Contacts of the helix formed by residues 410 - 427 (chain A) in PDB entry 5XJY
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 HIS 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ALA* 4.2 14.9 + - + +
408A VAL 3.7 0.4 - - - -
409A PHE* 1.3 79.9 - - + +
411A ASP* 1.3 68.1 + - - +
412A LEU 3.1 1.7 + - - -
413A GLU* 3.9 10.7 + - - +
414A GLY 4.3 2.4 + - - -
502A MET* 3.1 28.4 + - + -
503A GLU* 4.6 13.8 - - + +
505A VAL 4.2 10.6 + - - -
507A LEU* 4.1 29.3 - - + +
2302A NAG 6.4 0.9 - - - -
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA 4.9 6.2 - - - +
408A VAL* 4.5 2.6 + - - +
409A PHE* 3.3 0.8 - - - +
410A HIS* 1.3 82.6 - - - +
412A LEU* 1.3 55.6 + - - +
413A GLU 3.2 0.9 - - - -
414A GLY* 2.5 32.9 + - - +
415A MET* 3.0 5.4 + - - +
1568A SER 4.5 4.7 - - - +
1569A SER* 4.3 6.9 + - - +
1572A ARG* 3.1 39.7 - - - +
1573A PHE* 3.5 30.7 - - + -
1576A SER* 4.4 5.7 - - - -
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL 4.2 7.7 + - - +
409A PHE* 3.7 36.1 - - + +
410A HIS 3.1 1.8 - - - -
411A ASP* 1.3 75.9 - - - +
413A GLU* 1.3 64.3 + - - +
415A MET* 3.5 9.4 + - + +
416A TRP* 3.3 28.6 - - - +
495A ILE* 3.3 34.1 - - + +
498A ILE* 4.4 14.4 - - + -
499A SER* 5.4 0.9 - - - +
1573A PHE* 3.7 28.9 - - + -
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE 4.6 0.8 + - - -
410A HIS 3.9 9.2 + - - +
411A ASP 3.2 0.2 - - - -
412A LEU* 1.3 76.6 - - - +
414A GLY* 1.3 58.7 + - - +
416A TRP* 3.0 26.4 + - - +
417A GLU* 3.0 17.1 + - + +
495A ILE* 3.8 8.9 - - - +
496A ARG* 2.6 38.6 + - - -
499A SER* 3.0 36.8 + - - +
503A GLU* 5.5 5.6 - - - +
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Residues in contact with GLY 414 (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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410A HIS 4.3 1.0 + - - -
411A ASP* 2.5 23.6 + - - +
413A GLU* 1.3 73.3 - - - +
415A MET* 1.3 59.7 + - - +
417A GLU* 3.9 11.0 + - - +
418A GLU* 3.7 12.8 + - - +
1569A SER* 2.7 32.4 + - - -
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Residues in contact with MET 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ASP 3.0 6.2 + - - +
412A LEU* 3.8 11.2 - - + +
413A GLU 3.1 0.6 - - - -
414A GLY* 1.3 77.5 - - - +
416A TRP* 1.3 60.9 + - + +
417A GLU 3.1 0.7 - - - -
418A GLU* 2.6 24.4 + - - +
419A LEU* 2.6 48.7 + - + +
1569A SER* 3.3 25.8 - - - +
1570A ALA* 3.7 27.8 - - + -
1573A PHE* 3.8 48.7 - - + -
1574A LEU* 4.7 5.2 - - + -
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Residues in contact with TRP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 3.3 22.6 + - - +
413A GLU* 3.0 17.2 + - - +
415A MET* 1.3 78.6 - - + +
417A GLU* 1.3 63.3 + - - +
419A LEU* 6.5 0.2 - - + -
420A SER* 3.3 41.1 - - - +
421A PRO* 5.1 0.2 - - - +
423A ILE* 5.9 2.9 - - + -
488A PHE* 3.4 37.2 - + - -
491A THR* 3.6 38.8 - - + -
492A ASN* 5.0 18.8 - - + +
495A ILE* 3.3 32.7 - - + +
496A ARG* 5.6 5.9 + - - +
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Residues in contact with GLU 417 (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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413A GLU* 3.0 16.0 + - + +
414A GLY* 4.1 12.0 - - - +
415A MET 3.1 0.2 - - - -
416A TRP* 1.3 79.0 - - - +
418A GLU* 1.3 64.4 + - + +
421A PRO* 4.0 12.0 - - - +
1569A SER* 6.2 0.2 - - - -
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Residues in contact with GLU 418 (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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414A GLY 3.7 7.4 - - - +
415A MET* 2.6 12.4 + - - +
417A GLU* 1.3 76.5 - - + +
419A LEU* 1.3 78.5 + - + +
420A SER 3.2 1.9 + - - -
421A PRO* 3.8 8.5 - - - +
422A LYS* 4.1 27.3 + - - +
1565A ALA* 4.8 7.1 - - - +
1567A ASP* 2.9 29.0 - - - +
1569A SER* 3.5 15.6 + - - -
1570A ALA* 4.2 10.2 + - - +
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Residues in contact with LEU 419 (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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415A MET* 2.6 50.0 + - + +
416A TRP* 6.5 0.4 - - + -
418A GLU* 1.3 92.1 - - + +
420A SER* 1.3 56.3 + - - +
421A PRO 3.6 0.4 - - - -
422A LYS* 3.3 23.0 + - + +
423A ILE* 3.0 44.5 + - + +
1570A ALA* 5.4 3.6 - - + -
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A MET 3.9 1.0 + - - -
416A TRP* 3.3 49.3 - - - +
418A GLU 3.2 2.8 - - - -
419A LEU* 1.3 78.6 - - - +
421A PRO* 1.3 64.4 - - - +
423A ILE* 3.3 5.8 + - - +
424A TRP* 2.9 25.3 + - - +
488A PHE* 3.2 26.4 - - - -
492A ASN* 5.8 0.9 + - - -
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Residues in contact with PRO 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLU 4.0 11.0 - - - +
418A GLU 3.8 10.5 - - - +
420A SER* 1.3 90.1 - - - +
422A LYS* 1.3 60.2 + - + +
424A TRP* 3.9 9.2 - - + -
425A THR* 2.9 38.5 + - + +
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Residues in contact with LYS 422 (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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418A GLU* 4.1 30.1 + - + +
419A LEU* 3.5 23.7 - - + +
420A SER 3.2 0.6 - - - -
421A PRO* 1.3 78.9 - - + +
423A ILE* 1.3 59.2 + - + +
425A THR* 3.4 5.9 + - - -
426A PHE* 2.9 31.9 + - - +
1563A LYS* 3.6 36.3 - - + +
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Residues in contact with ILE 423 (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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416A TRP* 5.9 2.9 - - + -
419A LEU* 3.0 35.1 + - + +
420A SER* 3.7 4.7 - - - +
422A LYS* 1.3 78.2 - - + +
424A TRP* 1.3 58.6 + - - +
426A PHE* 3.7 13.9 - - + +
427A MET* 2.9 49.1 + - + +
488A PHE* 4.1 22.0 - - + -
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Residues in contact with TRP 424 (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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420A SER 2.9 18.3 + - - +
421A PRO* 3.2 10.3 + - + +
423A ILE* 1.3 78.3 - - - +
425A THR* 1.3 67.5 + - + +
427A MET* 3.9 4.6 - - - +
428A GLU* 3.3 25.3 + - + +
484A TRP* 3.8 31.5 - + - -
485A ARG* 4.9 21.1 - - + -
488A PHE* 3.5 44.9 - + + -
489A ASN* 5.3 1.6 - - - -
2303A NAG 4.2 19.3 - - - -
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Residues in contact with THR 425 (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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421A PRO* 2.9 23.9 + - + +
422A LYS* 3.4 7.8 + - - -
424A TRP* 1.3 84.2 - - + +
426A PHE* 1.3 61.6 + - - +
427A MET 3.2 2.0 - - - -
428A GLU* 2.9 6.7 + - + -
429A ASN* 2.5 46.6 + - - +
430A SER 3.4 3.3 + - - -
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Residues in contact with PHE 426 (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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122A MET* 4.9 22.4 - - + -
422A LYS 2.9 23.0 + - - +
423A ILE* 3.7 15.0 - - + +
425A THR* 1.3 77.2 + - - +
427A MET* 1.3 62.3 + - + +
428A GLU 3.2 2.3 + - - -
430A SER* 3.3 45.5 + - - -
432A GLU* 5.0 7.2 - - + -
433A MET* 3.5 23.8 - - + +
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Residues in contact with MET 427 (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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423A ILE* 2.9 31.7 + - + +
424A TRP* 3.9 4.7 - - - +
426A PHE* 1.3 81.0 - - + +
428A GLU* 1.3 59.9 + - - +
433A MET* 5.1 4.7 - - + -
468A ALA 5.8 0.2 - - - +
469A LYS 4.0 16.2 - - - +
470A HIS* 5.4 5.3 - - + +
471A PRO 5.3 2.1 - - - +
484A TRP* 3.4 64.4 - - + -
488A PHE* 6.4 1.3 - - - -
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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