Contacts of the helix formed by residues 365 - 381 (chain A) in PDB entry 2EIT
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ASP* 3.8 21.0 + - - -
363A VAL* 3.3 2.9 + - - +
364A VAL* 1.3 83.8 - - - +
366A ALA* 1.3 60.6 + - - +
367A GLU* 3.5 8.1 + - - +
368A GLN* 3.0 29.0 + - - +
369A GLU* 2.9 28.9 + - - +
397A TYR* 3.6 14.7 - - - -
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Residues in contact with ALA 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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365A SER* 1.3 73.2 - - - +
367A GLU* 1.3 56.4 + - - +
369A GLU* 3.3 7.3 + - - +
370A ARG* 2.9 29.5 + - - +
397A TYR* 3.4 36.1 + - + +
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Residues in contact with GLU 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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365A SER* 3.2 8.0 + - - +
366A ALA* 1.3 76.2 - - - +
368A GLN* 1.3 67.6 + - + +
370A ARG* 2.8 45.4 + - - +
371A LYS* 3.0 41.9 + - + +
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Residues in contact with GLN 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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183A TRP* 3.9 24.4 + - + +
320A GLN* 4.6 0.6 + - - +
363A VAL* 4.2 5.2 - - + -
364A VAL* 3.5 26.2 - - + +
365A SER* 3.0 28.9 + - - +
367A GLU* 1.3 77.6 - - + +
369A GLU* 1.3 62.8 + - - +
371A LYS* 3.1 35.5 + - - +
372A VAL* 2.9 31.8 + - + +
418A ILE 4.6 4.6 + - - -
419A PHE* 4.1 26.1 + - - +
1518A NAD 5.0 3.5 + - - -
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Residues in contact with GLU 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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363A VAL* 3.6 14.7 - - + +
365A SER 2.9 13.8 + - - +
366A ALA* 3.4 10.7 - - - +
368A GLN* 1.3 75.8 - - - +
370A ARG* 1.3 59.4 + - - +
372A VAL* 3.3 1.0 + - - +
373A LEU* 2.9 48.3 + - + +
391A ARG* 3.5 33.6 + - - +
396A GLY 4.2 2.4 - - - +
397A TYR* 3.3 43.8 - - + -
398A PHE 4.0 1.7 + - - -
399A ILE* 4.2 13.5 - - + -
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Residues in contact with ARG 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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366A ALA 2.9 18.6 + - - +
367A GLU* 2.8 40.0 + - - +
369A GLU* 1.3 78.5 + - - +
371A LYS* 1.3 68.5 + - - +
373A LEU* 3.3 7.1 + - - +
374A SER* 2.9 43.7 + - - -
391A ARG* 6.1 0.7 - - - +
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Residues in contact with LYS 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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367A GLU* 3.0 33.4 + - + +
368A GLN* 3.1 33.8 + - - +
370A ARG* 1.3 92.1 - - - +
372A VAL* 1.3 68.3 + - + +
374A SER* 3.2 8.2 + - - -
375A TYR* 3.0 39.0 + - + -
418A ILE 5.5 2.2 - - - +
1518A NAD 5.9 0.6 + - - -
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Residues in contact with VAL 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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363A VAL* 4.8 5.8 - - + -
368A GLN* 2.9 26.2 + - - +
371A LYS* 1.3 75.1 - - + +
373A LEU* 1.3 62.4 + - - +
375A TYR* 3.2 3.8 + - - +
376A ILE* 3.0 26.9 + - + +
399A ILE* 3.6 26.5 - - + -
418A ILE* 3.9 28.5 - - + +
419A PHE 4.1 4.5 - - - +
420A GLY* 4.0 12.3 - - - -
421A PRO* 4.1 9.9 - - + -
422A VAL* 4.0 24.9 - - + -
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Residues in contact with LEU 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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369A GLU* 2.9 30.6 + - + +
370A ARG* 3.9 5.6 - - - +
372A VAL* 1.3 76.1 - - - +
374A SER* 1.3 61.0 + - - +
376A ILE* 3.2 23.9 + - + +
377A GLU* 3.1 27.6 + - - +
389A GLY 5.3 1.3 - - - +
390A LYS* 4.3 4.5 - - - -
391A ARG* 3.2 66.9 - - + +
399A ILE* 4.3 11.2 - - + -
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Residues in contact with SER 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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370A ARG* 2.9 32.5 + - - -
371A LYS* 3.4 10.1 - - - -
373A LEU* 1.3 76.1 - - - +
375A TYR* 1.3 57.5 + - - +
377A GLU* 3.2 9.2 + - - +
378A ILE* 3.0 38.2 + - - +
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Residues in contact with TYR 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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371A LYS* 3.0 31.5 + - + -
372A VAL 3.6 7.6 - - - +
374A SER* 1.3 74.7 - - - +
376A ILE* 1.3 61.1 + - - +
378A ILE* 3.3 16.2 + - + +
379A GLY 2.8 24.4 + - - -
404A PHE* 4.9 0.4 - - - -
412A ARG* 4.3 15.7 + - + -
413A ILE* 3.6 17.1 - - + +
416A GLU* 2.6 47.3 + - + +
417A GLU 4.2 7.0 + - - -
418A ILE* 3.5 53.6 - - + -
422A VAL* 6.0 0.4 - - - -
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Residues in contact with ILE 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 VAL* 3.0 32.6 + - + +
373A LEU* 3.2 26.2 + - + +
375A TYR* 1.3 76.8 - - - +
377A GLU* 1.3 60.8 + - - +
379A GLY 3.2 0.9 + - - -
380A LYS* 3.0 39.0 + - - +
389A GLY* 3.6 32.5 - - - +
399A ILE* 4.2 8.1 - - + -
402A THR* 4.0 23.8 - - + +
404A PHE* 3.4 16.3 - - + -
422A VAL* 4.0 17.7 - - + -
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Residues in contact with GLU 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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373A LEU* 3.1 16.5 + - + +
374A SER* 3.2 10.3 + - - +
376A ILE* 1.3 77.5 - - - +
378A ILE* 1.3 65.1 - - + +
380A LYS* 2.9 51.7 + - - +
381A ASN* 3.7 12.5 + - - +
389A GLY 4.9 0.9 - - - +
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Residues in contact with ILE 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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374A SER* 3.0 25.2 + - - +
375A TYR* 3.5 22.9 - - + +
377A GLU* 1.3 75.9 - - + +
379A GLY* 1.3 63.7 + - - +
381A ASN* 3.0 17.3 + - - +
382A GLU* 3.4 36.6 + - + +
412A ARG* 3.5 45.1 - - + +
413A ILE* 4.4 4.3 - - + -
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Residues in contact with GLY 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 TYR 2.8 17.9 + - - -
376A ILE 3.2 4.6 + - - -
378A ILE* 1.3 69.8 - - - +
380A LYS* 1.3 54.4 + - - +
381A ASN 3.0 5.2 - - - -
382A GLU* 2.9 3.7 + - - -
383A GLY 2.9 31.4 + - - +
404A PHE* 3.3 17.2 - - - -
413A ILE* 3.7 22.9 - - - -
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Residues in contact with LYS 380 (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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376A ILE* 3.0 24.1 + - - +
377A GLU* 2.9 44.8 + - - +
378A ILE 3.3 0.6 - - - -
379A GLY* 1.3 75.4 - - - +
381A ASN* 1.3 67.7 + - - +
383A GLY 3.6 11.8 - - - +
385A LEU* 3.7 30.3 - - + -
389A GLY 4.1 9.8 + - - -
390A LYS* 6.2 0.4 - - - +
404A PHE* 3.8 13.0 - - + -
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Residues in contact with ASN 381 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A GLU 3.8 11.5 - - - +
378A ILE* 3.0 9.5 + - - +
379A GLY 3.0 0.6 - - - -
380A LYS* 1.3 88.0 + - - +
382A GLU* 1.3 61.5 + - + +
383A GLY 4.9 0.2 - - - -
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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