Contacts of the strand formed by residues 223 - 233 (chain A) in PDB entry 1WG8
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 LEU 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ARG* 4.4 4.3 + - - +
90A VAL* 3.6 6.5 - - - +
92A GLY* 4.0 10.8 - - - -
93A ILE* 3.8 24.0 - - + -
219A ALA 3.3 22.7 + - - +
220A ALA* 3.8 14.1 - - - +
221A GLU 3.3 1.7 - - - +
222A VAL* 1.3 76.1 - - - +
224A ALA* 1.3 65.1 + - - +
225A PRO* 4.7 0.3 - - - +
227A GLY 3.7 21.8 - - - +
228A ARG 3.7 18.8 - - - +
229A LEU* 3.9 24.0 - - + +
251A LEU* 4.7 6.5 - - + -
280A ALA 4.9 0.7 - - - +
282A LYS* 2.9 41.0 + - + +
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Residues in contact with ALA 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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89A ARG* 4.0 18.4 - - + -
90A VAL 2.8 24.0 + - - +
91A ASP* 4.3 13.9 - - - +
222A VAL 3.4 1.6 + - - -
223A LEU* 1.3 77.1 - - - +
225A PRO* 1.3 81.9 - - + +
226A GLY 3.2 0.3 + - - -
227A GLY* 2.8 16.2 + - - +
282A LYS* 3.5 5.0 - - - +
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Residues in contact with PRO 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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89A ARG* 5.4 2.7 - - + -
223A LEU 4.7 0.4 - - - +
224A ALA* 1.3 90.6 - - + +
226A GLY* 1.3 57.9 + - - +
227A GLY 3.2 2.4 + - - -
282A LYS* 4.2 3.8 - - + +
283A GLU 4.0 9.9 - - - +
284A ALA* 3.6 29.4 - - + +
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Residues in contact with GLY 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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225A PRO* 1.3 71.4 - - - +
227A GLY* 1.3 63.0 + - - +
228A ARG* 3.8 6.9 + - - +
281A GLU* 3.6 22.3 - - - +
282A LYS 2.6 22.2 + - - -
283A GLU* 4.4 2.8 + - - +
284A ALA 5.2 1.0 - - - -
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Residues in contact with GLY 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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91A ASP* 3.1 22.7 - - - -
223A LEU* 3.7 9.9 - - - +
224A ALA* 2.8 18.1 + - - -
225A PRO 3.1 2.0 + - - -
226A GLY* 1.3 79.8 - - - +
228A ARG* 1.3 60.1 + - - -
281A GLU* 3.4 2.4 - - - -
282A LYS* 2.9 27.4 + - - +
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Residues in contact with ARG 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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16A ASP 4.3 1.6 + - - -
17A LEU* 2.8 61.3 + - - +
18A LEU* 3.9 19.7 - - + +
19A ALA* 4.2 15.5 - - + +
91A ASP 3.5 5.8 + - - +
92A GLY* 3.3 3.1 - - - -
93A ILE 2.8 31.9 + - - +
223A LEU* 3.7 4.3 - - - +
226A GLY 4.2 5.8 + - - +
227A GLY* 1.3 73.7 - - - -
229A LEU* 1.3 54.9 + - - +
230A VAL* 4.4 4.9 - - + -
254A LEU* 3.4 33.9 - - + +
280A ALA 3.4 2.5 - - - +
281A GLU* 2.8 34.2 + - - -
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Residues in contact with LEU 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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93A ILE* 3.5 26.0 - - + +
215A PHE* 4.3 5.4 - - + -
216A LEU* 4.3 11.9 - - + +
219A ALA* 4.0 21.1 - - + -
220A ALA 5.0 0.7 - - - +
223A LEU* 3.9 17.1 - - + +
228A ARG* 1.3 72.1 - - - +
230A VAL* 1.3 63.5 + - - +
231A VAL* 3.8 19.9 - - + +
245A PHE* 4.2 15.9 - - + -
246A LEU* 3.9 26.7 - - + +
251A LEU* 4.3 9.9 - - + -
278A ARG 4.0 0.2 - - - +
279A ALA* 3.1 6.6 - - - +
280A ALA 2.9 32.0 + - - +
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Residues in contact with VAL 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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14A ALA* 4.3 8.5 - - - -
17A LEU* 3.9 24.9 - - + +
18A LEU* 3.7 25.1 - - + +
93A ILE 2.7 12.9 + - - +
94A LEU* 3.3 22.9 - - + +
95A ALA 2.9 24.8 + - - -
228A ARG* 4.4 2.5 - - + -
229A LEU* 1.3 79.1 - - - +
231A VAL* 1.3 66.6 + - - +
232A ILE* 5.1 0.2 - - + -
277A LEU* 3.9 33.7 - - + -
278A ARG 3.6 2.5 - - - -
279A ALA* 4.0 4.9 - - + -
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Residues in contact with VAL 231 (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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95A ALA* 3.3 17.3 - - + +
97A LEU* 3.9 20.4 - - + -
212A LEU* 5.0 2.2 - - + -
215A PHE* 4.5 0.4 - - + -
216A LEU* 4.0 17.9 - - + -
229A LEU* 3.8 23.8 - - + -
230A VAL* 1.3 79.1 - - - +
232A ILE* 1.3 66.7 + - - +
233A ALA 3.9 0.6 + - - +
242A VAL* 3.8 37.8 - - + +
246A LEU* 6.0 1.3 - - + -
276A LYS 3.5 2.1 - - - +
277A LEU* 3.3 2.0 - - - -
278A ARG* 2.8 41.2 + - - +
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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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9A VAL* 3.6 25.8 - - + +
10A LEU* 4.5 8.5 - - + -
14A ALA* 4.6 10.5 - - + -
36A HIS* 4.1 14.1 - - + +
94A LEU* 4.8 6.5 - - + -
95A ALA 2.8 13.0 + - - +
96A ASP* 4.1 16.4 - - + +
97A LEU* 3.1 27.5 + - - +
231A VAL* 1.3 76.5 - - - +
233A ALA* 1.3 60.1 + - - +
234A PHE* 3.4 31.0 - - + -
275A ALA* 3.9 18.2 - - + -
276A LYS 3.4 8.5 - - - +
277A LEU* 4.1 16.2 - - + -
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Residues in contact with ALA 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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97A LEU* 4.1 8.1 - - + -
231A VAL* 3.9 1.0 - - + +
232A ILE* 1.3 75.0 - - - +
234A PHE* 1.3 61.5 + - - +
235A HIS 5.1 0.2 - - - -
238A GLU* 3.8 9.6 - - + -
239A ASP* 3.6 47.1 - - + +
242A VAL* 4.5 8.1 - - + -
274A SER 3.5 1.6 - - - +
275A ALA* 3.5 3.1 - - - -
276A LYS* 2.8 34.5 + - - +
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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
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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