Contacts of the helix formed by residues 506 - 521 (chain A) in PDB entry 5E3H
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 THR 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A PHE* 3.4 13.4 - - + +
505A GLY* 1.3 86.3 - - - +
507A GLN* 1.3 65.5 + - - +
508A LYS* 3.6 18.0 + - - +
509A TYR* 3.3 10.9 + - - +
510A GLU 3.4 7.3 + - - -
549A ASN* 3.5 9.5 + - - +
553A ILE* 4.9 4.9 - - - -
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Residues in contact with GLN 507 (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 THR* 1.3 74.4 - - - +
508A LYS* 1.3 66.3 + - - +
510A GLU* 3.1 22.5 + - + +
511A GLN* 3.3 23.8 + - + +
553A ILE* 5.1 6.1 - - + +
8B A 2.6 62.9 + - - -
9B G 3.6 19.0 + - - +
7C U 5.0 0.4 + - - -
8C A 4.5 10.1 + - - -
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Residues in contact with LYS 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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504A PHE* 6.3 0.4 - - + -
506A THR* 3.6 10.5 + - - +
507A GLN* 1.3 81.9 - - - +
509A TYR* 1.3 61.2 + - - +
511A GLN* 3.6 7.1 + - - +
512A TRP* 3.6 16.6 + - - +
9B G 4.8 14.2 + - - +
10B C 6.4 0.7 - - - -
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Residues in contact with TYR 509 (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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479A MET* 3.3 23.9 - - + +
483A GLU* 3.4 17.7 + - - +
504A PHE* 3.0 49.6 - - + +
506A THR* 3.3 10.7 + - - +
507A GLN 3.2 0.4 - - - -
508A LYS* 1.3 77.6 - - - +
510A GLU* 1.3 64.5 + - - +
512A TRP* 3.3 47.7 + + - +
513A ILE* 3.3 29.0 + - + +
545A LEU* 3.5 26.4 - - - +
549A ASN* 3.4 15.9 - - + -
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Residues in contact with GLU 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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506A THR 3.4 2.9 + - - +
507A GLN* 3.1 19.4 + - + +
509A TYR* 1.3 77.8 - - - +
511A GLN* 1.3 68.1 + - + +
512A TRP 3.1 1.0 + - - -
513A ILE* 3.2 15.5 + - + +
514A VAL* 3.2 17.6 + - + +
546A ARG* 5.1 3.3 - - + +
549A ASN* 3.4 28.8 + - - +
550A ASP* 3.4 14.9 - - - +
553A ILE* 4.5 7.9 - - - +
8C A 2.3 49.7 + - - +
9C G 4.7 1.4 - - - +
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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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507A GLN* 3.3 19.3 + - + +
508A LYS* 4.0 8.3 - - - +
509A TYR 3.4 0.2 - - - -
510A GLU* 1.3 78.1 - - + +
512A TRP* 1.3 55.4 + - - +
514A VAL* 3.6 2.9 + - - +
515A THR* 2.6 33.9 + - - +
9B G 2.7 59.9 + - - +
10B C 4.1 12.5 + - - +
7C U 3.3 36.9 + - + +
8C A 5.3 2.9 - - - +
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Residues in contact with TRP 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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483A GLU* 3.2 36.3 - - - -
493A LEU* 4.8 28.5 - - + -
494A GLU* 5.1 17.5 + - - +
508A LYS 3.6 7.3 + - - +
509A TYR* 3.3 43.5 + + - +
510A GLU 3.0 0.4 - - - -
511A GLN* 1.3 77.1 - - - +
513A ILE* 1.3 57.4 + - + +
515A THR* 2.7 13.3 + - + -
516A VAL* 2.6 56.9 + - + +
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Residues in contact with ILE 513 (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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483A GLU* 5.7 0.2 - - - -
509A TYR* 3.4 39.7 - - + +
510A GLU* 3.2 8.4 + - + +
512A TRP* 1.3 87.8 - - + +
514A VAL* 1.3 57.3 + - + +
516A VAL* 3.6 10.0 - - + +
517A GLN* 3.1 30.4 + - + +
542A THR* 3.4 38.1 - - + +
545A LEU* 3.6 27.6 - - + -
546A ARG* 3.7 22.2 - - + +
549A ASN* 5.7 0.2 - - + -
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 3.2 19.9 + - + +
511A GLN 3.8 7.4 - - - +
512A TRP 3.1 0.4 - - - -
513A ILE* 1.3 77.2 - - + +
515A THR* 1.3 61.6 + - - +
517A GLN* 3.6 11.9 + - - +
518A LYS* 3.2 20.6 + - - +
546A ARG* 6.3 2.0 - - + -
7C U 3.5 35.0 - - - +
8C A 4.0 28.0 - - - +
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Residues in contact with THR 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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511A GLN* 2.6 20.5 + - - +
512A TRP* 2.7 23.7 + - + -
514A VAL* 1.3 71.4 - - - +
516A VAL* 1.3 56.9 + - - -
518A LYS* 3.2 8.3 + - + +
519A ALA* 2.9 28.9 + - + +
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Residues in contact with VAL 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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486A ALA* 6.2 2.7 - - + -
512A TRP* 2.6 53.5 + - + +
513A ILE* 3.6 15.3 - - + +
514A VAL 3.3 0.2 - - - -
515A THR* 1.3 74.3 - - - +
517A GLN* 1.3 56.7 + - - +
519A ALA* 2.9 9.7 + - + +
520A CYS* 2.8 39.0 + - - -
538A LEU* 6.4 0.2 - - + -
542A THR* 3.6 25.6 - - + -
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Residues in contact with GLN 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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513A ILE* 3.1 22.0 + - - +
514A VAL* 3.7 10.5 - - + +
516A VAL* 1.3 75.4 - - - +
518A LYS* 1.3 61.5 + - - +
520A CYS* 3.2 8.2 + - - +
521A MET* 3.1 48.1 + - + +
539A PHE* 3.8 19.4 + - + -
542A THR* 3.0 31.4 + - - +
543A SER* 3.5 28.7 + - - +
546A ARG* 5.4 2.2 - - - +
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Residues in contact with LYS 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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514A VAL* 3.2 12.8 + - + +
515A THR* 3.5 14.1 - - + +
516A VAL 3.2 0.2 - - - -
517A GLN* 1.3 79.8 - - - +
519A ALA* 1.3 60.1 + - - +
521A MET* 3.8 8.6 + - - +
522A VAL* 4.0 11.4 + - - +
904A LEU* 4.1 23.5 - - + +
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Residues in contact with ALA 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 THR* 2.9 15.3 + - + +
516A VAL* 2.9 11.6 + - + +
518A LYS* 1.3 79.5 - - - +
520A CYS* 1.3 61.2 + - - +
521A MET 3.3 0.2 - - - -
522A VAL* 3.4 21.9 - - - +
523A PHE* 4.1 4.3 + - - +
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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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490A CYS* 4.7 8.3 - - - -
516A VAL* 2.8 33.8 + - - +
517A GLN* 3.2 8.7 + - - +
519A ALA* 1.3 77.1 - - - +
521A MET* 1.3 60.8 + - + +
522A VAL 3.3 1.1 - - - -
523A PHE* 3.4 23.9 - - - +
535A CYS* 3.7 16.1 - - - +
538A LEU* 3.7 47.0 - - + +
539A PHE 5.6 0.7 - - - +
542A THR* 5.1 1.6 - - - -
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Residues in contact with MET 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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517A GLN* 3.1 33.3 + - + +
518A LYS* 3.8 1.3 + - - +
519A ALA 3.3 0.4 - - - -
520A CYS* 1.3 78.8 - - + +
522A VAL* 1.3 57.8 + - - +
523A PHE 3.3 4.6 - - - +
535A CYS* 5.1 6.8 - - + -
539A PHE* 3.8 34.5 - - + -
811A ARG* 3.6 46.9 - - + +
871A HIS* 5.8 0.4 - - - +
904A LEU* 3.6 41.6 - - + +
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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