Contacts of the helix formed by residues 260 - 269 (chain E) in PDB entry 4QOZ
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 ILE 260 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 3.9 25.6 - - + -
229E THR 3.1 17.2 + - - +
230E ASP* 4.1 12.1 - - + -
258E ILE* 3.4 3.6 + - - -
259E ASN* 1.3 73.3 - - - +
261E ARG* 1.3 59.1 + - - +
263E SER* 3.7 10.3 - - - -
264E TYR* 2.9 30.1 + - + +
280E MET* 4.5 14.4 - - + -
302E ILE* 4.3 11.0 - - + +
305E ILE* 3.8 27.4 - - + -
306E ALA* 4.0 23.6 - - + +
309E MET* 3.8 19.5 - - - -
316E LEU* 4.7 3.1 - - + -
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Residues in contact with ARG 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D C 2.8 41.9 + - - +
25D C 3.0 50.3 + - - -
230E ASP* 2.6 50.3 + - - +
231E GLY* 3.8 10.3 - - - +
259E ASN* 3.0 13.5 + - - +
260E ILE* 1.3 75.6 - - - +
262E LYS* 1.3 60.5 + - - +
264E TYR* 3.8 2.1 - - - +
265E GLY* 2.9 26.9 + - - -
275E THR* 3.2 47.2 + - + -
276E LYS* 4.1 9.5 - - - +
280E MET* 4.3 1.8 - - + -
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Residues in contact with LYS 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D C 3.0 30.4 + - - +
21D C 3.8 18.7 + - - +
259E ASN* 3.3 16.2 + - - +
261E ARG* 1.3 78.4 - - - +
263E SER* 1.3 58.2 + - - +
265E GLY* 3.3 1.2 + - - -
266E ASN* 2.9 39.9 + - - +
319E ASN* 3.1 31.2 + - - +
320E GLU* 3.7 24.5 - - - +
329E SER* 3.0 28.9 + - - -
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Residues in contact with SER 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ILE* 3.7 13.9 - - - +
259E ASN 3.2 12.7 + - - -
260E ILE* 3.6 10.3 - - - -
261E ARG 3.3 0.2 - - - -
262E LYS* 1.3 77.7 - - - +
264E TYR* 1.3 58.3 + - - +
266E ASN* 3.3 6.3 + - - +
267E PHE* 2.9 31.5 + - - +
309E MET* 3.7 14.4 - - - -
314E CYS* 4.8 4.5 - - - -
316E LEU* 4.0 12.9 - - - +
317E ARG 4.7 3.1 + - - -
319E ASN* 3.3 12.9 + - - +
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Residues in contact with TYR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 5.0 0.7 - - - +
260E ILE 2.9 18.0 + - - +
261E ARG 3.8 3.4 - - - +
263E SER* 1.3 74.8 - - - +
265E GLY* 1.3 59.6 + - - +
267E PHE* 4.4 0.4 - - - -
268E TYR* 2.9 53.3 + + - +
270E VAL* 3.4 26.9 - - + +
271E PRO 5.0 3.8 - - - -
275E THR* 4.8 4.9 - - + -
280E MET* 2.8 60.6 + - + -
283E LYS* 3.4 16.5 - - + +
284E LEU* 3.4 32.0 - - + +
305E ILE* 4.0 3.4 - - + -
309E MET* 3.5 23.6 - - + +
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Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E ARG 2.9 18.0 + - - -
262E LYS* 3.7 1.3 - - - -
264E TYR* 1.3 80.9 - - - +
266E ASN* 1.3 62.1 + - - +
269E LYS* 3.2 24.8 + - - +
270E VAL 4.2 9.4 + - - -
271E PRO* 5.6 1.3 - - - -
275E THR* 5.2 5.2 - - - -
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Residues in contact with ASN 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D G 4.0 42.2 + - + +
20D C 2.7 39.8 + - - -
104E LYS* 5.5 0.2 + - - -
262E LYS* 2.9 27.2 + - - +
263E SER* 3.9 5.2 - - - +
265E GLY* 1.3 76.4 - - - +
267E PHE* 1.3 59.3 + - - +
269E LYS* 2.8 31.9 + - - +
319E ASN* 5.9 0.8 - - - +
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Residues in contact with PHE 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LYS* 3.4 52.0 - - + +
263E SER 2.9 18.0 + - - +
264E TYR 3.8 2.7 - - - +
265E GLY 3.2 0.2 - - - -
266E ASN* 1.3 79.3 - - + +
268E TYR* 1.3 101.3 + + - +
269E LYS* 3.5 12.9 + - - +
309E MET* 4.3 2.5 - - + -
312E ASP* 3.6 28.0 - - + -
313E GLY 4.2 3.6 - - - -
314E CYS* 3.5 47.8 - - + -
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Residues in contact with TYR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASP* 3.3 24.9 - - - +
101E VAL* 3.7 30.3 - - + -
104E LYS* 4.3 8.5 - - + -
264E TYR* 2.9 47.3 + + + +
267E PHE* 1.3 100.5 - + - +
269E LYS* 1.3 71.6 + - - +
270E VAL* 3.3 18.1 + - + +
284E LEU* 3.7 22.5 - - + +
308E ARG* 3.9 2.6 - - - +
309E MET* 3.7 32.1 - - + +
312E ASP* 2.7 28.2 + - - +
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Residues in contact with LYS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D A 4.1 25.1 + - - -
19D G 5.5 9.2 - - - -
100E ASP* 4.6 9.2 - - + +
104E LYS* 4.1 6.7 - - - +
264E TYR 4.1 0.2 + - - -
265E GLY 3.2 15.9 + - - +
266E ASN* 2.8 28.8 + - - +
267E PHE 3.3 10.5 + - - +
268E TYR* 1.3 81.1 - - - +
270E VAL* 1.3 65.8 + - - +
271E PRO* 4.7 1.3 - - - +
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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