Contacts of the helix formed by residues 335 - 346 (chain E) in PDB entry 5LK5
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 ASP 335 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E PRO* 3.7 33.4 - - + +
92E VAL* 4.1 3.5 - - - +
333E THR* 3.5 11.8 + - - +
334E ASN* 1.3 81.6 - - - +
336E GLU* 1.3 60.8 + - - +
337E ALA* 3.6 11.3 - - - +
338E TYR* 3.0 29.1 + - + +
339E ALA* 3.0 24.1 + - - +
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Residues in contact with GLU 336 (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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90E THR* 4.2 13.1 + - + +
92E VAL* 4.0 8.2 - - + +
175E ILE* 3.6 35.8 - - + +
177E ARG* 2.7 46.2 + - - +
183E GLU* 4.4 1.9 - - - +
185E LYS* 5.3 8.3 + - - +
334E ASN 4.2 0.4 + - - -
335E ASP* 1.3 69.7 - - - +
337E ALA* 1.3 66.7 + - - +
339E ALA* 3.4 5.3 + - - +
340E GLU* 3.1 23.0 + - - +
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Residues in contact with ALA 337 (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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335E ASP* 3.3 11.1 + - - +
336E GLU* 1.3 79.3 - - - +
338E TYR* 1.3 56.8 + - - +
340E GLU* 3.2 10.0 + - - +
341E GLU* 3.0 39.7 + - - +
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Residues in contact with TYR 338 (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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19E PRO* 4.2 18.2 - - + -
21E VAL* 4.0 23.5 - - + +
24E LYS* 2.6 27.1 + - - -
331E LEU* 4.1 21.8 - - + -
333E THR* 4.0 15.0 - - - -
335E ASP* 3.0 29.6 + - + +
336E GLU 3.3 0.6 - - - -
337E ALA* 1.3 72.6 - - - +
339E ALA* 1.3 67.2 + - - +
341E GLU* 3.1 26.8 + - + +
342E PHE* 2.9 32.5 + + + +
345E GLU* 5.3 5.6 + - - -
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Residues in contact with ALA 339 (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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92E VAL* 3.6 31.4 - - + -
94E GLN* 3.0 23.8 + - - +
173E THR* 4.8 2.7 - - + -
175E ILE* 6.1 0.4 - - + -
331E LEU* 3.8 15.9 - - + -
333E THR* 4.1 4.7 - - + -
335E ASP 3.0 12.1 + - - +
336E GLU* 3.5 10.1 - - - +
338E TYR* 1.3 77.5 - - - +
340E GLU* 1.3 56.3 + - - +
342E PHE 3.4 0.2 + - - -
343E GLY* 2.9 23.7 + - - -
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Residues in contact with GLU 340 (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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185E LYS* 3.7 19.7 + - - +
188E ASN* 3.1 43.9 + - - +
336E GLU 3.1 14.0 + - - +
337E ALA* 3.2 11.8 + - - +
339E ALA* 1.3 73.3 - - - +
341E GLU* 1.3 66.3 + - + +
344E ASN* 3.0 32.0 + - - +
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Residues in contact with GLU 341 (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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335E ASP* 5.6 0.2 - - - +
337E ALA* 3.0 28.3 + - - +
338E TYR* 3.4 29.5 + - + +
340E GLU* 1.3 77.2 - - + +
342E PHE* 1.3 63.0 + - - +
344E ASN* 3.1 9.4 + - - +
345E GLU* 3.0 34.1 + - - +
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Residues in contact with PHE 342 (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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24E LYS* 3.5 36.6 - - + -
26E GLN* 3.7 37.9 - - + -
94E GLN* 4.1 6.7 - - - -
329E ASN* 3.9 15.9 - - + -
330E PHE 4.1 3.8 - - - -
331E LEU* 3.7 39.9 - - + -
338E TYR* 2.9 26.5 + - + +
339E ALA 3.8 2.9 - - - +
341E GLU* 1.3 73.2 - - - +
343E GLY* 1.3 58.5 + - - +
345E GLU* 3.2 15.7 + - + -
346E THR* 2.7 54.0 + - + +
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Residues in contact with GLY 343 (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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94E GLN* 3.5 15.4 - - - +
171E LEU* 3.8 17.7 - - - -
188E ASN* 3.9 5.8 - - - -
339E ALA 2.9 12.8 + - - -
340E GLU 3.7 2.5 - - - -
341E GLU 3.2 0.4 - - - -
342E PHE* 1.3 77.3 - - - +
344E ASN* 1.3 56.6 + - - +
346E THR* 3.6 6.1 - - - -
347E TRP* 3.1 15.1 + - - +
348E GLY 3.0 20.1 + - - -
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Residues in contact with ASN 344 (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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188E ASN* 2.9 21.9 + - - +
340E GLU* 3.0 26.2 + - - +
341E GLU* 3.1 9.2 + - - +
343E GLY* 1.3 77.4 - - - +
345E GLU* 1.3 59.7 + - + +
346E THR 3.3 0.2 - - - -
347E TRP* 4.0 13.0 - - - -
348E GLY* 3.4 25.2 - - - +
349E VAL* 3.6 5.5 + - - +
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Residues in contact with GLU 345 (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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338E TYR* 5.3 5.5 + - - -
341E GLU* 3.0 26.1 + - - +
342E PHE* 3.2 21.7 + - + +
344E ASN* 1.3 77.5 - - + +
346E THR* 1.3 64.5 + - + +
349E VAL* 3.4 21.1 - - - +
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Residues in contact with THR 346 (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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26E GLN* 3.9 6.5 - - - +
171E LEU* 4.8 3.8 - - - +
329E ASN* 3.4 41.3 - - - +
342E PHE* 2.7 49.2 + - + +
343E GLY* 3.3 7.6 + - - -
344E ASN 3.3 0.2 - - - -
345E GLU* 1.3 82.2 - - + +
347E TRP* 1.3 74.0 + - - +
348E GLY 3.2 0.2 - - - -
349E VAL* 3.0 13.3 + - - +
350E THR* 3.0 19.4 + - - -
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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