Contacts of the helix formed by residues 507 - 521 (chain A) in PDB entry 5E92
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 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A TRP* 3.9 29.7 - + - +
463A ALA* 3.5 38.7 - - + +
504A TRP 3.7 3.2 + - - +
505A LEU 3.3 2.0 - - - +
506A ASN* 1.3 76.8 - - - +
508A GLN* 1.3 58.2 + - + +
509A GLY* 2.9 36.9 + - - -
510A ILE* 3.2 19.1 + - + +
511A GLN* 3.1 27.9 + - - +
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Residues in contact with GLN 508 (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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506A ASN 3.7 3.8 + - - +
507A HIS* 1.3 71.2 + - + +
509A GLY* 1.3 64.6 + - - +
511A GLN* 3.5 16.5 - - - +
512A MET* 3.1 22.9 + - - +
543A HIS 5.6 6.1 - - - +
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Residues in contact with GLY 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TRP* 3.4 28.2 - - - -
507A HIS* 2.9 13.4 + - - -
508A GLN* 1.3 74.4 - - - +
510A ILE* 1.3 58.3 + - - +
512A MET* 3.3 4.5 + - - +
513A VAL* 3.0 31.5 + - - +
541A LEU* 4.2 10.0 - - - +
543A HIS 5.4 5.1 + - - -
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Residues in contact with ILE 510 (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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344A TRP* 3.7 4.0 - - + -
347A LEU* 3.6 28.5 - - + -
458A THR* 3.9 14.4 - - + -
461A CYS* 3.8 15.9 - - + -
463A ALA* 3.9 12.6 - - + +
464A VAL* 3.8 26.9 - - + -
504A TRP* 3.2 30.3 - - + +
507A HIS* 3.2 25.6 + - + +
509A GLY* 1.3 73.7 - - - +
511A GLN* 1.4 52.0 + - - +
513A VAL* 3.2 4.9 + - - +
514A CYS* 2.8 39.9 + - - -
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Residues in contact with GLN 511 (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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505A LEU* 3.6 41.3 - - + +
507A HIS 3.1 17.5 + - - +
508A GLN* 3.5 16.9 - - - +
509A GLY 3.3 0.2 - - - -
510A ILE* 1.4 76.3 - - - +
512A MET* 1.4 55.4 + - - +
514A CYS* 3.5 2.6 + - - +
515A GLU* 3.0 49.6 + - - +
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Residues in contact with MET 512 (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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508A GLN 3.1 13.2 + - - +
509A GLY 3.3 8.7 + - - +
511A GLN* 1.4 71.6 - - - +
513A VAL* 1.4 56.3 + - - +
515A GLU* 3.3 13.3 + - - +
516A THR* 2.7 42.7 + - - +
537A ARG* 5.2 13.9 - - + +
541A LEU* 4.2 22.2 - - + -
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Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TRP* 4.1 19.5 - - + -
347A LEU* 4.7 8.7 - - + -
454A LEU* 5.0 5.6 - - + +
458A THR* 3.3 27.6 - - + +
509A GLY 3.0 17.9 + - - +
510A ILE* 3.6 10.1 - - - +
512A MET* 1.4 73.8 - - - +
514A CYS* 1.3 55.8 + - - +
516A THR* 3.3 8.1 + - - -
517A LEU* 3.0 35.0 + - + +
538A PHE* 4.0 36.8 - - + -
541A LEU* 4.2 7.2 - - + -
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Residues in contact with CYS 514 (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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458A THR* 4.0 14.6 - - - -
500A ILE* 3.8 31.9 - - + -
504A TRP* 3.9 17.5 - - - -
505A LEU* 3.8 21.5 - - + -
510A ILE* 2.8 27.6 + - - +
511A GLN 3.8 0.7 - - - +
513A VAL* 1.3 69.3 - - - +
515A GLU* 1.3 58.2 + - - +
517A LEU* 3.7 10.5 - - - +
518A THR* 2.7 37.1 + - - -
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Residues in contact with GLU 515 (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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505A LEU* 6.0 2.0 - - + -
511A GLN* 3.0 50.0 + - + +
512A MET* 3.3 12.3 + - + +
514A CYS* 1.3 74.8 - - - +
516A THR* 1.3 63.2 + - - +
518A THR* 3.6 5.2 + - - -
519A GLU* 3.3 34.4 + - - +
537A ARG* 4.9 3.0 + - - +
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Residues in contact with THR 516 (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 LEU* 5.6 1.8 - - + -
512A MET* 2.7 24.0 + - - +
513A VAL* 3.3 8.7 + - - -
515A GLU* 1.3 75.0 - - - +
517A LEU* 1.3 61.8 + - - +
519A GLU* 3.4 6.7 + - - +
520A CYS* 3.2 25.4 + - - -
529A LEU* 4.0 3.5 - - + +
534A VAL* 4.0 37.5 - - + -
537A ARG* 3.2 44.1 + - + +
538A PHE* 5.1 6.3 - - + -
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Residues in contact with LEU 517 (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 ALA* 3.4 23.3 - - + +
454A LEU* 4.0 19.7 - - + +
455A TRP* 3.9 26.5 - - + +
458A THR* 4.2 10.1 - - - +
500A ILE* 4.1 7.4 - - + -
513A VAL* 3.0 23.0 + - + +
514A CYS* 3.7 17.9 - - - +
516A THR* 1.3 74.1 - - - +
518A THR* 1.4 61.6 + - - +
520A CYS* 3.0 8.3 + - - -
521A TRP* 3.0 68.5 + - + -
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Residues in contact with THR 518 (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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500A ILE* 3.5 21.5 - - - +
514A CYS 2.7 23.1 + - - -
515A GLU* 3.9 6.7 - - - -
517A LEU* 1.4 75.2 - - - +
519A GLU* 1.3 61.5 + - + +
521A TRP* 3.2 36.3 + - + +
522A ASP* 3.6 8.0 + - - +
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Residues in contact with GLU 519 (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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515A GLU* 3.3 16.2 + - - +
516A THR 3.5 7.4 - - - +
517A LEU 3.3 0.4 - - - -
518A THR* 1.3 77.0 - - + +
520A CYS* 1.4 59.7 + - - +
522A ASP* 3.3 24.2 - - - +
527A ALA 3.8 9.7 - - - +
528A ARG* 3.3 13.2 - - - -
529A LEU* 3.5 21.9 - - + +
537A ARG* 2.8 44.4 + - - -
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Residues in contact with CYS 520 (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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447A VAL* 3.7 17.8 - - + +
448A TYR* 3.4 12.8 + - - -
450A MET* 4.3 3.1 - - - -
451A ALA* 3.6 15.5 - - + -
454A LEU* 5.7 1.1 - - - -
516A THR* 3.2 16.0 + - - +
517A LEU* 3.0 10.8 + - - +
519A GLU* 1.4 77.8 - - - +
521A TRP* 1.3 57.5 + - - +
522A ASP 3.4 1.3 - - - -
528A ARG* 3.1 27.4 - - - -
529A LEU* 3.8 16.6 - - - -
534A VAL* 3.5 31.6 - - - -
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Residues in contact with TRP 521 (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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448A TYR* 3.7 24.4 - - + +
451A ALA* 3.8 14.1 - - + -
452A LEU* 3.9 17.0 - - + -
455A TRP* 3.7 19.3 - + + -
497A ARG* 2.9 60.2 + - + +
498A PRO* 3.4 37.2 - - + -
500A ILE* 3.8 22.9 - - + -
517A LEU* 3.0 33.9 + - + -
518A THR* 3.2 40.2 + - + +
519A GLU 3.3 0.6 - - - -
520A CYS* 1.3 75.9 - - - +
522A ASP* 1.3 66.9 + - - +
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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