Contacts of the helix formed by residues 292 - 300 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28M GLU* 2.6 35.8 + - - -
291N ILE* 1.3 78.4 - - - +
293N GLU* 1.3 63.2 + - - +
294N GLU* 3.7 6.6 + - - +
295N LEU* 3.2 16.3 + - - +
296N GLN* 3.1 21.7 + - - +
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Residues in contact with GLU 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292N SER* 1.3 73.4 - - - +
294N GLU* 1.3 64.4 + - - +
296N GLN* 5.0 1.1 - - - -
297N ASP* 3.2 28.0 + - - +
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Residues in contact with GLU 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M LEU* 6.0 5.6 - - + -
76M TYR* 4.6 8.8 + - - +
292N SER* 3.3 6.8 + - - +
293N GLU* 1.3 79.0 - - - +
295N LEU* 1.3 60.1 + - - +
297N ASP* 4.6 0.4 - - - +
298N ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M LEU* 5.4 11.4 - - + +
28M GLU* 3.3 29.4 - - - +
29M LEU* 6.1 4.9 - - + -
291N ILE* 4.8 4.3 - - + -
292N SER* 3.2 4.8 + - - +
294N GLU* 1.3 77.3 - - - +
296N GLN* 1.3 66.1 + - - +
298N ALA* 3.3 5.8 + - - +
299N LEU* 3.3 23.4 + - - +
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Residues in contact with GLN 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291N ILE* 3.7 20.5 - - + +
292N SER 3.1 19.8 + - - +
293N GLU* 4.8 1.1 - - - +
295N LEU* 1.3 80.1 - - - +
297N ASP* 1.3 63.1 + - - +
298N ALA 3.4 0.2 + - - -
299N LEU* 3.4 10.6 + - - +
300N GLY 3.7 12.8 + - - +
301N VAL* 5.8 0.5 - - - +
304N LYS* 6.5 0.7 - - + -
308N PRO* 6.3 5.2 - - + -
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Residues in contact with ASP 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N GLU 3.2 20.7 + - - +
294N GLU 4.6 0.2 - - - +
296N GLN* 1.3 79.7 - - - +
298N ALA* 1.3 62.9 + - - +
300N GLY* 3.3 13.2 + - - +
301N VAL* 6.5 0.4 - - - -
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Residues in contact with ALA 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M TYR* 3.5 55.5 - - + +
294N GLU 3.0 22.5 + - - +
295N LEU* 3.7 6.3 - - - +
296N GLN 3.2 0.6 - - - -
297N ASP* 1.3 79.6 - - - +
299N LEU* 1.3 60.4 + - - +
300N GLY* 3.3 1.6 + - - -
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Residues in contact with LEU 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322J TRP 5.7 0.5 - - - +
323J LEU* 5.9 6.9 - - - -
73M ILE* 6.2 2.9 - - + -
74M LYS 4.7 17.0 - - - +
75M LEU* 5.9 0.7 - - - +
76M TYR 5.3 1.3 - - - +
295N LEU 3.3 12.2 + - - +
296N GLN* 4.0 5.8 - - - +
297N ASP 3.3 0.6 - - - -
298N ALA* 1.3 78.7 - - - +
300N GLY* 1.3 61.2 + - - +
308N PRO* 6.4 2.9 - - + -
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Residues in contact with GLY 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286J PHE* 6.2 0.4 - - - -
296N GLN 3.7 9.5 + - - +
297N ASP* 3.3 12.1 + - - -
298N ALA 3.2 4.9 - - - -
299N LEU* 1.3 82.7 - - - +
301N VAL* 1.3 65.4 + - - +
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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