Contacts of the helix formed by residues 293 - 306 (chain A) in PDB entry 1LMU
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A PRO 3.7 1.4 + - - -
292A PHE* 1.3 76.9 - - - +
294A LEU* 1.3 65.0 + - - +
295A SER* 3.4 7.8 + - - -
296A THR* 2.6 49.7 + - - +
297A LEU* 2.9 7.3 + - - +
331A SER* 3.7 8.1 - - - -
332A ASP* 3.5 27.6 - - - -
333A CYS 4.0 6.5 - - - -
334A ARG* 4.1 8.5 + - - +
384A ILE* 4.1 4.3 - - - -
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Residues in contact with LEU 294 (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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293A SER* 1.3 73.2 - - - +
295A SER* 1.3 58.5 + - - +
297A LEU* 3.2 4.5 + - + +
298A GLN* 2.8 58.5 + - + +
312A VAL* 4.5 4.0 - - + -
313A LEU* 3.7 33.4 - - + -
316A CYS* 4.3 20.6 - - - -
329A PRO 3.3 23.3 - - - +
330A ARG* 4.5 7.0 - - + -
331A SER 3.1 14.2 + - - +
332A ASP* 5.3 0.2 - - - +
384A ILE* 3.8 9.0 - - + +
525A GLU* 3.5 30.3 - - + +
526A ALA 5.6 0.2 - - - +
529A ALA* 6.2 0.2 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER* 3.4 10.4 + - - -
294A LEU* 1.3 78.0 - - - +
296A THR* 1.3 64.1 + - - +
298A GLN* 2.9 15.6 + - - +
299A ILE* 2.7 36.7 + - - +
497A LEU* 3.8 21.5 - - - -
501A THR* 4.0 13.9 + - - +
520A ASP* 5.3 1.0 + - - -
525A GLU* 6.3 0.2 - - - +
528A ARG* 3.8 23.5 + - - +
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Residues in contact with THR 296 (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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292A PHE* 2.8 28.6 - - - -
293A SER* 2.6 49.4 + - - +
295A SER* 1.3 79.9 + - - +
297A LEU* 1.3 61.2 + - - +
299A ILE* 3.3 7.9 + - - +
300A GLU* 3.0 18.7 + - - +
334A ARG* 2.9 40.4 - - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.6 18.8 - - + -
293A SER 2.9 8.1 + - - +
294A LEU* 3.5 9.9 - - + +
296A THR* 1.3 80.9 + - - +
298A GLN* 1.3 58.0 + - - +
300A GLU* 3.1 1.0 + - - -
301A ALA* 2.8 29.1 + - + +
312A VAL* 3.9 15.9 - - + -
316A CYS* 3.5 32.8 - - - -
384A ILE* 4.8 8.5 - - + -
402A VAL* 4.5 5.4 - - + +
405A LEU* 3.0 46.4 - - + -
406A ILE* 4.1 26.5 - - + -
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 2.8 45.8 + - + +
295A SER* 2.9 20.9 + - - +
297A LEU* 1.3 76.6 - - - +
299A ILE* 1.3 59.9 + - + +
301A ALA* 3.3 3.1 + - - +
302A ALA* 2.9 30.7 + - - +
307A LEU 4.6 1.9 - - - +
308A SER 5.7 0.2 - - - +
309A ALA* 3.3 42.0 + - + +
312A VAL* 3.2 26.4 - - + +
313A LEU* 4.7 1.6 - - - +
497A LEU* 3.7 17.1 - - + +
525A GLU 5.4 1.7 + - - +
528A ARG* 5.0 4.4 + - - +
529A ALA* 4.0 11.7 - - - +
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Residues in contact with ILE 299 (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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295A SER* 2.7 38.3 + - - +
296A THR* 3.8 7.9 - - - +
297A LEU 3.2 0.2 - - - -
298A GLN* 1.3 74.2 - - - +
300A GLU* 1.3 64.1 + - - +
302A ALA* 3.2 6.2 + - - +
303A LYS* 3.0 50.9 + - - +
494A ALA* 3.6 27.1 - - + +
497A LEU* 2.9 38.8 - - + -
498A SER* 3.9 16.8 - - - +
501A THR* 4.9 4.0 - - + -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 4.2 11.9 - - + -
296A THR 3.0 16.5 + - - +
299A ILE* 1.3 77.6 - - - +
301A ALA* 1.3 63.3 + - - +
303A LYS* 3.3 21.8 + - - +
304A ARG* 3.1 43.7 + - - +
405A LEU* 3.3 39.3 - - + -
408A ARG* 4.2 10.6 + - - +
454A GLU* 4.3 6.9 - - - +
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Residues in contact with ALA 301 (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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297A LEU 2.8 16.9 + - - +
298A GLN* 3.8 3.4 - - - +
300A GLU* 1.3 76.2 - - - +
302A ALA* 1.3 58.2 + - - +
305A PHE* 2.8 49.4 + - + +
306A GLY 3.2 4.0 + - - -
307A LEU* 3.8 14.5 + - + +
312A VAL* 4.0 23.8 - - + -
402A VAL* 4.8 3.8 - - + -
405A LEU* 3.8 8.2 - - + +
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Residues in contact with ALA 302 (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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298A GLN 2.9 18.2 + - - +
299A ILE* 3.6 4.5 - - - +
301A ALA* 1.3 76.3 - - - +
303A LYS* 1.3 60.7 + - - +
306A GLY* 2.8 26.2 + - - -
307A LEU 3.4 22.4 + - - +
308A SER 5.8 0.2 - - - -
309A ALA 6.0 0.2 - - - +
493A ASP* 3.9 11.0 - - + -
494A ALA* 3.5 29.6 - - - +
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Residues in contact with LYS 303 (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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299A ILE* 3.0 39.3 + - + +
300A GLU* 3.3 22.5 + - - +
302A ALA* 1.3 80.1 - - - +
304A ARG* 1.3 68.4 + - + +
306A GLY* 4.4 0.5 + - - -
494A ALA* 3.5 17.0 - - + -
498A SER* 6.4 0.7 - - - -
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Residues in contact with ARG 304 (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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300A GLU* 3.1 28.3 + - - +
303A LYS* 1.3 85.8 - - + +
305A PHE* 1.3 105.0 - - + +
401A LYS 4.4 3.2 + - - -
404A THR* 5.0 7.7 - - - +
405A LEU* 3.8 33.4 - - - +
408A ARG* 4.1 17.0 - - - +
454A GLU* 4.2 20.8 + - - +
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Residues in contact with PHE 305 (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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301A ALA* 2.8 37.8 + - + +
304A ARG* 1.3 121.3 - - + +
306A GLY* 1.3 59.5 + - - +
307A LEU* 3.6 26.0 - - + +
401A LYS* 3.2 67.6 + - + +
402A VAL* 5.1 1.6 - - + -
405A LEU* 4.9 5.6 - - + -
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Residues in contact with GLY 306 (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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301A ALA 3.2 0.2 + - - -
302A ALA* 2.8 25.0 + - - -
303A LYS 4.4 0.8 + - - -
304A ARG 3.6 0.4 - - - -
305A PHE* 1.3 74.5 - - - +
307A LEU* 1.4 65.5 + - - +
308A SER 3.9 1.0 + - - -
493A ASP* 4.5 9.2 - - - +
543A LYS* 4.9 5.2 + - - -
546A ARG* 6.5 1.3 - - - -
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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