C LYS 6.0 0.9 - - - +
77C MET* 4.1 32.3 - - + +
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Residues in contact with ASP 227 (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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223A SER* 2.9 36.0 + - - +
226A ARG* 1.3 84.0 + - - +
228A TYR* 1.3 60.6 + - - +
229A VAL 3.4 0.2 - - - -
230A LYS* 3.4 27.8 - - + +
231A LYS* 2.8 29.3 + - - +
268A VAL* 3.9 25.8 - - + +
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Residues in contact with TYR 228 (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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224A TYR* 3.0 27.1 + - + +
225A TYR* 4.0 4.5 - - - +
226A ARG 3.2 0.6 - - - -
227A ASP* 1.3 75.6 - - - +
229A VAL* 1.3 65.2 + - - +
231A LYS* 3.3 19.7 + - + +
232A ILE* 3.4 26.3 + - + +
267A ASP* 5.7 1.1 - - - -
268A VAL* 3.5 27.8 - - + +
269A PHE* 5.4 6.5 - + + -
372A LYS* 5.0 12.4 - - + +
375A TYR* 3.2 31.3 - + - +
557A HIS* 5.2 0.4 - + - -
558A PRO* 3.6 39.9 - - + +
559A VAL* 4.1 18.8 - - + -
12C GLU* 4.2 14.3 + - - -
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Residues in contact with VAL 229 (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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225A TYR 3.5 14.1 + - - +
226A ARG 3.5 6.8 + - - +
228A TYR* 1.3 75.1 - - - +
230A LYS* 1.3 62.9 + - - +
232A ILE* 3.1 18.8 + - - +
233A LEU* 3.3 13.5 + - + +
558A PRO 4.3 7.9 - - - +
559A VAL* 4.6 12.8 - - + -
562A ALA* 3.7 19.5 - - + -
13C PHE* 4.5 19.5 - - + -
73C MET* 3.9 30.5 - - + +
77C MET* 4.2 19.5 - - + -
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Residues in contact with LYS 230 (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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226A ARG* 3.0 31.4 + - - +
227A ASP* 3.4 28.0 - - - +
229A VAL* 1.3 78.6 - - - +
231A LYS* 1.3 55.8 + - - +
233A LEU* 4.8 0.4 - - - +
234A LYS* 3.0 44.9 + - + +
76C LYS 4.8 3.0 + - - -
77C MET* 3.7 41.1 + - + +
78C LYS 4.8 5.2 + - - +
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASP 2.8 16.3 + - - +
228A TYR* 3.7 15.9 - - + +
229A VAL 3.2 0.8 - - - -
230A LYS* 1.3 77.8 - - - +
232A ILE* 1.3 62.5 + - + +
234A LYS* 4.9 2.5 - - - -
235A LYS* 3.2 33.2 + - + +
266A GLU 4.3 5.1 + - - -
267A ASP* 2.6 43.4 + - - +
268A VAL* 4.7 15.3 - - + +
372A LYS* 5.3 4.6 - - - +
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Residues in contact with ILE 232 (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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228A TYR* 3.4 33.2 - - + +
229A VAL* 3.1 16.5 + - - +
231A LYS* 1.3 77.9 - - + +
233A LEU* 1.3 63.0 + - - +
235A LYS* 3.3 21.2 - - - +
559A VAL* 4.3 5.2 - - + -
5C LEU* 6.4 0.4 - - + -
9C GLN* 3.6 39.8 + - + +
12C GLU* 3.4 26.9 - - - +
13C PHE* 4.1 33.4 - - + -
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Residues in contact with LEU 233 (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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229A VAL* 3.3 12.6 + - + +
230A LYS 4.4 1.6 - - - +
232A ILE* 1.3 78.5 - - + +
234A LYS* 1.3 64.4 + - - +
235A LYS 3.1 2.5 + - - -
236A LYS* 4.1 10.2 + - - +
237A LYS* 5.8 1.4 + - - -
2C ALA 4.3 14.8 - - - +
3C ASP* 5.2 4.7 - - + +
5C LEU* 3.8 29.8 - - + +
9C GLN* 5.2 3.0 - - - +
13C PHE* 6.0 7.2 - - + -
73C MET 4.6 3.6 - - - +
74C ALA* 3.9 27.4 - - + +
77C MET* 4.3 6.3 - - + +
78C LYS* 3.8 38.4 - - + +
79C ASP 5.8 0.4 - - - +
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Residues in contact with LYS 234 (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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230A LYS* 3.0 28.4 + - + +
231A LYS* 4.8 2.5 - - - +
233A LEU* 1.3 73.8 - - - +
235A LYS* 1.3 56.2 + - - +
236A LYS* 2.9 11.9 + - - +
237A LYS* 3.1 37.7 + - + +
238A PRO* 3.3 12.7 - - + +
77C MET 5.5 1.7 + - - +
78C LYS* 6.3 0.2 - - - +
79C ASP* 2.5 54.0 + - + +
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Residues in contact with LYS 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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231A LYS* 3.2 30.2 + - + +
232A ILE* 3.3 13.9 - - - +
233A LEU 3.1 1.6 - - - -
234A LYS* 1.3 75.6 - - - +
236A LYS* 1.3 51.9 + - - +
237A LYS 3.2 0.6 + - - -
238A PRO* 3.3 11.4 - - + +
239A THR* 2.3 42.1 + - - +
376A ARG* 5.2 9.7 - - - +
8C GLU* 5.0 8.7 + - - -
9C GLN* 3.7 19.6 - - + +
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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