Contacts of the helix formed by residues 363 - 381 (chain A) in PDB entry 5DO7
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 GLY 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A PRO* 1.3 81.6 - - - +
364A VAL* 1.3 53.2 + - - -
365A PHE* 3.1 13.0 - - - -
366A SER* 2.8 16.6 + - - -
367A LYS 2.4 33.3 + - - -
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO 3.6 2.6 + - - +
363A GLY* 1.3 69.8 - - - +
365A PHE* 1.3 68.6 + - + +
367A LYS* 2.8 41.6 + - - +
368A LEU* 3.4 11.3 + - - +
461A TRP* 4.7 10.3 - - + -
462A GLN* 3.4 32.3 - - - +
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY* 4.6 7.0 - - - -
364A VAL* 1.3 89.8 - - + +
366A SER* 1.3 61.2 + - - +
368A LEU* 4.5 5.8 + - - +
369A GLY* 4.3 8.1 + - - -
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY* 2.8 16.1 + - - -
365A PHE* 1.3 81.1 - - - +
367A LYS* 1.3 67.6 + - - +
369A GLY* 3.2 14.4 + - - -
370A VAL* 3.7 3.8 + - - +
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.2 27.4 - - + +
361A SER* 3.3 32.1 + - - -
362A PRO 3.6 8.2 + - - +
363A GLY 2.4 24.6 + - - +
364A VAL* 2.8 25.8 + - + +
366A SER* 1.3 69.1 - - - +
368A LEU* 1.3 57.5 + - - +
370A VAL* 2.6 37.3 - - - +
371A LEU* 6.0 0.2 - - + -
457A LEU 3.8 24.4 + - - +
458A TYR* 4.2 13.3 - - + +
459A GLN 5.9 0.2 - - - +
462A GLN* 4.2 15.0 + - + +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL 3.4 7.4 + - - +
365A PHE* 4.9 6.1 - - - +
367A LYS* 1.3 75.5 - - - +
369A GLY* 1.3 75.1 + - - +
370A VAL 3.0 2.2 - - - -
371A LEU* 2.8 25.9 + - + +
372A LEU* 2.8 16.2 + - + +
461A TRP* 5.0 0.2 - - - +
462A GLN* 3.8 42.0 - - + +
465A LEU* 3.7 32.3 - - + -
466A ALA* 5.3 2.2 - - + -
469A LEU* 4.7 15.3 - - + -
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Residues in contact with GLY 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE 4.3 3.6 + - - -
366A SER 3.2 11.8 + - - -
368A LEU* 1.3 88.2 - - - +
370A VAL* 1.3 60.6 + - - +
372A LEU* 3.3 9.8 + - - +
373A ARG* 3.1 19.2 + - - +
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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
----------------------------------------------------------
150A TYR* 3.8 24.2 - - + +
153A LEU* 3.7 37.2 - - + +
154A LEU* 4.1 29.4 - - + -
366A SER 3.7 4.9 + - - +
367A LYS* 2.6 32.9 + - - +
368A LEU 3.0 1.0 - - - -
369A GLY* 1.3 71.7 - - - +
371A LEU* 1.3 75.4 + - - +
373A ARG* 2.8 19.2 + - + +
374A ARG* 2.8 12.6 + - + +
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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
----------------------------------------------------------
154A LEU* 3.9 20.4 - - + -
367A LYS* 6.0 0.2 - - + -
368A LEU* 2.8 20.8 + - - +
370A VAL* 1.3 78.2 - - + +
372A LEU* 1.3 57.1 + - - +
374A ARG* 3.3 37.4 - - - +
375A VAL* 2.8 34.9 + - - +
458A TYR* 3.2 41.1 - - + -
462A GLN* 3.8 19.3 - - + -
463A MET* 3.9 22.7 - - + +
466A ALA* 4.2 6.1 - - + -
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Residues in contact with LEU 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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368A LEU* 2.8 14.3 + - + +
369A GLY* 3.4 13.7 - - - +
371A LEU* 1.3 72.9 - - - +
373A ARG* 1.3 64.4 + - + +
375A VAL* 2.8 4.3 + - - -
376A THR* 2.7 48.6 + - + +
466A ALA* 4.0 15.8 - - + +
469A LEU* 3.6 35.0 - - + -
470A HIS* 4.0 17.3 - - + +
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Residues in contact with ARG 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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149A HIS* 3.9 20.8 + - - -
150A TYR* 3.1 41.2 + - + +
153A LEU* 4.4 8.7 - - - +
161A PRO* 6.3 0.2 - - - +
369A GLY 3.1 8.2 + - - +
370A VAL* 2.8 16.4 + - - +
372A LEU* 1.3 78.3 - - + +
374A ARG* 1.3 62.9 + - - +
376A THR* 3.1 9.0 + - - +
377A ARG* 2.9 55.7 + - - +
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Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 6.1 1.2 - - - +
139A LEU* 3.1 37.2 - - + +
142A LEU* 4.1 7.5 - - + +
147A THR* 4.2 22.4 + - - +
150A TYR* 3.8 49.0 - - + +
151A THR* 4.3 9.2 + - - +
154A LEU* 5.7 0.8 - - - +
370A VAL 2.8 14.1 + - - +
371A LEU* 3.3 31.7 - - - +
373A ARG* 1.3 72.0 - - - +
375A VAL* 1.3 61.0 + - - +
377A ARG* 2.8 7.1 + - - +
378A ASN* 2.8 27.0 + - - +
448A VAL* 4.7 1.0 - - - +
452A GLU* 2.8 35.1 + - - -
458A TYR* 3.5 16.0 + - - -
463A MET* 4.4 4.4 - - - +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 5.9 1.1 - - + -
371A LEU 2.8 21.4 + - - +
372A LEU* 2.8 11.6 + - - +
374A ARG* 1.3 73.9 - - + +
376A THR* 1.3 66.1 + - - +
377A ARG 3.1 0.3 + - - -
378A ASN* 3.1 8.4 + - + +
379A LEU* 2.8 24.9 + - + +
445A LEU* 3.4 39.7 - - + -
463A MET* 3.9 15.0 - - + -
466A ALA* 4.3 8.5 - - + -
467A TYR* 4.6 2.0 - - - +
470A HIS* 3.2 34.5 - - + +
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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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372A LEU* 2.7 36.1 + - + +
373A ARG* 3.1 14.6 + - - -
375A VAL* 1.3 75.1 - - - +
377A ARG* 1.3 55.1 + - - +
379A LEU* 4.0 5.1 - - - +
380A VAL* 2.8 34.7 + - - +
470A HIS* 3.3 33.2 - - + +
473A PRO* 6.0 2.0 - - + -
474A PHE* 4.5 16.1 - - + -
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Residues in contact with ARG 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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142A LEU* 3.9 4.9 - - + -
146A GLU* 3.7 19.0 + - - +
150A TYR* 3.1 35.3 + - - -
373A ARG* 2.9 46.4 + - - +
374A ARG 2.8 11.7 + - - +
376A THR* 1.3 72.3 - - - +
378A ASN* 1.3 69.8 + - - +
380A VAL* 3.0 24.8 - - + +
381A ARG* 3.0 38.9 + - - +
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Residues in contact with ASN 378 (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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139A LEU* 3.7 40.0 - - + +
140A SER* 4.6 2.4 + - - +
141A SER* 3.1 32.3 + - - +
142A LEU* 3.7 13.3 - - + +
374A ARG 2.8 14.3 + - - +
375A VAL* 3.2 13.2 - - + +
377A ARG* 1.3 76.5 - - - +
379A LEU* 1.3 63.2 + - - +
381A ARG* 2.8 17.8 + - - -
382A ASN* 3.9 8.7 + - - +
444A VAL* 5.3 4.0 - - - +
445A LEU* 4.9 14.8 - - + +
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Residues in contact with LEU 379 (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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375A VAL* 2.8 20.7 + - + +
376A THR* 4.0 4.9 - - - +
378A ASN* 1.3 78.9 - - - +
380A VAL* 1.3 58.2 + - - +
382A ASN* 4.0 11.9 - - - +
385A ALA* 4.7 1.2 - - + +
386A VAL* 2.8 36.3 + - + +
389A ARG* 3.5 25.6 - - - -
441A LEU* 3.3 30.7 - - + -
445A LEU* 6.5 1.1 - - + -
467A TYR* 4.5 0.2 - - + -
470A HIS* 2.8 42.6 - - + +
474A PHE* 3.9 16.4 - - + -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR 2.8 17.3 + - - +
377A ARG* 3.0 27.6 - - + +
378A ASN 3.0 0.2 - - - -
379A LEU* 1.3 76.9 - - - +
381A ARG* 1.3 62.3 + - + +
382A ASN 3.0 11.2 + - - -
383A LYS* 4.7 8.0 + - - +
386A VAL* 3.8 16.3 - - + +
474A PHE* 5.1 12.8 - - + -
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER* 3.5 32.7 + - - +
142A LEU* 4.4 3.0 - - - +
143A THR* 4.3 10.7 - - - +
146A GLU* 2.7 36.0 + - - -
184A LEU* 6.2 2.0 - - + +
377A ARG* 3.0 41.1 + - - +
378A ASN 2.8 10.6 + - - +
380A VAL* 1.3 74.8 - - + +
382A ASN* 1.3 58.0 + - - +
383A LYS* 3.9 17.6 - - - +
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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
------------------------------------------------------------
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