Contacts of the helix formed by residues 380 - 394 (chain A) in PDB entry 5KZX
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A TYR 3.3 1.4 + - - -
379A SER* 1.3 79.7 + - - +
381A THR* 1.3 53.8 + - - +
382A ALA* 3.5 9.9 + - - +
383A ILE* 3.2 30.4 + - - +
384A THR* 2.7 35.8 + - - -
420A GLY* 3.4 22.7 - - - -
421A PHE* 3.5 8.5 - - - -
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Residues in contact with THR 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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380A SER* 1.3 69.4 - - - +
382A ALA* 1.3 58.3 + - - +
384A THR* 3.6 0.7 - - - -
385A ARG* 2.7 55.7 + - - +
420A GLY 2.9 15.6 + - - +
421A PHE* 3.7 28.2 - - + -
423A ASP* 2.6 30.9 + - - +
424A PHE* 3.9 14.4 - - - -
427A MET* 3.8 22.2 - - + +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER* 3.3 9.1 + - - +
381A THR* 1.3 82.3 + - - +
383A ILE* 1.3 62.3 - - + +
385A ARG* 3.4 14.4 + - - +
386A GLN* 3.1 33.0 + - - +
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Residues in contact with ILE 383 (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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377A GLY 4.8 2.7 - - - +
378A TYR* 3.9 33.0 - - + -
379A SER* 3.5 24.7 - - - +
380A SER* 3.2 19.5 + - - +
382A ALA* 1.3 77.7 - - + +
384A THR* 1.3 63.0 - - - +
386A GLN* 3.1 32.1 + - - +
387A VAL* 3.3 8.8 + - - +
1D NAG 3.6 11.2 - - + +
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Residues in contact with THR 384 (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 TYR* 3.6 9.0 + - + +
380A SER 2.7 23.3 + - - -
381A THR 3.2 4.7 + - - -
383A ILE* 1.3 76.5 - - - +
385A ARG* 1.3 62.0 + - - +
387A VAL* 3.2 23.5 + - - +
388A VAL* 3.7 7.6 + - - +
401A GLN* 3.5 34.5 - - + +
403A ASN* 3.1 30.5 + - - +
421A PHE* 4.1 0.7 - - - -
427A MET* 3.7 22.7 - - + -
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Residues in contact with ARG 385 (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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381A THR* 2.7 50.0 + - - +
382A ALA* 3.6 11.3 - - - +
384A THR* 1.3 73.9 - - - +
386A GLN* 1.3 56.0 + - - +
388A VAL* 3.3 10.2 + - - +
389A GLU* 3.0 27.0 + - - +
423A ASP* 2.7 32.3 + - - -
426A ALA* 4.3 1.6 - - - +
427A MET* 3.7 28.5 - - + +
430A GLU* 2.9 37.5 + - - +
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Residues in contact with GLN 386 (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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382A ALA* 3.1 25.1 + - - +
383A ILE* 3.1 21.5 + - - +
385A ARG* 1.3 72.9 - - - +
387A VAL* 1.3 55.1 + - - +
389A GLU* 4.1 16.8 - - - +
390A ASN* 2.8 41.4 + - - +
1D NAG 2.9 43.5 + - + +
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Residues in contact with VAL 387 (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* 3.3 34.8 - - + -
378A TYR* 3.5 40.6 - - + +
383A ILE 3.5 13.5 - - - +
384A THR* 3.2 12.0 + - - +
386A GLN* 1.3 74.4 - - - +
388A VAL* 1.3 58.6 + - - +
390A ASN* 3.2 1.7 + - - -
391A MET* 2.8 34.8 + - + +
398A LEU* 4.9 0.2 - - + -
401A GLN* 3.3 17.3 - - - +
685A TYR* 3.7 14.4 - - + +
1D NAG 3.9 8.1 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR 3.7 7.2 + - - +
385A ARG* 3.3 10.0 + - - +
387A VAL* 1.3 76.3 - - - +
389A GLU* 1.3 54.9 + - - +
391A MET* 3.4 1.7 + - - +
392A THR* 2.8 46.8 + - - +
398A LEU* 4.0 15.7 - - + -
401A GLN* 3.6 22.2 - - + +
431A LEU* 3.8 27.8 - - + -
436A ARG* 4.1 26.9 - - - +
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Residues in contact with GLU 389 (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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385A ARG 3.0 16.0 + - - +
386A GLN* 3.6 19.0 + - - +
387A VAL 3.3 0.2 - - - -
388A VAL* 1.3 77.8 - - - +
390A ASN* 1.3 62.1 + - - +
392A THR* 3.4 5.0 + - - -
393A ARG* 2.9 53.8 + - + +
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Residues in contact with ASN 390 (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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386A GLN* 2.8 23.3 + - - +
389A GLU* 1.3 75.1 - - - +
391A MET* 1.3 63.7 + - - +
393A ARG* 2.7 34.9 + - - +
394A ALA* 3.4 23.4 + - - +
685A TYR* 3.6 32.5 - - + +
1D NAG 1.4 62.9 + - - +
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Residues in contact with MET 391 (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 PHE* 3.6 24.9 - - + -
373A LEU* 4.0 15.5 - - + -
387A VAL 2.8 23.9 + - - +
388A VAL 3.7 4.3 - - - +
390A ASN* 1.3 71.5 - - - +
392A THR* 1.3 63.7 + - - +
394A ALA 3.3 3.3 + - - -
395A HIS 3.1 4.3 + - - -
396A PHE* 2.9 52.8 + - + +
397A PRO 3.4 26.9 - - - +
398A LEU* 4.0 17.9 - - + -
684A PRO* 4.0 18.6 - - + -
685A TYR* 3.7 22.0 - - + -
699A LEU* 4.8 0.4 - - + -
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Residues in contact with THR 392 (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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388A VAL* 2.8 25.6 + - - +
389A GLU* 3.8 5.6 - - - -
391A MET* 1.3 76.9 - - - +
393A ARG* 1.3 63.9 + - - +
395A HIS* 3.0 19.4 + - - -
396A PHE 4.7 0.9 - - - -
436A ARG* 3.4 25.5 + - - +
831A LEU* 4.0 25.7 - - + +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLU* 2.9 43.3 + - + +
390A ASN* 2.7 38.2 + - - +
392A THR* 1.3 77.8 - - - +
394A ALA* 1.3 58.6 + - + +
395A HIS* 3.4 16.3 + - - -
1D NAG 3.3 28.4 + - - -
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Residues in contact with ALA 394 (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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390A ASN 3.4 14.2 + - - +
391A MET 3.3 1.6 + - - -
392A THR 3.1 0.8 - - - -
393A ARG* 1.3 78.1 - - + +
395A HIS* 1.3 68.0 + - - +
396A PHE* 3.3 26.7 + - + -
685A TYR* 4.3 5.4 - - + -
692A GLN* 3.8 11.7 - - - +
696A ARG* 2.8 32.4 + - - +
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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