Contacts of the helix formed by residues 271 - 282 (chain J) in PDB entry 2QKK
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 GLU 271 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210J ASN* 5.2 2.4 - - - +
263J GLY 4.5 3.8 - - - +
264J HIS* 4.1 19.5 - - - +
265J SER 3.9 3.9 - - - +
267J PHE 4.4 6.1 - - - +
268J ILE* 4.7 12.8 - - + -
269J GLY 3.7 0.4 - - - +
270J ASN* 1.3 111.3 + - - +
272J GLU* 1.3 58.3 + - - +
273J ALA 3.5 0.4 - - - -
274J ASP* 3.4 19.4 - - - +
275J ARG* 3.1 21.0 + - - +
13K C 5.5 3.1 + - - -
268W ILE* 5.8 3.2 - - + +
271W GLU* 3.5 34.7 - - + +
275W ARG* 3.2 31.2 + - - +
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Residues in contact with GLU 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J TYR* 2.9 44.4 + - + -
166J PRO* 5.1 2.3 - - - +
268J ILE* 4.9 1.3 - - + -
269J GLY* 3.3 23.6 - - - +
270J ASN 3.3 0.2 - - - -
271J GLU* 1.3 79.2 - - - +
273J ALA* 1.3 55.2 + - - +
274J ASP 3.0 1.3 - - - -
275J ARG* 2.9 8.8 + - + +
276J LEU* 2.5 40.3 + - + +
268W ILE* 4.2 30.0 - - + +
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Residues in contact with ALA 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J TYR* 3.9 38.8 - - + +
144J THR 4.3 2.5 - - - +
145J ASP* 4.2 15.7 - - + +
161J GLY* 4.1 6.3 - - - +
163J TYR* 4.1 9.5 - - + +
269J GLY 4.2 1.8 - - - +
270J ASN 4.2 7.3 - - - +
272J GLU* 1.3 78.6 - - - +
274J ASP* 1.3 58.1 + - - +
276J LEU* 3.0 11.2 + - - +
277J ALA* 2.8 31.9 + - - +
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Residues in contact with ASP 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ASP* 3.2 16.7 - - - +
270J ASN 2.8 20.3 - - - +
271J GLU* 3.4 23.2 - - + +
273J ALA* 1.3 79.5 - - - +
275J ARG* 1.3 62.1 + - - +
276J LEU 3.1 1.0 + - - -
277J ALA 3.2 3.8 + - - -
278J ARG* 3.1 45.0 + - - +
1008J CA 2.4 30.0 - - - -
13K C 4.3 12.3 + - - +
14K C 4.9 0.3 + - - -
271W GLU* 5.5 2.9 - - - +
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Residues in contact with ARG 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J GLU 3.1 11.0 + - - +
272J GLU* 2.9 12.0 + - + +
274J ASP* 1.3 78.7 - - - +
276J LEU* 1.3 60.8 + - - +
278J ARG* 3.9 10.9 + - - +
279J GLU* 3.8 20.3 + - - +
264W HIS 5.8 3.8 - - - +
265W SER 5.3 8.5 - - - +
266W GLY 5.9 1.8 - - - +
268W ILE* 6.5 1.1 - - + -
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Residues in contact with LEU 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J ILE 4.5 0.2 - - - -
161J GLY* 4.7 1.6 - - - -
162J VAL 3.4 31.2 - - - +
163J TYR* 4.2 10.8 - - + -
171J ASN* 4.1 23.1 - - + +
172J VAL* 4.0 22.9 - - - +
173J GLY* 3.4 19.4 - - - +
272J GLU* 2.5 18.7 + - + +
273J ALA* 3.0 7.2 + - - +
275J ARG* 1.3 74.6 - - - +
277J ALA* 1.3 62.7 + - - +
278J ARG 3.4 0.2 - - - -
279J GLU* 3.3 22.7 - - + +
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Residues in contact with ALA 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ASP* 3.2 31.9 - - - +
147J CYS* 3.3 17.4 - - - -
159J GLY* 3.4 14.8 - - - +
160J ILE 3.6 9.6 + - - -
161J GLY* 3.8 6.0 - - - -
273J ALA 2.8 12.6 + - - +
274J ASP 3.2 3.8 + - - +
276J LEU* 1.3 72.2 - - - +
278J ARG* 1.3 67.8 + - - +
279J GLU 3.0 2.0 - - - -
280J GLY 3.3 0.5 + - - -
281J ALA 3.0 18.0 + - - -
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Residues in contact with ARG 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ASP* 2.9 25.5 + - - -
147J CYS* 3.0 35.6 - - - +
274J ASP* 3.1 51.5 + - - +
275J ARG* 4.1 9.6 - - - +
276J LEU 3.4 0.4 - - - -
277J ALA* 1.3 78.1 - - - +
279J GLU* 1.3 64.3 + - + +
281J ALA* 3.0 16.6 - - - +
282J LYS* 3.3 21.0 + - - +
13K C 4.6 5.2 - - - -
14K C 2.6 31.2 + - - -
264W HIS* 4.3 23.3 - - + +
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Residues in contact with GLU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLY* 4.6 4.3 - - - +
275J ARG 3.8 12.3 + - - +
276J LEU* 3.3 17.0 + - + +
277J ALA 3.0 0.2 - - - -
278J ARG* 1.3 75.6 - - - +
280J GLY* 1.3 69.0 + - - +
281J ALA 3.0 0.9 - - - -
282J LYS* 2.8 45.1 + - - +
283J GLN* 3.7 5.7 + - - +
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Residues in contact with GLY 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLY 3.2 29.3 + - - -
174J ILE 3.5 9.4 - - - -
175J ARG* 3.0 12.4 - - - +
276J LEU 3.4 5.3 + - - -
277J ALA 3.3 5.2 + - - -
279J GLU* 1.3 78.3 - - - +
281J ALA* 1.3 64.4 + - - +
283J GLN* 2.7 27.8 + - - +
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Residues in contact with ALA 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J CYS* 3.8 15.9 - - - -
149J SER* 6.3 1.6 - - - -
157J ARG* 3.9 18.2 + - + +
158J ALA* 3.7 22.2 - - - +
159J GLY* 3.9 1.8 - - - -
175J ARG* 3.2 19.1 + - - -
277J ALA 3.0 14.0 + - - +
278J ARG* 3.0 17.7 - - - +
280J GLY* 1.3 75.5 - - - +
282J LYS* 1.3 56.5 + - + +
283J GLN 3.0 6.9 + - - +
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Residues in contact with LYS 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ARG* 3.6 24.7 + - - +
278J ARG* 3.3 24.0 - - - +
279J GLU* 2.8 34.1 + - - +
281J ALA* 1.3 75.5 - - + +
283J GLN* 1.3 60.3 + - - +
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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