Contacts of the helix formed by residues 292 - 300 (chain C) in PDB entry 5LXY
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 SER 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLU* 2.9 35.0 + - - -
291C ILE* 1.3 77.3 - - - +
293C GLU* 1.3 59.4 + - - +
294C GLU* 3.4 10.0 + - - +
295C LEU 3.1 14.0 + - - -
296C GLN* 2.9 28.3 + - - +
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C SER* 1.3 74.0 - - - +
294C GLU* 1.3 57.3 + - - +
296C GLN* 3.2 8.3 + - - +
297C ASP* 2.8 31.2 + - - +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 4.1 18.2 + - - +
24B GLU* 5.5 6.1 - - - +
25B LEU* 4.2 17.5 + - + +
28B GLU* 5.5 1.2 - - - +
76B TYR* 4.3 13.7 + - - +
292C SER* 3.2 8.9 + - - +
293C GLU* 1.3 79.9 - - - +
295C LEU* 1.3 60.9 + - - +
297C ASP* 3.5 6.5 + - - +
298C ALA* 3.1 21.1 + - - +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.6 25.9 - - + +
28B GLU* 3.7 22.9 - - + +
29B LEU* 4.0 35.4 - - + +
32B GLN* 5.7 0.2 - - + -
75B LEU* 4.2 14.8 - - + -
291C ILE* 3.8 27.8 - - + -
292C SER* 3.1 18.5 + - - +
294C GLU* 1.3 73.6 - - - +
296C GLN* 1.3 66.6 + - - +
298C ALA* 3.1 8.7 + - + -
299C LEU* 2.9 34.8 + - + +
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Residues in contact with GLN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ILE* 3.9 19.4 - - + +
292C SER 2.9 18.7 + - - +
293C GLU* 3.2 9.4 + - - +
295C LEU* 1.3 76.4 - - - +
297C ASP* 1.3 61.1 + - - +
299C LEU* 3.2 4.3 + - - +
300C GLY 3.1 17.7 + - - -
301C VAL* 3.2 29.0 + - + +
304C LYS* 6.0 6.1 - - - -
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Residues in contact with ASP 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 4.6 9.5 - - + +
293C GLU 2.8 19.8 + - - +
294C GLU* 3.7 7.0 - - - +
296C GLN* 1.3 73.3 - - - +
298C ALA* 1.3 61.6 + - - +
300C GLY* 3.3 11.8 + - - +
301C VAL 5.3 0.2 - - - +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.9 18.2 - - + -
74B LYS 3.9 3.3 - - - +
75B LEU* 4.2 6.5 - - + -
76B TYR* 3.0 56.6 + - + -
77B GLY 4.8 0.7 + - - -
294C GLU 3.1 14.4 + - - +
295C LEU* 3.1 15.3 + - + +
297C ASP* 1.3 77.9 - - - +
299C LEU* 1.3 59.7 + - - +
300C GLY 3.6 0.3 + - - -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 5.2 0.7 - - + -
73B ILE* 3.8 21.3 - - + -
74B LYS* 3.5 23.2 - - - +
75B LEU* 3.9 11.7 - - + -
291C ILE* 3.8 28.5 - - + -
295C LEU* 2.9 26.1 + - + +
296C GLN 3.2 0.8 + - - +
298C ALA* 1.3 76.8 - - - +
300C GLY* 1.3 62.2 + - - +
301C VAL* 3.8 15.7 - - + -
308C PRO* 4.4 2.7 - - + -
309C PHE* 4.0 22.9 - - + -
318F TYR* 5.3 0.9 + - - -
322F TRP 4.8 6.6 - - - +
323F LEU* 4.0 27.5 - - + +
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Residues in contact with GLY 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C GLN 3.1 4.6 + - - -
297C ASP* 3.3 8.0 + - - -
298C ALA 3.3 3.8 + - - -
299C LEU* 1.3 81.1 - - - +
301C VAL* 1.3 60.3 + - - +
302C THR* 3.2 8.8 + - - -
285F ARG 4.6 12.3 + - - -
286F PHE* 4.4 6.6 + - - +
318F TYR* 3.5 11.5 + - - -
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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