Contacts of the helix formed by residues 269 - 283 (chain t) in PDB entry 6QX2
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 ASN 269 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113t MET 3.7 5.1 + - - -
114t ASP 3.1 25.6 + - - +
115t GLY* 3.3 16.6 - - - -
267t GLN 3.9 2.6 + - - +
268t VAL* 1.3 71.9 - - - +
270t LYS* 1.3 58.1 + - - +
271t ALA* 3.0 7.1 + - - +
272t ARG* 3.0 64.5 + - + +
273t MET* 2.9 30.8 + - - +
4w C 5.0 3.0 + - - +
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Residues in contact with LYS 270 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113t MET* 3.1 28.3 + - - +
114t ASP* 3.2 26.5 + - - +
264t ILE* 3.9 20.2 - - + -
268t VAL 3.5 4.0 + - - -
269t ASN* 1.3 69.1 - - - +
271t ALA* 1.3 63.5 + - - +
273t MET* 3.2 10.8 + - + +
274t ILE* 3.0 36.3 + - + +
294t ASP* 2.6 32.1 + - - +
296t THR* 3.5 32.8 + - - +
302t VAL* 4.4 15.5 - - + -
304t VAL* 4.2 12.3 - - + -
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Residues in contact with ALA 271 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114t ASP* 3.0 45.1 + - + +
269t ASN* 3.0 1.8 + - - +
270t LYS* 1.3 74.8 - - - +
272t ARG* 1.3 61.6 + - - +
274t ILE* 3.5 9.3 + - - +
275t GLU* 3.1 22.7 + - - +
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Residues in contact with ARG 272 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267t GLN 5.9 0.6 + - - -
269t ASN* 3.0 51.5 + - + +
271t ALA* 1.3 73.6 - - - +
273t MET* 1.3 58.9 + - - +
275t GLU* 3.1 22.0 + - - +
276t LYS* 2.9 28.2 + - + +
326t PRO* 5.8 1.1 - - + -
3w G 3.6 46.2 + - - -
4w C 3.3 28.9 + - - -
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Residues in contact with MET 273 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245t SER* 4.6 0.7 - - - -
261t VAL* 5.1 0.4 - - + -
264t ILE* 4.2 24.2 - - + -
265t PRO* 5.0 0.2 - - - -
268t VAL* 4.1 17.5 - - + -
269t ASN 2.9 17.4 + - - +
270t LYS* 3.5 8.7 - - - +
272t ARG* 1.3 76.7 - - - +
274t ILE* 1.3 71.8 + - + +
276t LYS* 3.4 5.6 + - - +
277t ILE* 3.3 31.5 + - + +
304t VAL* 4.8 12.8 - - + -
325t THR* 5.0 0.2 - - - -
326t PRO* 4.0 30.0 - - + +
327t LEU* 3.5 44.6 - - + +
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Residues in contact with ILE 274 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270t LYS* 3.0 27.6 + - + +
271t ALA* 3.7 10.3 - - - +
273t MET* 1.3 78.7 - - + +
275t GLU* 1.3 56.4 + - - +
277t ILE* 3.0 11.7 + - + +
278t ALA* 2.9 32.6 + - + +
292t LEU* 3.5 21.4 - - + +
294t ASP* 3.6 40.8 - - + +
304t VAL* 3.9 25.4 - - + -
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Residues in contact with GLU 275 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271t ALA 3.1 12.5 + - - +
272t ARG* 3.1 26.9 + - - +
274t ILE* 1.3 78.2 - - - +
276t LYS* 1.3 51.3 + - - +
278t ALA* 3.3 8.0 + - - +
279t GLU* 2.8 46.8 + - + +
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Residues in contact with LYS 276 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272t ARG* 2.9 12.7 + - + +
273t MET* 3.6 10.1 - - - +
274t ILE 3.3 0.2 - - - -
275t GLU* 1.3 76.6 + - - +
277t ILE* 1.3 56.3 + - - +
279t GLU* 3.4 11.5 + - - +
280t LEU* 3.0 33.8 + - + +
324t GLN 5.7 0.9 - - - +
325t THR* 4.7 5.8 - - + -
326t PRO* 4.5 19.1 - - + -
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Residues in contact with ILE 277 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273t MET* 3.3 32.0 + - + +
274t ILE* 3.0 14.1 + - + +
276t LYS* 1.3 72.7 - - - +
278t ALA* 1.3 66.9 + - - +
280t LEU* 3.2 7.8 + - + +
281t VAL* 3.1 24.1 + - + +
286t ILE* 6.0 0.2 - - + -
289t ILE* 4.4 14.4 - - + -
292t LEU* 3.7 24.2 - - + -
304t VAL* 5.6 1.3 - - + -
306t ILE* 4.3 19.3 - - + -
321t LEU* 3.9 20.6 - - + -
325t THR* 3.7 23.6 - - + +
327t LEU* 4.5 10.3 - - + -
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Residues in contact with ALA 278 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274t ILE* 2.9 16.8 + - + +
275t GLU* 3.7 8.7 - - - +
277t ILE* 1.3 75.3 - - - +
279t GLU* 1.3 51.7 + - - +
281t VAL* 3.3 7.7 + - - +
282t ARG* 2.8 36.1 + - - +
292t LEU* 3.6 16.9 - - + +
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Residues in contact with GLU 279 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275t GLU* 2.8 29.4 + - + +
276t LYS* 3.5 10.0 - - - +
278t ALA* 1.3 73.8 - - - +
280t LEU* 1.3 62.1 + - + +
282t ARG* 3.8 6.2 - - + +
283t ASP* 3.0 52.6 + - - +
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Residues in contact with LEU 280 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276t LYS* 3.0 15.8 + - + +
277t ILE* 3.2 9.4 + - - +
279t GLU* 1.3 78.5 - - + +
281t VAL* 1.3 60.0 + - - +
283t ASP* 3.6 1.9 + - + -
284t LYS 3.3 2.6 + - - -
285t LYS* 2.8 50.7 + - + -
286t ILE* 3.6 23.9 + - + -
321t LEU* 5.3 0.9 - - + -
324t GLN* 3.4 45.3 - - + +
325t THR* 3.8 19.5 - - + -
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Residues in contact with VAL 281 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277t ILE* 3.1 16.6 + - + +
278t ALA* 3.6 9.6 - - - +
280t LEU* 1.3 73.2 - - - +
282t ARG* 1.3 67.1 + - - +
284t LYS* 2.9 15.9 + - - +
286t ILE* 3.9 21.7 - - + +
289t ILE* 3.8 50.0 - - + +
292t LEU* 6.0 0.9 - - + -
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Residues in contact with ARG 282 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278t ALA 2.8 21.3 + - - +
279t GLU* 3.8 9.6 - - - +
281t VAL* 1.3 73.3 - - - +
283t ASP* 1.3 65.6 + - - +
284t LYS* 3.4 3.6 + - - +
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Residues in contact with ASP 283 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279t GLU* 3.0 39.8 + - - +
280t LEU* 4.2 2.9 - - + +
281t VAL 3.2 0.2 - - - -
282t ARG* 1.3 82.4 - - - +
284t LYS* 1.3 68.0 + - - +
285t LYS* 2.9 12.4 + - + +
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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