Contacts of the helix formed by residues 529 - 548 (chain A) in PDB entry 2XNF
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 529 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LEU* 5.2 11.0 - - + +
467A ASN* 5.8 2.6 - - - +
527A PRO* 3.4 6.3 - - - +
528A TYR* 1.3 76.8 - - + +
530A GLN* 1.3 64.1 + - - +
531A SER* 3.1 14.9 + - - -
532A GLY* 2.7 33.9 + - - -
533A PHE* 3.5 19.1 + - - +
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A CYS* 4.7 11.1 - - + +
507A GLU* 2.8 48.2 + - + +
508A VAL 4.5 11.7 - - - +
509A ARG* 4.1 9.6 - - - +
510A VAL* 3.9 29.6 - - + -
528A TYR 3.2 5.8 + - - +
529A ASP* 1.3 72.2 - - - +
531A SER* 1.3 83.0 + - - +
534A VAL* 2.7 40.8 + - - +
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Residues in contact with SER 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASP* 3.1 14.8 + - - -
530A GLN* 1.3 98.0 + - - +
532A GLY* 1.3 58.5 + - - +
534A VAL* 4.3 1.6 - - - +
535A ASN* 3.1 29.3 + - - +
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Residues in contact with GLY 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 5.0 0.5 - - - +
464A LEU* 4.1 13.1 - - - +
529A ASP* 2.7 19.3 + - - -
531A SER* 1.3 71.5 - - - +
533A PHE* 1.3 64.6 - - - +
535A ASN* 3.4 6.5 + - - +
536A GLY* 3.0 19.8 + - - -
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Residues in contact with PHE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 4.3 0.2 - - + -
461A LEU* 3.7 21.5 - - + +
464A LEU* 3.8 17.7 - - + +
465A PHE* 3.6 29.6 - + - -
497A CYS* 3.7 14.8 - - - -
510A VAL* 3.4 33.4 - - + -
511A LEU 4.5 5.6 - - - -
512A MET* 3.5 29.6 - - + -
527A PRO* 3.5 24.5 - - + -
529A ASP 3.5 12.4 + - - +
530A GLN 3.3 1.2 + - - -
532A GLY* 1.3 73.9 - - - +
534A VAL* 1.3 60.3 + - - +
536A GLY* 3.1 3.8 + - - -
537A ILE* 2.9 50.1 + - + +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A HIS* 3.6 28.5 - - + +
507A GLU* 3.6 23.6 - - - +
510A VAL* 3.7 18.6 - - + -
530A GLN* 2.7 28.8 + - - +
531A SER 4.4 1.3 - - - +
533A PHE* 1.3 71.6 - - - +
535A ASN* 1.3 51.2 + - - +
537A ILE* 3.1 7.3 + - - +
538A ARG* 2.7 49.2 + - + +
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Residues in contact with ASN 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 3.1 21.9 + - - +
532A GLY* 3.4 7.9 - - - +
534A VAL* 1.3 76.7 - - - +
536A GLY* 1.3 63.3 + - - +
538A ARG* 3.3 12.0 + - - +
539A GLN* 3.2 38.2 + - - +
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Residues in contact with GLY 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 4.2 21.3 - - - +
532A GLY 3.0 14.0 + - - -
533A PHE 3.1 3.8 + - - -
535A ASN* 1.3 78.3 + - - +
537A ILE* 1.3 61.4 + - - +
539A GLN* 3.2 20.8 + - - +
540A VAL* 3.1 25.9 + - - +
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Residues in contact with ILE 537 (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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451A GLN* 6.4 0.2 - - + -
453A ILE* 4.4 14.4 - - + -
458A LEU* 4.2 6.5 - - + -
461A LEU* 4.2 11.2 - - + -
497A CYS* 3.5 36.8 - - + -
499A HIS* 4.1 7.6 - - + +
512A MET* 4.1 12.3 - - + -
533A PHE* 2.9 38.6 + - + +
534A VAL* 3.6 7.6 - - - +
536A GLY* 1.3 73.4 - - - +
538A ARG* 1.3 54.1 + - - +
540A VAL* 3.0 11.0 + - + +
541A ILE* 2.7 60.7 + - + +
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Residues in contact with ARG 538 (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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412A PRO* 6.3 0.2 - - - +
413A LYS* 6.4 0.4 - - - +
414A PRO* 6.1 3.2 - - - +
534A VAL* 2.7 39.5 + - + +
535A ASN* 3.3 14.1 - - - +
536A GLY 3.3 0.2 - - - -
537A ILE* 1.3 71.5 - - - +
539A GLN* 1.3 58.1 + - + +
541A ILE* 3.4 38.4 - - - +
542A THR* 2.8 45.0 + - - +
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU* 5.5 0.4 - - - -
461A LEU* 5.8 0.9 - - - +
535A ASN* 3.3 22.2 - - - +
536A GLY* 3.2 23.0 - - - +
537A ILE 3.2 0.4 - - - -
538A ARG* 1.3 77.3 - - + +
540A VAL* 1.3 58.8 + - + +
542A THR* 3.2 10.9 - - - +
543A ASN* 2.9 32.8 + - - +
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ILE* 3.7 30.5 - - + -
454A PRO* 3.8 22.9 - - + +
457A LEU* 3.9 40.4 - - + +
458A LEU* 5.0 1.1 - - - +
461A LEU* 5.0 4.0 - - + -
536A GLY 3.2 15.3 - - - +
537A ILE* 3.0 19.4 + - + +
539A GLN* 1.3 78.6 - - + +
541A ILE* 1.3 50.9 + - - +
543A ASN* 3.6 2.6 + - - +
544A LEU* 2.8 35.9 + - - +
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Residues in contact with ILE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PRO* 3.9 26.7 - - + -
413A LYS* 5.6 2.2 - - + +
451A GLN* 5.1 11.0 - - + -
453A ILE* 4.0 14.8 - - + -
499A HIS* 5.1 7.4 - - + -
537A ILE* 2.7 43.6 + - + +
538A ARG* 3.4 38.1 - - - +
540A VAL* 1.3 69.7 - - - +
542A THR* 1.3 60.3 + - - +
544A LEU* 3.1 7.7 + - + +
545A GLU* 2.8 36.8 + - + +
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Residues in contact with THR 542 (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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538A ARG* 2.8 34.6 + - - +
539A GLN* 3.2 14.1 - - - +
541A ILE* 1.3 74.0 - - - +
543A ASN* 1.3 61.0 + - + +
545A GLU* 3.8 6.2 - - - +
546A HIS* 2.9 29.1 + - - +
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Residues in contact with ASN 543 (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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454A PRO* 5.8 1.0 - - - +
457A LEU* 3.4 29.6 - - + +
539A GLN 2.9 18.7 + - - +
540A VAL 3.6 2.2 - - - +
542A THR* 1.3 81.0 - - + +
544A LEU* 1.3 61.4 + - - +
546A HIS* 3.2 9.7 + - - +
547A HIS* 2.8 39.8 + - - +
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Residues in contact with LEU 544 (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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412A PRO* 5.5 5.6 - - + -
451A GLN* 4.6 4.9 - - - +
452A LEU 3.9 13.9 - - - +
453A ILE* 3.9 11.4 - - + -
454A PRO* 3.8 35.4 - - + -
494A PHE* 5.1 5.2 - - + -
540A VAL 2.8 18.0 + - - +
541A ILE* 3.4 6.5 - - + +
543A ASN* 1.3 82.4 - - - +
545A GLU* 1.3 52.3 + - + +
547A HIS* 3.6 8.1 - - + +
548A HIS* 2.6 33.8 + - - +
549A HIS* 5.5 4.3 - - + +
550A HIS* 3.3 39.6 + - + +
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Residues in contact with GLU 545 (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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411A LYS* 4.7 5.5 - - - +
412A PRO* 3.5 19.9 - - + +
413A LYS* 2.7 68.6 + - + +
422A LYS* 5.8 0.7 + - - -
541A ILE* 2.8 27.5 + - + +
542A THR* 3.8 7.2 - - - +
544A LEU* 1.3 77.1 - - + +
546A HIS* 1.3 65.7 + - - +
548A HIS* 3.4 35.0 - - - +
550A HIS* 5.3 3.0 + - - -
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Residues in contact with HIS 546 (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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542A THR 2.9 18.4 + - - +
543A ASN* 3.5 9.9 - - - +
545A GLU* 1.3 77.2 - - - +
547A HIS* 1.3 65.0 + - - +
548A HIS* 4.8 0.2 - - - +
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Residues in contact with HIS 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ASN* 2.8 25.5 + - - +
544A LEU* 3.6 11.0 - - + +
546A HIS* 1.3 83.6 - - - +
548A HIS* 1.3 70.2 + - - +
549A HIS* 3.8 33.7 + - + +
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Residues in contact with HIS 548 (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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411A LYS* 3.9 23.0 - - + +
413A LYS* 5.6 1.8 - - - -
422A LYS* 6.3 0.2 - - - -
544A LEU 2.6 19.8 + - - -
545A GLU* 3.4 35.2 - - - +
546A HIS 4.8 0.4 - - - +
547A HIS* 1.3 78.8 - - - +
549A HIS* 1.3 58.1 + - - +
550A HIS* 3.3 37.3 + + - +
551A HIS 5.3 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