Contacts of the helix formed by residues 266 - 276 (chain B) in PDB entry 3CUQ
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 3.8 22.2 - - + +
264B MET 3.7 1.2 + - - -
265B SER* 1.3 71.1 - - - +
267B THR* 1.3 58.1 + - - +
269B VAL* 3.0 7.1 + - + +
270B TYR* 2.7 31.4 + - - +
287B LEU* 4.1 16.3 - - + +
288B VAL* 3.5 35.9 - - + -
291B CYS* 4.2 7.9 - - - -
303B LEU* 4.4 7.0 - - + -
311B MET* 2.9 38.3 + - + +
312B VAL 4.4 0.4 - - - +
313B ILE* 3.2 39.5 - - + -
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.1 22.7 - - - +
154A LEU* 4.3 33.4 - - + +
155A GLY 6.0 0.2 - - - +
156A THR 5.2 9.2 - - - +
157A GLY* 5.7 5.4 - - - -
158A PHE* 5.5 6.8 - - + -
265B SER* 3.2 13.9 - - - +
266B LEU* 1.3 73.2 - - - +
268B GLU* 1.3 65.5 + - - +
270B TYR* 3.8 2.1 - - - +
271B CYS* 3.2 27.3 + - - -
351B LEU* 5.7 4.0 - - + -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 6.3 0.2 - - - -
260B ARG* 3.9 12.8 + - - -
263B ILE 5.0 0.3 - - - +
264B MET* 3.1 39.6 - - + +
265B SER* 3.2 29.2 + - - +
267B THR* 1.3 77.1 + - - +
269B VAL* 1.3 57.6 + - - +
271B CYS* 3.6 7.0 + - - +
272B LEU* 3.0 22.0 + - - +
349B SER* 4.0 23.6 + - - -
351B LEU* 5.6 1.6 - - - +
352B LEU* 5.3 2.1 - - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.9 26.2 - - + -
257B LEU* 5.8 0.4 - - + -
264B MET* 3.7 28.3 - - + -
265B SER 3.1 17.7 + - - +
266B LEU* 3.0 15.4 + - + +
268B GLU* 1.3 74.4 - - - +
270B TYR* 1.3 67.7 + - - +
272B LEU* 3.0 13.1 + - - +
273B VAL* 3.1 24.4 + - + +
287B LEU* 3.7 25.6 - - + -
313B ILE* 4.6 14.4 - - + -
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Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 2.6 36.2 + - - +
101A GLY* 4.6 2.4 - - - -
102A VAL* 3.8 18.6 - - + -
105A ILE* 4.0 18.8 - - + -
151A LEU* 4.1 13.3 - - + +
154A LEU* 3.9 15.7 - - + -
266B LEU 2.7 20.0 + - - +
267B THR 3.8 3.4 - - - +
269B VAL* 1.3 73.3 - - - +
271B CYS* 1.3 61.7 + - - +
273B VAL* 4.1 1.6 - - - +
274B ASN* 3.0 47.1 + - - +
282B LEU* 3.2 14.4 - - + -
283B SER 4.6 1.3 - - - -
284B PRO* 3.7 35.4 - - + +
287B LEU* 4.0 21.3 - - + +
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 4.1 26.7 - - + -
105A ILE* 3.7 37.5 - - - -
106A GLU* 4.8 6.5 - - + +
252A GLU* 6.2 0.2 - - - +
267B THR 3.2 15.7 + - - +
268B GLU* 3.7 10.5 - - - +
269B VAL 3.2 0.4 - - - -
270B TYR* 1.3 72.0 - - - +
272B LEU* 1.3 68.6 + - - +
273B VAL 2.9 3.1 + - - -
275B ARG* 3.2 37.0 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 4.5 11.0 - - + +
253B LEU* 4.1 18.8 - - + -
256B PRO* 4.1 30.7 - - + -
260B ARG* 4.3 18.8 - - - +
264B MET* 4.7 6.5 - - + -
268B GLU 3.0 17.5 + - - +
269B VAL* 3.0 10.5 + - - +
271B CYS* 1.3 77.8 - - - +
273B VAL* 1.3 59.6 + - + +
275B ARG* 4.5 21.3 - - - +
276B ALA* 3.7 20.6 + - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LEU* 4.3 15.3 - - + -
252B ILE* 4.3 17.9 - - + -
253B LEU* 4.1 15.7 - - + -
269B VAL* 3.1 31.4 + - + +
270B TYR* 4.1 4.0 - - - +
271B CYS 2.9 2.0 + - - -
272B LEU* 1.3 77.7 - - - +
274B ASN* 1.3 68.0 + - - +
275B ARG 3.3 2.1 + - - -
276B ALA* 3.5 10.4 + - - +
277B ARG* 3.7 24.7 - - - +
282B LEU* 4.1 25.1 - - + -
287B LEU* 4.8 0.9 - - + -
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Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR 5.1 0.4 - - - -
99A GLU* 5.2 2.4 - - - +
102A VAL* 3.9 14.4 - - + -
270B TYR* 3.0 50.3 + - - +
273B VAL* 1.3 76.1 - - - +
275B ARG* 1.3 63.7 - - - +
276B ALA 3.3 0.2 - - - -
277B ARG* 3.5 26.6 + - - +
281B LEU* 3.3 30.4 - - + +
282B LEU* 2.7 43.4 - - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLU* 5.5 4.0 - - - -
102A VAL* 4.5 12.0 - - + +
106A GLU* 3.2 30.9 + - - -
252A GLU* 3.5 31.4 + - - -
271B CYS* 3.2 26.2 + - - +
272B LEU* 4.5 26.5 - - - +
274B ASN* 1.3 78.5 - - - +
276B ALA* 1.3 55.9 + - - +
277B ARG 3.1 9.8 + - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.7 17.3 + - + +
273B VAL* 3.5 5.8 + - - +
274B ASN 3.3 0.8 - - - -
275B ARG* 1.3 76.1 - - - +
277B ARG* 1.3 65.1 + - - +
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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