Contacts of the helix formed by residues 369 - 382 (chain A) in PDB entry 2XXA
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A SER* 3.8 24.6 - - - -
370A ASP* 1.3 77.9 + - - +
371A LYS* 3.4 7.1 - - - +
372A VAL* 3.5 33.6 + - - +
373A LEU* 4.0 5.2 + - - +
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Residues in contact with ASP 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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347A MET* 3.5 31.7 - - - +
349A SER* 4.0 10.0 + - - -
369A ASP* 1.3 86.2 + - - +
371A LYS* 1.3 63.9 + - + +
372A VAL 3.5 0.3 + - - -
373A LEU* 3.8 9.3 + - - +
374A VAL* 3.5 22.2 + - - +
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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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369A ASP 3.4 4.4 - - - +
370A ASP* 1.3 77.0 - - + +
372A VAL* 1.4 64.5 + - + +
374A VAL* 3.6 8.6 + - - +
375A ARG* 3.3 42.9 + - - +
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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
----------------------------------------------------------
369A ASP* 3.5 28.7 - - - +
370A ASP 3.3 0.8 - - - -
371A LYS* 1.4 77.7 - - + +
373A LEU* 1.4 56.5 + - - +
375A ARG* 3.4 8.9 + - - +
376A MET* 3.0 42.4 + - + +
415A ARG* 4.1 22.8 + - - +
419A GLN* 5.1 6.5 - - - +
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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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338A LEU* 3.8 25.2 - - + +
341A MET* 3.8 39.7 - - + -
342A LYS* 3.8 38.8 + - + -
347A MET* 4.5 13.7 - - + -
369A ASP 4.0 5.2 + - - +
370A ASP 3.8 9.1 + - - +
371A LYS 3.5 0.6 - - - -
372A VAL* 1.4 74.3 - - - +
374A VAL* 1.4 65.2 + - + +
376A MET* 3.5 11.6 + - - +
377A GLU 3.4 16.5 + - - -
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Residues in contact with VAL 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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342A LYS* 3.7 19.7 + - - +
370A ASP* 3.5 24.5 - - - +
371A LYS* 3.6 7.6 + - - +
372A VAL 3.4 0.6 - - - -
373A LEU* 1.4 77.0 - - + +
375A ARG* 1.4 61.7 + - + +
377A GLU* 3.6 12.1 + - - +
378A ALA* 3.7 11.3 + - - +
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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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371A LYS* 3.3 32.4 + - + +
372A VAL* 3.6 7.9 - - - +
373A LEU 3.4 0.2 - - - -
374A VAL* 1.4 74.8 - - + +
376A MET* 1.4 61.7 + - - +
378A ALA* 3.5 14.0 + - - +
379A ILE* 3.4 23.8 + - + +
408A MET* 3.7 38.0 - - + +
412A ASP* 4.1 18.3 + - - +
415A ARG* 5.5 4.7 - - - +
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Residues in contact with MET 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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334A PHE* 3.7 33.4 - - + -
338A LEU* 4.6 9.2 - - + -
372A VAL* 3.0 28.7 + - - +
373A LEU* 3.7 12.3 - - - +
374A VAL 3.4 0.4 - - - -
375A ARG* 1.4 74.2 - - - +
377A GLU* 1.3 62.7 + - - +
379A ILE* 3.7 1.2 + - - -
380A ILE* 3.4 29.1 + - + +
415A ARG* 3.5 19.3 - - - +
416A LEU* 3.4 34.9 - - + +
419A GLN* 3.4 29.2 - - + +
420A PHE* 6.4 0.7 - - + -
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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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335A LEU* 3.8 17.2 - - + +
338A LEU* 4.6 14.2 - - + +
339A ARG* 3.5 28.1 + - - +
342A LYS* 3.2 42.9 + - - +
373A LEU 3.4 5.0 + - - +
374A VAL 3.8 4.6 - - - +
375A ARG 3.3 0.4 - - - -
376A MET* 1.3 78.1 - - - +
378A ALA* 1.4 53.7 + - - +
380A ILE* 3.5 4.4 + - - +
381A ASN* 2.8 50.7 + - - +
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Residues in contact with ALA 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 VAL 3.7 8.1 + - - +
375A ARG* 3.5 12.7 + - - +
376A MET 3.4 0.4 - - - -
377A GLU* 1.4 75.0 - - - +
379A ILE* 1.3 62.7 + - - +
381A ASN* 3.4 11.5 + - - +
382A SER* 3.2 26.7 + - - -
406A SER* 3.7 20.2 + - - +
408A MET* 5.1 4.7 - - + -
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Residues in contact with ILE 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 ARG* 3.4 23.2 + - + +
376A MET* 4.4 0.7 - - - -
377A GLU 3.4 0.4 - - - -
378A ALA* 1.3 72.1 - - - +
380A ILE* 1.4 63.3 + - - +
382A SER 3.4 8.8 + - - -
383A MET* 3.5 13.7 - - + +
402A ILE* 3.5 25.3 - - + +
406A SER* 3.9 15.9 - - - +
408A MET* 4.1 12.8 - - + -
412A ASP* 4.1 29.4 - - + +
413A VAL* 4.0 20.0 - - + -
415A ARG* 4.6 6.5 - - - +
416A LEU* 3.7 39.5 - - + -
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Residues in contact with ILE 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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331A LEU* 3.8 37.5 - - + +
334A PHE* 3.8 30.5 - - + -
335A LEU* 3.8 25.8 - - + -
338A LEU* 3.8 14.8 - - + -
376A MET* 3.4 19.1 - - + +
377A GLU* 3.5 2.1 + - - +
378A ALA 3.5 0.4 - - - -
379A ILE* 1.4 72.5 - - - +
381A ASN* 1.4 62.2 + - - +
383A MET* 3.3 20.5 + - - +
388A ARG* 3.3 18.6 + - + -
416A LEU* 3.8 25.4 - - + -
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Residues in contact with ASN 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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335A LEU* 3.9 5.3 - - - +
339A ARG* 3.4 23.6 + - - +
377A GLU* 2.8 49.9 + - - +
378A ALA* 3.5 11.6 - - - +
379A ILE 3.3 0.2 - - - -
380A ILE* 1.4 77.9 - - - +
382A SER* 1.3 58.1 + - - +
383A MET 3.7 0.7 - - - +
388A ARG* 3.2 20.8 + - - +
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Residues in contact with SER 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 ALA 3.2 13.5 + - - -
379A ILE 3.7 9.2 - - - -
380A ILE 3.3 0.6 - - - -
381A ASN* 1.3 74.3 - - - +
383A MET* 1.3 59.2 + - - +
401A ARG* 3.0 30.1 + - - -
402A ILE* 4.0 23.8 - - - -
405A GLY* 4.3 4.6 + - - -
406A SER* 3.7 19.9 + - - -
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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