Contacts of the helix formed by residues 363 - 377 (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 ASP 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLY 3.9 0.2 + - - -
362A VAL* 1.4 72.7 - - - +
364A LYS* 1.3 61.7 + - - +
365A ARG* 2.9 62.9 + - - +
366A ILE* 3.3 15.3 + - + +
367A THR* 3.0 28.5 + - - +
475A GLU* 3.1 15.8 + - - +
482A LEU* 4.0 17.3 - - + +
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Residues in contact with LYS 364 (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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255A ASN* 4.7 4.9 - - - -
256A GLU* 3.9 23.5 + - - -
259A MET* 5.5 3.2 - - - +
357A GLU* 2.9 48.2 + - + +
358A GLU* 6.3 0.6 - - - +
362A VAL 3.8 1.6 + - - +
363A ASP* 1.3 74.9 + - - +
365A ARG* 1.4 57.9 + - + +
367A THR* 3.4 7.2 - - - -
368A ARG* 3.0 70.2 + - - +
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Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 4.2 8.6 - - - +
110A SER* 4.6 18.2 - - - -
111A LEU* 3.9 38.4 - - + +
119A LEU* 5.6 0.2 - - - +
363A ASP* 2.9 32.8 + - - +
364A LYS* 1.4 77.6 - - + +
366A ILE* 1.4 57.9 + - - +
368A ARG* 4.5 8.9 + - - +
369A PHE* 4.7 7.1 + - - +
482A LEU* 3.4 33.2 - - + +
485A GLN* 3.5 29.3 + - - +
486A ASP* 2.8 36.3 + - - -
489A LEU* 5.2 4.8 - - - +
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Residues in contact with ILE 366 (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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111A LEU* 6.0 0.4 - - + -
119A LEU* 3.7 31.9 - - + -
362A VAL* 3.5 17.9 - - + -
363A ASP* 3.3 12.7 + - + +
364A LYS 3.1 0.4 - - - -
365A ARG* 1.4 80.3 - - - +
367A THR* 1.4 58.4 + - - +
368A ARG 3.3 1.6 - - - -
369A PHE* 3.4 4.1 + - - +
370A VAL* 3.0 36.2 + - + +
471A ALA* 3.2 37.5 - - + +
474A VAL* 5.4 0.2 - - + -
475A GLU* 3.6 23.8 - - + +
478A SER* 5.2 0.2 - - - -
482A LEU* 4.0 31.0 - - + -
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Residues in contact with THR 367 (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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353A PHE* 3.5 4.6 - - - -
356A LEU* 4.1 18.2 - - + -
357A GLU* 3.2 27.2 + - + +
362A VAL* 3.7 28.9 - - + -
363A ASP 3.0 21.1 + - - +
364A LYS* 3.3 5.6 + - - -
366A ILE* 1.4 71.7 - - - +
368A ARG* 1.3 64.7 + - - +
369A PHE 3.1 2.2 - - - -
370A VAL* 4.8 1.8 - - - -
371A LEU* 3.2 43.2 + - + +
372A PRO* 3.4 1.4 - - - +
471A ALA* 4.2 8.1 - - + -
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Residues in contact with ARG 368 (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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103A SER* 3.3 35.3 - - - +
104A LEU* 3.6 8.4 - - - +
106A THR* 2.9 28.8 + - - -
107A GLY* 4.0 13.9 - - - +
110A SER* 5.3 1.6 + - - -
252A ASN* 2.8 36.5 + - - +
255A ASN* 3.2 31.2 + - - +
256A GLU* 4.9 3.2 - - - +
353A PHE* 4.1 13.5 - - + -
357A GLU* 4.8 1.3 + - - +
364A LYS* 3.0 52.2 + - - +
365A ARG* 4.7 3.1 - - - +
366A ILE 3.3 0.2 - - - -
367A THR* 1.3 76.6 - - - +
369A PHE* 1.4 56.5 + - - +
372A PRO* 3.3 17.5 - - - +
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Residues in contact with PHE 369 (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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104A LEU* 3.9 6.1 - - + -
107A GLY 5.6 4.9 - - - +
108A LEU* 3.7 38.1 - - + -
111A LEU* 6.1 2.9 - - + -
116A SER 5.7 2.0 - - - -
119A LEU* 4.6 14.8 - - + -
120A GLY* 3.7 31.9 - - - -
123A ALA* 3.7 19.1 - - + -
124A VAL* 5.7 4.5 - - + -
127A TYR* 5.3 0.2 - + - -
231A ILE* 4.5 9.9 - - + -
365A ARG 4.7 8.5 + - - +
366A ILE* 3.4 7.3 + - - +
367A THR 3.1 0.2 - - - -
368A ARG* 1.4 79.2 - - - +
370A VAL* 1.4 72.7 + - + +
371A LEU 3.5 0.7 - - - -
372A PRO* 3.4 1.6 - - - +
373A VAL* 3.3 50.8 + - + +
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Residues in contact with VAL 370 (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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119A LEU* 5.8 0.9 - - + -
123A ALA* 4.5 3.8 - - + -
127A TYR* 2.6 35.6 + - + +
366A ILE* 3.0 22.1 + - + +
367A THR* 4.8 0.2 - - - -
369A PHE* 1.4 83.1 - - + +
371A LEU* 1.4 53.5 + - - +
374A GLY* 2.8 21.3 + - - -
467A ASP* 3.7 12.9 - - - +
470A GLY* 4.0 4.7 - - - -
471A ALA* 3.5 35.7 - - + +
474A VAL* 4.1 33.2 - - + -
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Residues in contact with LEU 371 (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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349A LEU* 3.3 18.6 - - + +
352A THR* 3.8 22.9 - - + +
353A PHE* 3.7 45.1 - - + +
356A LEU* 3.7 34.3 - - + -
367A THR* 3.2 29.4 + - + +
370A VAL* 1.4 76.5 - - - +
372A PRO* 1.4 57.4 - - + +
375A ALA 3.0 24.6 + - - -
467A ASP* 4.1 24.8 - - + +
471A ALA* 5.3 1.1 - - + -
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Residues in contact with PRO 372 (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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100A ILE* 4.5 13.8 - - + +
103A SER* 4.1 9.0 - - - -
104A LEU* 3.9 21.8 - - + -
223A ILE* 5.5 1.2 - - - +
227A VAL* 4.1 7.6 - - - +
349A LEU* 4.1 15.9 - - + +
353A PHE* 3.8 16.8 - - + -
367A THR 3.4 13.2 - - - +
368A ARG 3.3 22.4 - - - +
369A PHE 3.4 7.2 - - - +
371A LEU* 1.4 89.2 - - + +
373A VAL* 1.4 59.3 + - - +
375A ALA* 3.6 11.6 + - - +
376A THR* 3.7 11.8 - - - +
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Residues in contact with VAL 373 (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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104A LEU* 3.9 7.6 - - + -
124A VAL* 6.1 2.0 - - + -
127A TYR* 3.6 23.3 - - + +
227A VAL* 4.1 6.7 - - + -
231A ILE* 3.9 29.2 - - + -
369A PHE* 3.3 38.8 + - + +
372A PRO* 1.4 72.6 - - - +
374A GLY* 1.3 60.2 + - - +
376A THR* 3.2 8.9 + - - +
377A ILE* 3.0 44.3 + - + +
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Residues in contact with GLY 374 (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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127A TYR* 3.3 15.8 + - - -
370A VAL 2.8 24.1 + - - -
373A VAL* 1.3 73.2 - - - +
375A ALA* 1.3 56.3 + - - +
378A ASN* 2.9 36.6 + - - +
467A ASP* 3.1 21.1 - - - +
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Residues in contact with ALA 375 (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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223A ILE* 6.2 2.9 - - + -
345A SER* 3.5 26.5 + - - +
346A SER* 4.8 7.8 - - - -
349A LEU* 3.8 23.3 - - + -
371A LEU 3.0 18.4 + - - +
372A PRO 3.7 7.4 - - - +
373A VAL 3.2 0.4 - - - -
374A GLY* 1.3 75.6 - - - +
376A THR* 1.4 56.5 + - - +
379A MET* 3.2 18.1 - - - +
422A GLY* 3.9 5.9 - - - -
467A ASP* 3.3 9.3 + - - +
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Residues in contact with THR 376 (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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223A ILE* 4.7 14.6 - - - +
224A LEU* 4.2 24.8 + - + +
227A VAL* 4.2 21.3 - - + -
372A PRO 3.7 11.2 - - - +
373A VAL* 3.4 15.3 - - + +
375A ALA* 1.4 79.6 - - - +
377A ILE* 1.4 62.6 + - + +
379A MET* 3.9 3.1 - - - -
418A ILE 3.2 8.5 + - - +
420A ALA 3.3 7.4 + - - +
421A ALA* 5.5 1.6 - - - -
422A GLY 5.1 4.2 + - - +
601A NA 2.2 26.9 - - - -
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Residues in contact with ILE 377 (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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124A VAL* 5.3 9.4 - - + -
127A TYR* 3.6 30.3 - - + -
131A THR* 4.7 2.3 - - - +
224A LEU* 5.2 10.3 - - + -
373A VAL* 3.0 31.7 + - + +
376A THR* 1.4 93.1 - - + +
378A ASN* 1.4 62.7 + - - +
379A MET 3.2 7.7 + - - -
417A SER* 3.5 8.7 + - - +
418A ILE* 3.7 39.6 - - + +
601A NA 3.5 8.4 - - - -
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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