Contacts of the helix formed by residues 267 - 271 (chain E) in PDB entry 1KYZ
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 267 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL 3.5 20.9 - - - +
208E GLY* 4.0 9.4 - - - -
252E MET* 4.0 27.1 - - + -
264E MET* 3.3 30.1 - - + +
265E LYS* 3.3 16.1 - - - +
266E TRP* 1.3 80.1 - - - +
268E CYS* 1.3 71.0 + - - +
269E HIS 3.2 1.3 - - - -
270E ASP* 2.9 14.2 + - - +
271E TRP* 3.4 21.9 - - + -
279E PHE* 3.9 19.7 - - + -
297E GLU* 3.0 1.6 + - - -
1697E SAH 3.9 26.0 - - + +
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Residues in contact with CYS 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E MET* 3.8 26.2 - - - +
267E ILE* 1.3 80.5 - - - +
269E HIS* 1.3 62.3 + - - +
270E ASP 3.0 1.4 + - - -
271E TRP 3.0 13.5 + - - +
276E CYS* 3.4 19.6 - - - -
279E PHE* 4.1 13.0 - - - -
280E LEU* 4.7 11.7 - - - -
295E VAL* 4.3 16.8 - - - -
297E GLU* 3.0 8.1 + - - +
330E ARG* 2.9 21.5 + - - +
335E PHE* 4.3 15.9 - - + -
338E LEU* 5.0 3.4 - - + -
361E PHE* 5.6 1.3 - - - -
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Residues in contact with HIS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E MET* 5.7 5.7 - - + +
266E TRP* 3.7 43.3 + + + +
267E ILE 3.1 0.6 + - - -
268E CYS* 1.3 75.0 - - - +
270E ASP* 1.3 73.4 + - - +
271E TRP 3.3 0.4 - - - -
297E GLU* 3.0 25.0 + - + +
316E ILE* 4.0 16.6 - - + +
320E MET* 3.7 11.5 - - - +
327E GLY* 3.1 2.4 - - - -
328E LYS 2.8 44.7 + - - +
329E GLU* 2.7 32.1 + - - +
330E ARG* 4.0 1.6 - - - +
335E PHE* 5.8 2.9 - - + -
1698E FER 4.8 7.1 - - + +
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Residues in contact with ASP 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E MET* 6.1 1.0 - - - +
266E TRP 4.0 7.0 - - - +
267E ILE 2.9 13.6 + - - +
269E HIS* 1.3 95.5 + - + +
271E TRP* 1.3 81.8 + - + +
320E MET* 3.5 3.5 - - - +
324E ASN* 2.8 48.0 + - - +
326E GLY* 5.3 0.2 - - - -
327E GLY* 3.7 2.7 - - - -
1697E SAH 5.1 7.4 - - - -
1698E FER 3.1 30.1 - - - -
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Residues in contact with TRP 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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252E MET* 3.4 24.5 - - + -
253E PHE* 3.5 19.0 - + - -
267E ILE* 3.4 32.3 + - + -
268E CYS 3.0 11.0 + - - +
269E HIS 3.3 0.6 - - - -
270E ASP* 1.3 98.6 - - + +
272E SER* 1.3 55.3 + - - +
275E HIS* 3.4 42.8 - + + -
276E CYS* 4.2 7.6 - - - -
279E PHE* 4.2 6.3 - + + -
326E GLY* 3.4 10.3 - - - +
327E GLY* 4.3 1.2 - - - -
328E LYS 4.9 0.2 + - - -
330E ARG* 2.8 29.1 + - - -
1697E SAH 3.4 42.6 - + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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