Contacts of the helix formed by residues 276 - 286 (chain B) in PDB entry 2Z9I
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 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PRO* 5.4 1.6 - - - +
237B ASN* 4.3 13.2 - - - -
243B GLY 3.7 13.7 - - - -
244B ALA* 3.5 3.6 - - - +
274B ILE* 3.1 23.8 + - - +
275B ASN* 1.3 83.5 - - - +
277B ALA* 1.3 66.1 + - - +
278B ASP* 3.7 11.0 + - - +
279B ALA* 3.6 19.2 + - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL 3.4 22.2 - - - +
236B THR* 3.5 19.5 - - + -
237B ASN* 3.4 21.6 + - - +
244B ALA* 3.9 10.1 - - - -
276B SER* 1.3 75.6 - - - +
278B ASP* 1.3 63.2 + - - +
280B LEU* 2.9 23.2 + - - +
281B VAL* 3.2 17.5 + - + +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 4.0 13.5 - - + -
142B VAL 6.4 0.7 - - - -
143B SER* 6.2 2.7 - - - -
154B VAL* 3.8 17.8 - - + +
236B THR* 6.1 0.5 - - - +
276B SER* 3.7 9.6 + - - +
277B ALA* 1.3 77.9 - - - +
279B ALA* 1.3 56.6 + - - +
281B VAL* 3.4 9.8 + - - +
282B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 3.8 23.0 - - + +
273B PRO 5.0 2.2 - - - +
274B ILE* 3.7 24.5 - - + +
275B ASN* 4.2 3.6 - - + +
276B SER* 3.6 25.2 + - - +
277B ALA 3.1 0.6 - - - -
278B ASP* 1.3 79.0 - - - +
280B LEU* 1.3 56.1 + - - +
282B ALA* 3.7 1.7 - - - +
283B ALA* 3.0 30.2 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.7 24.7 - - + -
233B VAL* 4.8 8.3 - - + -
235B VAL* 5.6 4.7 - - - +
244B ALA* 4.0 26.0 - - + +
246B ILE* 5.4 2.5 - - + -
266B VAL* 4.4 16.4 - - + -
269B VAL* 4.0 24.2 - - + -
274B ILE* 4.2 12.5 - - + +
276B SER 3.8 1.0 + - - +
277B ALA 2.9 14.4 + - - +
279B ALA* 1.3 72.7 - - - +
281B VAL* 1.3 58.3 - - + +
283B ALA* 4.4 2.0 - - + -
284B VAL* 2.8 50.5 + - + +
295B LEU* 5.2 0.9 - - + -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 4.1 21.3 - - + -
235B VAL 6.1 0.4 - - - +
277B ALA* 3.2 16.3 + - + +
278B ASP* 3.6 11.4 - - - +
280B LEU* 1.3 78.0 - - + +
282B ALA* 1.3 53.4 + - - +
284B VAL* 3.8 3.7 - - - +
285B ARG* 2.7 73.3 + - + +
3H THR 5.1 4.0 - - - +
4H VAL* 4.8 18.4 - - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 3.7 15.7 - - + -
154B VAL* 3.6 21.5 - - + +
155B LEU 3.6 15.5 - - - +
156B ASP* 3.4 17.4 - - + +
278B ASP 2.9 21.7 + - - +
279B ALA 3.7 3.1 - - - +
281B VAL* 1.3 73.7 - - - +
283B ALA* 1.3 56.7 + - - +
285B ARG* 3.9 3.7 - - - +
286B SER* 2.9 28.9 + - - -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 4.7 4.7 + - - +
269B VAL* 3.5 34.3 - - + -
279B ALA 3.0 18.7 + - - +
280B LEU* 3.8 4.5 - - - +
282B ALA* 1.3 74.5 - - - +
284B VAL* 1.3 55.7 + - - +
286B SER* 3.6 7.0 - - - -
287B LYS* 2.6 41.4 - - - +
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Residues in contact with VAL 284 (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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229B ALA* 3.4 33.2 - - + +
230B SER 4.1 1.1 - - - +
231B LEU* 3.7 36.3 - - + +
269B VAL* 5.7 2.0 - - + -
280B LEU* 2.8 43.4 + - + +
281B VAL* 4.0 3.8 - - - +
283B ALA* 1.3 69.8 - - - +
285B ARG* 1.3 60.0 + - - +
287B LYS* 2.8 28.7 + - - +
311B LEU* 4.5 12.6 - - + -
4H VAL 3.9 11.7 - - - +
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Residues in contact with ARG 285 (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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86B THR* 4.5 26.7 + - - +
87B SER* 6.5 1.6 - - - -
153B THR* 6.0 0.8 - - - +
154B VAL* 4.7 20.7 + - - +
212B GLN* 4.8 4.1 - - - +
215B ARG* 3.8 15.6 + - - -
216B ILE* 5.8 1.6 - - - +
228B HIS* 4.4 21.4 - - + +
229B ALA* 3.8 20.2 + - - +
281B VAL* 2.7 52.5 + - - +
282B ALA* 4.2 4.5 - - - +
284B VAL* 1.3 72.8 - - - +
286B SER* 1.3 56.6 + - - +
287B LYS 3.1 5.4 + - - +
3H THR* 5.8 2.4 - - - +
4H VAL 4.6 18.6 - - - +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.5 23.7 + - - +
212B GLN* 3.6 33.1 + - - +
215B ARG* 4.9 2.7 + - - -
282B ALA 2.9 20.4 + - - -
283B ALA* 3.6 9.3 + - - -
284B VAL 3.2 0.2 - - - -
285B ARG* 1.3 74.8 - - - +
287B LYS* 1.3 72.9 + - - +
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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