Contacts of the helix formed by residues 264 - 274 (chain E) in PDB entry 3K75
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 GLN 264 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E SER* 4.3 19.9 + - - -
260E ILE* 3.6 12.7 - - + +
261E PRO* 2.7 23.0 + - + +
263E ASP* 1.3 93.8 + - - +
265E TYR* 1.3 67.4 + - - +
266E TYR 3.6 1.6 - - - -
267E CYS* 3.5 7.0 + - - +
268E GLY* 3.3 14.4 + - - -
295E GLU 4.3 1.6 - - - +
296E TYR* 3.2 53.9 + - + +
297E THR* 4.0 12.6 - - + +
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Residues in contact with TYR 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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174E ILE* 3.8 20.9 - - + -
175E ALA 3.4 2.1 - - - -
176E THR* 2.6 35.3 + - - -
194E LEU* 2.6 46.5 + - + -
195E LEU 3.8 4.7 - - - -
196E THR* 3.3 33.4 - - + -
260E ILE* 3.9 13.3 - - + +
261E PRO 2.9 8.1 + - - +
262E LYS* 3.2 15.0 + - + +
263E ASP 3.6 0.2 - - - -
264E GLN* 1.3 77.9 - - - +
266E TYR* 1.3 84.3 + + + +
267E CYS 3.0 0.2 - - - -
268E GLY* 2.9 19.6 + - - -
269E VAL* 3.0 25.5 + - + +
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Residues in contact with TYR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 4.1 20.3 - - + +
262E LYS* 3.4 27.7 + - - -
265E TYR* 1.3 96.6 - + + +
267E CYS* 1.3 56.4 + - - +
269E VAL* 3.8 11.5 - - + +
270E LEU* 3.1 25.6 + - - +
313E VAL* 4.1 12.2 + - + +
314E ASP* 3.5 29.6 + - - -
315E SER* 3.5 36.1 - - - +
316E GLU* 4.1 10.9 - - + +
319E ILE* 3.6 6.6 - - - +
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Residues in contact with CYS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E ASP 5.9 1.1 - - - -
264E GLN* 3.5 7.9 + - - +
265E TYR 3.0 1.0 - - - -
266E TYR* 1.3 77.9 - - - +
268E GLY* 1.3 62.8 + - - +
270E LEU* 3.6 5.5 + - - +
271E TYR* 3.1 21.0 + - - +
293E ILE* 5.6 4.8 - - - +
294E ASN 4.4 2.9 - - - +
295E GLU* 3.2 19.0 - - - +
296E TYR 3.7 11.9 - - - +
297E THR* 3.8 30.3 - - - -
298E ILE* 4.2 4.0 - - - -
313E VAL* 4.8 11.5 - - - +
319E ILE* 3.8 28.3 - - - -
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Residues in contact with GLY 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E LEU* 3.7 11.0 - - - -
260E ILE* 4.7 7.0 - - - -
264E GLN 3.3 5.2 + - - -
265E TYR 2.9 7.7 + - - -
267E CYS* 1.3 77.6 - - - +
269E VAL* 1.3 53.5 + - - +
271E TYR* 3.1 4.1 + - - -
272E PHE* 2.7 42.7 + - - +
295E GLU* 3.2 19.6 + - - -
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Residues in contact with VAL 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E THR* 4.1 11.9 - - + +
178E CYS* 4.2 6.1 - - - -
182E ARG* 3.4 35.4 - - - +
194E LEU* 3.7 15.4 - - + +
265E TYR* 3.0 51.7 + - + +
266E TYR* 3.8 11.9 - - + +
268E GLY* 1.3 73.1 - - - +
270E LEU* 1.3 66.4 + - - +
273E THR* 2.6 32.6 + - - +
316E GLU* 3.7 7.4 - - + +
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Residues in contact with LEU 270 (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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266E TYR 3.1 16.4 + - - +
267E CYS* 3.6 7.4 - - - +
269E VAL* 1.3 79.0 - - - +
271E TYR* 1.3 58.5 + - - +
273E THR* 4.8 0.2 - - - -
274E GLY* 2.8 27.9 + - - -
278E PHE* 4.1 15.3 - - + -
279E ASN* 3.5 5.4 - - - +
282E MET* 3.4 44.9 - - + -
293E ILE* 4.7 13.0 - - + -
316E GLU* 3.8 12.6 - - + +
319E ILE* 3.6 26.5 - - + -
320E PHE* 4.4 9.6 - - + -
333E ARG* 4.2 10.8 - - - +
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Residues in contact with TYR 271 (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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267E CYS 3.1 13.3 + - - +
268E GLY 3.1 4.3 + - - +
270E LEU* 1.3 82.3 - - + +
272E PHE* 1.3 101.4 + + - +
273E THR 3.4 1.0 + - - -
274E GLY 3.8 1.0 + - - -
279E ASN* 2.9 33.6 + - - +
283E ARG* 3.6 33.2 - - - -
293E ILE* 6.5 0.9 - - + -
294E ASN 5.4 0.2 - - - -
295E GLU* 3.9 33.7 - - + +
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Residues in contact with PHE 272 (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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178E CYS* 3.9 4.0 - - + +
179E GLY* 3.4 18.4 + - - -
192E ASP* 4.2 20.5 - - - +
194E LEU* 4.0 25.6 - - + -
258E ARG* 4.0 37.9 - - - -
260E ILE* 5.2 4.3 - - + -
268E GLY* 2.7 26.7 + - - +
271E TYR* 1.3 95.1 - + - +
273E THR* 1.3 60.3 + - - +
295E GLU* 2.8 38.8 - - + -
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Residues in contact with THR 273 (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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178E CYS* 3.4 17.5 - - - +
179E GLY* 3.8 10.0 - - - +
182E ARG* 2.8 48.8 + - + +
183E ARG* 2.8 25.7 + - + -
269E VAL 2.6 22.6 + - - -
270E LEU 4.0 0.7 - - - -
271E TYR 4.1 0.7 - - - -
272E PHE* 1.3 81.0 - - - +
274E GLY* 1.3 77.9 - - - +
330E PRO* 4.4 2.0 - - + -
333E ARG* 4.2 10.1 - - - +
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Residues in contact with GLY 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ARG* 2.4 26.9 + - - -
270E LEU 2.8 19.9 + - - -
271E TYR 3.8 0.8 + - - -
273E THR* 1.3 96.7 - - - +
275E SER* 1.3 54.8 + - - -
278E PHE* 4.2 9.6 - - - -
279E ASN* 3.5 17.0 - - - -
333E ARG* 4.7 8.2 - - - +
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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