Contacts of the helix formed by residues 296 - 305 (chain E) in PDB entry 1LT9
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 ASN 296 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E TRP* 5.9 0.2 - - - -
269E TYR 2.9 19.1 + - - +
270E LYS* 3.5 1.9 + - - -
293E TRP* 2.8 37.0 - - - +
295E GLY* 1.3 67.6 - - - -
297E ASP* 1.3 67.0 + - - +
299E ILE* 3.9 5.2 - - - +
300E SER* 2.9 26.5 + - - -
331E VAL* 5.2 2.3 - - + +
338E TYR* 3.4 42.4 - - + +
375E PHE* 3.4 34.9 - - - -
403E TRP* 5.2 3.6 - - - -
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Residues in contact with ASP 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E LYS* 3.0 43.6 + - - +
271E GLN* 4.8 4.3 + - - +
296E ASN* 1.3 76.1 - - - +
298E LYS* 1.3 66.4 + - + +
300E SER* 3.7 4.2 - - - -
301E GLN* 3.1 22.9 + - - +
334E GLU* 4.2 5.0 + - - +
338E TYR* 2.6 32.1 + - - -
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Residues in contact with LYS 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E VAL* 6.2 3.1 - - + -
236E TYR* 3.4 66.2 + - + +
237E ARG 5.3 0.6 + - - -
270E LYS 4.9 0.6 + - - +
271E GLN 4.4 12.2 + - - +
294E LEU* 3.6 29.1 + - + +
295E GLY* 3.0 9.0 + - - +
297E ASP* 1.3 78.0 - - + +
299E ILE* 1.3 65.8 + - - +
301E GLN* 3.2 7.7 + - - +
302E LEU* 3.1 28.6 + - - +
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Residues in contact with ILE 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E ILE* 4.0 49.1 - - + +
293E TRP* 3.6 38.1 - - + -
294E LEU* 4.2 7.9 - - + -
295E GLY 2.8 28.8 + - - +
296E ASN* 3.9 6.5 - - - +
298E LYS* 1.3 71.0 - - - +
300E SER* 1.3 63.8 + - - +
302E LEU* 3.2 9.3 + - - +
303E THR* 3.1 28.6 + - + +
329E PHE* 4.5 2.0 - - + -
331E VAL* 4.0 22.7 - - + -
403E TRP* 5.4 3.1 - - + -
454E ILE* 5.5 1.1 - - + -
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Residues in contact with SER 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E ASN 2.9 18.6 + - - -
297E ASP* 3.7 6.3 - - - -
299E ILE* 1.3 76.1 - - - +
301E GLN* 1.3 60.5 - - - +
303E THR* 3.1 6.2 + - - -
304E ARG* 3.1 29.7 - - - +
331E VAL* 2.6 31.6 + - - +
332E GLN* 3.2 20.7 - - - -
333E ASN* 3.2 11.8 + - - +
338E TYR* 4.6 1.6 - - - -
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Residues in contact with GLN 301 (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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229E PRO* 3.2 33.4 - - - +
230E ASP* 3.5 28.4 - - + +
233E VAL* 5.9 2.7 - - + +
236E TYR* 4.7 1.0 + - - -
297E ASP 3.1 17.2 + - - +
298E LYS* 3.6 6.1 + - - +
299E ILE 3.2 0.4 - - - -
300E SER* 1.3 75.6 - - - +
302E LEU* 1.3 71.5 + - - +
304E ARG* 3.6 4.3 + - - +
305E MET* 3.1 37.6 + - - +
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Residues in contact with LEU 302 (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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209E LYS 4.1 8.7 - - - +
210E GLU* 4.2 16.6 - - + -
227E ILE* 4.5 3.4 - - + -
229E PRO* 3.6 27.4 - - + -
236E TYR* 3.7 17.0 - - - +
250E THR* 4.5 9.2 - - + -
294E LEU* 3.9 19.7 - - + -
298E LYS 3.1 16.2 + - - +
299E ILE* 3.2 5.6 + - - +
301E GLN* 1.3 76.6 - - - +
303E THR* 1.3 66.4 + - - +
305E MET* 3.1 24.2 + - - +
306E GLY 4.2 0.3 + - - -
308E THR* 3.5 7.7 + - - +
454E ILE* 3.7 30.7 - - + -
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Residues in contact with THR 303 (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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299E ILE* 3.1 15.6 + - + +
300E SER 3.1 10.2 + - - -
302E LEU* 1.3 75.7 - - - +
304E ARG* 1.3 60.9 + - - +
306E GLY 3.0 20.6 - - - +
308E THR* 3.2 15.2 + - + -
329E PHE* 3.5 39.7 - - + +
330E THR* 3.4 29.1 - - - +
331E VAL* 3.0 25.1 + - + +
454E ILE* 4.9 4.0 - - + -
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Residues in contact with ARG 304 (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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300E SER* 3.1 29.9 + - - +
301E GLN* 3.9 5.4 - - - +
302E LEU 3.2 0.6 - - - -
303E THR* 1.3 79.4 + - - +
305E MET* 1.3 65.4 + - - +
306E GLY* 3.1 5.0 + - - -
330E THR* 5.2 4.3 - - + -
331E VAL 4.0 4.5 - - - +
332E GLN* 3.5 30.7 + - - +
333E ASN* 4.2 23.6 - - - +
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Residues in contact with MET 305 (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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209E LYS* 3.1 44.2 - - + +
210E GLU* 4.9 6.5 - - + -
229E PRO* 3.0 44.2 - - - +
301E GLN* 3.1 32.6 + - - +
302E LEU* 3.1 19.1 + - - +
304E ARG* 1.3 77.6 - - - +
306E GLY* 1.3 56.3 + - - +
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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