Contacts of the helix formed by residues 267 - 275 (chain A) in PDB entry 1GOT
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 LYS 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LEU* 3.8 22.4 - - + -
265A ASN 3.2 1.4 - - - -
266A LYS* 1.3 77.4 - - - +
268A ASP* 1.3 56.3 + - - +
270A PHE* 3.9 1.3 - - - -
271A GLU* 2.8 34.1 + - - +
292A TYR* 3.5 30.6 + - + +
319A MSE 3.6 35.0 - - + -
320A THR* 3.2 19.9 + - - +
321A CYS* 4.0 8.8 - - + +
324A ASP* 5.7 1.6 + - - -
327A ASN* 3.9 19.0 - - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 4.8 6.1 + - - -
266A LYS* 3.4 7.4 - - - -
267A LYS* 1.3 74.3 - - + +
269A LEU* 1.3 74.6 + - - +
271A GLU* 3.5 11.3 + - - +
272A GLU* 3.5 25.3 + - - +
321A CYS* 3.7 18.9 - - + -
323A THR* 4.5 0.7 + - - -
355G GDP 2.9 45.0 + - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.9 34.3 - - + +
172A ARG* 5.5 2.5 - - - +
224A SER* 3.8 15.7 - - - +
266A LYS* 3.2 17.7 + - + +
268A ASP* 1.3 78.8 + - - +
270A PHE* 1.3 59.8 + - - +
272A GLU* 3.3 7.8 + - + +
273A LYS* 2.8 31.3 + - - +
355G GDP 3.5 36.8 - - + +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU* 3.5 39.5 - - + -
224A SER* 4.0 7.1 - - - +
226A TYR* 3.6 31.4 - + - -
266A LYS 2.9 17.3 + - - +
267A LYS* 3.6 4.3 - - - +
269A LEU* 1.3 77.1 - - - +
271A GLU* 1.3 54.6 + - - +
273A LYS* 3.1 2.3 + - - -
274A ILE* 2.8 42.3 + - + +
279A LEU* 5.1 0.4 - - + -
292A TYR* 3.8 37.9 - + - -
295A ALA* 4.0 14.6 - - + -
296A GLY* 3.7 35.4 - - - -
299A ILE* 3.8 13.9 - - + -
319A MSE 6.0 0.4 - - + -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LYS 2.8 22.1 + - - +
268A ASP* 3.7 10.6 - - - +
270A PHE* 1.3 74.0 - - - +
272A GLU* 1.3 72.7 + - - +
274A ILE* 3.5 15.1 - - - +
275A LYS* 4.2 8.1 + - - +
292A TYR* 3.5 34.6 - - + +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASP 3.5 13.4 + - - +
269A LEU* 3.3 8.9 + - + +
270A PHE 3.1 0.6 - - - -
271A GLU* 1.3 88.8 - - - +
273A LYS* 1.3 67.4 + - - +
275A LYS* 3.2 20.1 + - - +
276A LYS* 3.8 4.3 + - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER* 3.8 3.4 + - - -
224A SER* 2.8 33.3 + - - +
226A TYR* 3.4 19.5 - - + +
227A ASP* 2.7 38.8 + - - +
228A LEU* 3.7 17.4 - - - +
269A LEU* 2.8 18.5 + - - +
270A PHE* 3.8 3.1 - - - +
272A GLU* 1.3 77.6 - - - +
274A ILE* 1.3 52.5 + - - +
276A LYS* 2.5 56.9 + - + +
277A SER* 2.8 13.2 + - - +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR* 3.1 27.0 + - + +
270A PHE* 2.8 26.6 + - + +
271A GLU 3.5 16.2 - - - +
273A LYS* 1.3 72.7 - - - +
275A LYS* 1.3 67.0 + - + +
276A LYS 3.2 0.7 + - - -
277A SER 3.7 5.9 + - - +
279A LEU* 4.5 2.9 - - + +
290A ASN* 3.3 54.9 - - - +
291A THR* 3.9 8.7 - - - -
292A TYR* 3.6 25.6 - - + +
295A ALA* 3.8 18.8 - - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU 4.3 10.1 - - - +
272A GLU* 3.2 13.5 + - - +
273A LYS 2.8 1.0 + - - -
274A ILE* 1.3 83.9 - - + +
276A LYS* 1.3 58.3 + - - +
290A ASN 5.3 5.6 - - - +
291A THR* 6.2 3.1 - - - +
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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