Contacts of the helix formed by residues 280 - 292 (chain A) in PDB entry 2XIK
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 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.9 31.2 - - + +
119A THR* 3.9 26.5 - - + +
120A ILE* 3.9 27.8 - - + +
148A LEU* 3.9 16.9 - - + +
152A GLY* 3.5 21.5 - - - +
154A VAL* 3.6 21.5 - - + -
277A THR* 3.0 15.3 + - + +
279A PHE* 1.3 75.2 - - + +
281A THR* 1.4 57.4 + - - +
282A GLU 3.1 2.7 - - - -
283A LEU* 2.9 25.8 + - + +
284A ILE* 3.4 12.7 + - - +
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Residues in contact with THR 281 (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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150A GLU 3.4 16.4 - - - +
151A GLN* 3.4 36.1 - - - +
152A GLY 3.6 1.6 - - - +
278A SER* 2.7 22.3 + - - +
280A LEU* 1.4 76.6 - - - +
282A GLU* 1.4 55.9 + - - +
284A ILE* 3.2 9.8 + - + +
285A ASP* 2.9 42.0 + - - +
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Residues in contact with GLU 282 (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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116A TYR* 3.6 22.4 - - - +
279A PHE* 3.4 12.4 + - + +
280A LEU 3.1 1.0 - - - -
281A THR* 1.4 78.7 + - - +
283A LEU* 1.4 57.0 + - - +
285A ASP* 3.5 10.9 + - - +
286A ARG* 3.0 27.7 + - - +
289A ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 283 (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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106A LEU* 3.7 26.8 - - + +
112A LEU* 3.7 35.0 - - + -
116A TYR* 3.7 48.0 - - + -
120A ILE* 4.0 17.5 - - + -
280A LEU* 2.9 15.3 + - + +
282A GLU* 1.4 73.3 - - - +
284A ILE* 1.4 61.3 + - - +
286A ARG* 3.5 27.7 + - - +
287A TYR* 3.0 27.5 + - - +
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Residues in contact with ILE 284 (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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99A GLY 4.8 0.4 - - - +
100A GLY* 3.9 27.1 - - - +
106A LEU* 4.1 18.8 - - + -
148A LEU* 4.5 5.8 - - + -
149A SER 3.2 27.1 - - - +
150A GLU* 4.1 13.7 - - + +
152A GLY* 4.0 13.5 - - - +
280A LEU 3.8 6.5 - - - +
281A THR* 3.2 24.6 + - - +
283A LEU* 1.4 75.9 - - - +
285A ASP* 1.4 60.3 + - - +
287A TYR* 3.2 5.7 + - + +
288A LYS* 2.9 52.5 + - + +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 2.9 28.9 + - - +
282A GLU* 3.7 9.1 - - - +
284A ILE* 1.4 79.9 - - - +
286A ARG* 1.3 54.8 + - - +
288A LYS* 3.3 9.5 + - - +
289A ARG* 2.9 49.3 + - + +
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Residues in contact with ARG 286 (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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106A LEU 2.8 27.3 + - - -
109A PRO* 3.6 19.2 - - + +
110A GLY* 2.9 32.8 + - - +
111A PRO* 3.0 22.4 + - - +
112A LEU* 3.7 10.9 - - - +
282A GLU 3.0 18.3 + - - +
283A LEU* 3.7 22.0 + - - +
284A ILE 3.3 0.2 - - - -
285A ASP* 1.3 74.3 - - - +
287A TYR* 1.4 54.8 + - - +
289A ARG* 3.4 26.4 + - - +
290A TRP* 3.1 28.9 + - - +
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Residues in contact with TYR 287 (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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100A GLY 5.0 6.1 - - - -
101A GLY* 6.1 0.7 - - - -
105A ASP* 3.2 35.7 - - + -
106A LEU* 3.7 20.4 - - + -
108A LYS* 3.7 14.6 + - - -
109A PRO* 3.8 13.6 - - + +
283A LEU 3.0 17.8 + - - +
284A ILE* 3.2 6.0 + - + +
286A ARG* 1.4 72.7 - - - +
288A LYS* 1.4 64.5 + - + +
290A TRP* 3.2 24.8 + + - +
291A LYS* 2.9 40.6 + - + +
1294A J60 3.2 44.2 - - - +
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Residues in contact with LYS 288 (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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99A GLY 4.3 9.2 + - - -
150A GLU* 2.8 28.7 + - - -
284A ILE* 2.9 35.6 + - + +
285A ASP* 3.3 11.0 + - - +
287A TYR* 1.4 80.2 - - + +
289A ARG* 1.3 62.6 + - + +
291A LYS* 4.1 4.6 - - - +
292A SER* 3.1 26.5 + - - -
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Residues in contact with ARG 289 (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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282A GLU 5.0 1.6 + - - -
285A ASP* 2.9 38.4 + - + +
286A ARG* 3.6 31.4 - - - +
287A TYR 3.3 0.2 - - - -
288A LYS* 1.3 76.7 - - + +
290A TRP* 1.3 61.4 + - - +
292A SER* 3.8 16.4 + - - -
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Residues in contact with TRP 290 (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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108A LYS* 3.7 41.3 + - + -
109A PRO* 3.7 31.3 + - + +
286A ARG 3.1 16.4 + - - +
287A TYR* 3.2 35.9 + + - +
289A ARG* 1.3 76.7 - - - +
291A LYS* 1.4 80.2 + - + +
292A SER 4.5 2.6 - - - -
1294A J60 6.3 0.4 - - + -
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Residues in contact with LYS 291 (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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287A TYR* 2.9 35.2 + - + +
288A LYS* 4.2 4.9 - - - +
290A TRP* 1.4 82.7 - - + +
292A SER* 1.4 64.1 + - - +
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Residues in contact with SER 292 (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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288A LYS 3.1 19.6 + - - -
289A ARG* 4.0 14.4 - - - -
290A TRP 3.5 2.8 - - - -
291A LYS* 1.4 80.4 - - - +
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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