Contacts of the helix formed by residues 365 - 382 (chain A) in PDB entry 3DL2
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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364A VAL* 1.3 77.0 - - - +
366A HIS* 1.3 63.7 + - - +
367A THR* 2.8 25.6 + - - +
368A SER* 3.2 18.6 + - - -
369A GLN* 3.1 22.5 + - - +
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Residues in contact with HIS 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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364A VAL 3.4 4.9 + - - +
365A SER* 1.3 71.0 + - - +
367A THR* 1.3 62.5 + - + +
369A GLN* 3.3 14.8 + - - +
370A VAL* 2.9 57.5 + - + +
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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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365A SER* 2.8 13.1 + - - +
366A HIS* 1.3 82.5 - - + +
368A SER* 1.3 67.8 + - - +
370A VAL* 3.4 6.8 + - - +
371A GLN* 3.0 45.1 + - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 4.8 7.9 - - - -
365A SER* 3.2 23.2 + - - -
367A THR* 1.3 83.5 + - - +
369A GLN* 1.3 58.2 + - - +
371A GLN* 3.5 13.0 + - - +
372A LEU* 2.9 29.6 + - - +
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Residues in contact with GLN 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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341A LYS* 4.3 14.6 - - - +
357A TRP* 3.3 57.7 - - + +
364A VAL* 3.8 23.9 - - + +
365A SER 3.1 17.0 + - - +
366A HIS* 3.7 14.1 + - - +
368A SER* 1.3 73.4 - - - +
370A VAL* 1.3 57.8 + - + +
372A LEU* 3.5 8.3 + - + +
373A SER* 2.7 37.7 + - - +
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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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366A HIS* 2.9 51.1 + - + +
367A THR* 3.7 5.6 - - - +
369A GLN* 1.3 73.3 - - + +
371A GLN* 1.3 61.9 + - + +
373A SER* 3.3 5.7 + - - -
374A ASN* 2.8 54.9 + - - +
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Residues in contact with GLN 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 THR* 3.0 31.7 + - - +
368A SER* 3.8 14.8 + - - +
370A VAL* 1.3 78.5 - - + +
372A LEU* 1.3 63.2 + - - +
374A ASN* 3.5 7.0 + - - +
375A ARG* 3.1 62.5 + - - +
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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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330A ILE* 4.4 17.3 - - + -
334A LEU* 3.8 24.7 - - + -
336A ALA* 3.9 27.6 - - + -
337A GLN 5.3 4.5 - - - +
338A THR* 4.8 3.8 - - + +
357A TRP* 4.2 22.7 - - + -
368A SER 2.9 19.3 + - - +
369A GLN* 3.7 7.9 - - + +
371A GLN* 1.3 74.5 - - - +
373A SER* 1.3 59.5 + - - +
375A ARG* 3.2 9.3 + - - +
376A ALA* 2.9 28.9 + - - +
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Residues in contact with SER 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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330A ILE* 5.6 1.6 - - - -
355A LEU* 3.8 30.6 - - - +
357A TRP* 3.0 31.3 + - - -
369A GLN* 2.7 22.2 + - - +
370A VAL* 3.6 6.5 - - - -
372A LEU* 1.3 77.6 - - - +
374A ASN* 1.3 57.9 - - - +
376A ALA* 4.0 3.5 - - - +
377A MET* 2.9 32.6 + - - +
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Residues in contact with ASN 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 VAL* 2.8 40.3 + - - +
371A GLN* 3.8 8.3 - - - +
373A SER* 1.3 73.5 - - - +
375A ARG* 1.3 60.3 + - + +
377A MET* 3.4 5.4 + - - +
378A GLU* 3.0 36.2 + - + +
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Residues in contact with ARG 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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334A LEU* 4.9 10.1 - - + -
371A GLN* 3.1 56.7 + - - +
372A LEU* 3.7 7.0 - - - +
374A ASN* 1.3 76.5 - - + +
376A ALA* 1.3 63.2 - - - +
378A GLU* 3.2 9.2 + - - +
379A LEU* 3.1 29.7 + - + +
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Residues in contact with ALA 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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326A LEU* 3.6 25.3 - - + +
329A ILE* 3.9 18.5 - - + +
330A ILE* 3.7 25.8 - - + -
334A LEU* 4.1 7.5 - - + +
372A LEU 2.9 16.8 + - - +
373A SER* 4.0 3.1 - - - +
375A ARG* 1.3 75.6 - - - +
377A MET* 1.3 57.9 + - - +
379A LEU* 3.3 4.3 + - - +
380A LEU* 3.0 23.9 + - - +
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Residues in contact with MET 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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326A LEU* 3.8 7.1 - - + +
345A VAL* 4.1 16.2 - - + -
353A LYS* 3.4 52.7 - - + +
355A LEU* 3.6 36.8 - - + -
373A SER 2.9 20.2 + - - +
374A ASN* 3.6 6.7 - - - +
376A ALA* 1.3 75.1 - - - +
378A GLU* 1.3 60.9 + - + +
380A LEU* 3.3 6.3 + - - +
381A ARG* 2.9 47.2 + - - +
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Residues in contact with GLU 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 ASN* 3.0 22.7 + - + +
375A ARG* 3.2 9.6 + - - +
377A MET* 1.3 75.5 - - + +
379A LEU* 1.3 64.5 + - + +
381A ARG* 3.0 41.5 + - - +
382A VAL* 3.6 14.4 + - - +
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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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329A ILE* 3.7 31.2 - - + -
333A VAL* 4.4 11.9 - - + -
334A LEU* 3.9 26.0 - - + -
375A ARG* 3.1 18.9 + - + +
376A ALA 3.6 6.7 - - - +
377A MET 3.3 0.2 - - - -
378A GLU* 1.3 76.7 - - + +
380A LEU* 1.3 62.4 + - - +
382A VAL* 3.4 21.7 - - + +
383A LYS* 3.6 14.6 - - - +
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Residues in contact with LEU 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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322A ASP* 3.6 30.1 - - + +
325A ARG* 3.5 43.5 + - + +
326A LEU* 4.2 9.9 - - + +
329A ILE* 3.8 11.4 - - + +
345A VAL* 3.9 16.4 - - + -
353A LYS* 3.8 26.1 - - + -
376A ALA 3.0 13.9 + - - +
377A MET* 3.6 13.5 - - - +
378A GLU 3.3 0.2 - - - -
379A LEU* 1.3 77.3 - - - +
381A ARG* 1.3 62.8 + - - +
383A LYS* 3.2 25.5 + - + +
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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
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351A GLU* 2.8 38.3 + - - +
352A ASP* 5.1 0.6 - - - +
353A LYS* 3.8 35.3 - - + +
377A MET* 2.9 38.6 + - - +
378A GLU* 3.0 33.8 + - - +
380A LEU* 1.3 76.4 - - - +
382A VAL* 1.3 60.7 + - - +
383A LYS 3.2 5.7 + - - +
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Residues in contact with VAL 382 (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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378A GLU 3.6 10.1 + - - +
379A LEU* 3.4 20.9 - - + +
381A ARG* 1.3 78.1 - - - +
383A LYS* 1.3 66.5 + - + +
384A GLY 3.7 1.4 + - - -
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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