Contacts of the helix formed by residues 332 - 343 (chain A) in PDB entry 5LLU
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 ILE 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.4 16.9 + - + +
329A ILE* 3.5 8.3 - - + +
331A GLY* 1.3 71.5 - - - +
333A LEU* 1.3 61.2 + - - +
334A GLN 3.3 2.7 - - - -
335A ALA* 3.2 15.9 + - + +
336A LEU* 3.3 38.7 + - + +
352A THR* 4.8 2.9 - - + +
355A CYS* 3.7 20.9 - - + -
356A LEU* 3.7 27.4 - - + +
360A ASN* 3.5 19.1 - - - +
464A VAL* 5.4 2.2 - - + -
465A LEU* 3.9 12.3 - - + -
468A ALA* 3.7 26.9 - - + -
469A LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 333 (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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51A LEU* 3.7 29.4 - - + -
55A VAL* 5.2 2.7 - - + -
329A ILE* 3.0 25.6 + - + +
330A ALA* 3.4 22.2 - - + +
331A GLY 3.2 2.6 - - - -
332A ILE* 1.3 77.4 - - - +
334A GLN* 1.4 60.6 + - - +
336A LEU* 3.4 18.6 + - + +
337A ILE* 3.2 42.7 + - + +
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Residues in contact with GLN 334 (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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50A LEU* 3.7 38.4 - - - +
51A LEU* 3.8 32.0 - - + +
54A THR* 4.6 10.9 - - + +
266A MET* 4.1 21.4 - - + +
331A GLY 4.4 0.7 + - - +
332A ILE 3.3 0.6 - - - -
333A LEU* 1.4 75.7 - - - +
335A ALA* 1.4 51.2 + - - +
337A ILE* 3.7 7.5 + - - +
338A THR* 2.9 40.0 + - + +
351A ILE* 4.1 3.1 - - + -
355A CYS* 3.8 10.3 - - - -
359A ASN* 3.0 32.1 + - - +
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Residues in contact with ALA 335 (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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332A ILE* 3.2 12.5 + - + +
334A GLN* 1.4 76.2 - - - +
336A LEU* 1.3 58.5 + - - +
338A THR* 3.1 16.3 + - - -
339A ALA* 3.1 18.2 + - - +
348A THR* 4.3 4.9 - - - -
351A ILE* 3.6 8.9 - - + +
352A THR* 3.6 44.6 - - + +
355A CYS* 3.8 7.2 - - + -
464A VAL* 4.3 6.3 - - + +
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Residues in contact with LEU 336 (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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329A ILE* 4.0 12.8 - - + -
332A ILE* 3.3 32.2 + - + +
333A LEU* 3.4 28.5 + - + +
334A GLN 3.4 0.2 - - - -
335A ALA* 1.3 75.2 - - - +
337A ILE* 1.4 58.4 + - + +
338A THR 3.3 0.2 - - - -
339A ALA* 3.1 5.1 + - - -
340A LEU 3.0 23.7 + - - -
461A MET* 3.3 55.8 - - + +
464A VAL* 4.2 6.1 - - + -
465A LEU* 3.8 24.2 - - + +
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Residues in contact with ILE 337 (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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51A LEU* 4.7 2.0 - - + +
54A THR* 3.4 40.8 - - + +
55A VAL* 3.8 31.6 - - + -
58A VAL* 3.8 15.5 - - + -
273A ILE* 4.2 11.5 - - + +
333A LEU* 3.2 34.6 + - + +
334A GLN* 4.1 5.8 - - - +
335A ALA 3.5 0.2 - - - -
336A LEU* 1.4 76.1 - - + +
338A THR* 1.4 60.8 + - + +
340A LEU* 3.4 13.7 - - + +
341A GLY* 3.3 15.9 + - - -
461A MET* 4.6 5.2 - - + -
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Residues in contact with THR 338 (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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54A THR* 5.5 3.1 - - + -
88A LEU* 5.4 1.8 - - + -
92A LEU* 5.5 1.6 - - + -
269A ALA* 4.4 11.4 - - + -
273A ILE* 3.7 27.6 - - + -
334A GLN* 2.9 21.0 + - + +
335A ALA* 3.1 17.5 + - - -
337A ILE* 1.4 74.9 - - + +
339A ALA* 1.4 57.9 + - - +
341A GLY* 3.3 0.9 + - - -
342A THR* 2.9 34.6 + - - +
348A THR* 3.3 16.7 - - - +
351A ILE* 3.8 27.1 - - + +
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Residues in contact with ALA 339 (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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335A ALA 3.1 16.1 + - - +
336A LEU* 3.1 10.8 + - - +
338A THR* 1.4 73.1 - - - +
340A LEU* 1.3 59.4 + - - +
342A THR* 3.9 1.8 - - - -
343A SER* 2.9 29.1 + - - -
348A THR* 3.5 10.7 - - - +
457A ARG 3.9 2.3 - - - +
460A THR* 3.6 24.1 - - + +
461A MET* 4.0 12.6 - - + -
464A VAL* 3.9 16.6 - - + -
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Residues in contact with LEU 340 (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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58A VAL* 3.8 39.7 - - + -
277A ILE* 4.3 9.7 - - + +
336A LEU 3.0 5.8 + - - +
337A ILE* 3.4 13.9 - - + +
338A THR 3.3 0.2 - - - -
339A ALA* 1.3 77.0 - - - +
341A GLY* 1.3 57.9 + - - +
454A LEU* 6.2 1.3 - - + -
457A ARG* 3.0 54.1 + - + +
458A PHE* 3.8 24.9 - - + -
461A MET* 3.5 30.2 - - + +
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Residues in contact with GLY 341 (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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89A MET* 5.2 0.2 - - - +
273A ILE* 4.2 12.6 - - - -
276A LEU* 3.4 18.5 - - - +
277A ILE* 3.7 19.7 - - - -
337A ILE 3.3 7.5 + - - -
338A THR 3.3 6.1 + - - -
340A LEU* 1.3 79.5 - - - +
342A THR* 1.3 56.4 + - - +
457A ARG* 2.8 25.6 + - - -
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Residues in contact with THR 342 (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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88A LEU* 5.5 0.9 - - + -
89A MET* 3.4 45.0 - - + +
92A LEU* 4.2 17.9 - - + -
273A ILE* 5.0 3.8 - - + -
276A LEU* 3.9 9.4 - - + -
338A THR* 2.9 24.0 + - - +
339A ALA 3.8 1.6 + - - -
341A GLY* 1.3 70.7 - - - +
343A SER* 1.4 70.1 + - - +
344A SER* 3.2 18.7 + - - -
347A ALA* 4.5 3.8 - - + -
348A THR* 3.2 22.7 - - + +
424A PRO* 4.2 6.4 - - - +
457A ARG* 4.1 4.0 + - - -
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Residues in contact with SER 343 (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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339A ALA 2.9 18.0 + - - -
340A LEU 4.3 0.2 + - - -
341A GLY 3.6 0.8 - - - -
342A THR* 1.4 80.0 + - - +
344A SER* 1.3 52.0 + - - +
424A PRO* 3.3 14.0 - - - +
456A ASP* 2.7 45.6 + - - +
457A ARG* 3.2 27.2 + - - -
460A THR* 3.4 9.4 - - - -
602A ASP 2.8 26.9 + - - -
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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