Contacts of the helix formed by residues 515 - 529 (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 THR 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A THR* 5.2 0.2 - - - -
513A ILE* 3.3 10.1 - - - +
514A ALA* 1.3 88.3 - - + +
516A GLU* 1.3 64.6 + - - +
517A VAL* 4.0 10.5 - - - +
518A TRP* 3.0 57.2 + - + +
519A LEU 3.2 6.8 + - - -
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Residues in contact with GLU 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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386A THR* 4.0 23.0 - - + +
514A ALA 4.3 3.1 - - - +
515A THR* 1.3 75.9 - - - +
517A VAL* 1.3 70.2 + - + +
519A LEU* 3.1 15.0 + - + +
520A ILE* 2.9 37.8 + - + +
537A VAL* 4.7 14.1 - - + -
557A ARG* 5.5 0.4 - - - +
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Residues in contact with VAL 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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515A THR* 4.0 15.0 - - - +
516A GLU* 1.3 86.5 - - + +
518A TRP* 1.3 73.8 + - + +
520A ILE* 3.2 12.6 + - + +
521A ASN* 3.0 29.1 + - - +
2304A NAG 5.3 7.6 - - + +
1C NAG 5.1 12.6 - - - +
2C NAG 5.4 12.3 - - - +
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Residues in contact with TRP 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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513A ILE* 4.7 8.5 - - + -
514A ALA* 5.4 8.5 - - + -
515A THR* 3.0 41.1 + - + +
517A VAL* 1.3 80.0 - - + +
519A LEU* 1.3 57.9 + - - +
521A ASN* 4.4 3.1 - - - +
522A LYS* 2.9 36.5 + - + +
2304A NAG 3.3 41.3 + - + +
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Residues in contact with LEU 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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384A LEU* 3.6 21.1 - - + +
385A TYR* 3.4 40.2 - - - +
386A THR* 3.6 11.2 - - + -
513A ILE* 4.0 17.6 - - + +
515A THR 3.2 4.2 + - - -
516A GLU* 3.1 22.3 + - - +
518A TRP* 1.3 79.6 - - - +
520A ILE* 1.3 50.3 + - + +
522A LYS* 4.4 0.4 - - - +
523A SER* 2.6 39.3 + - - +
535A GLY* 5.0 6.3 - - - -
536A ILE 5.1 0.2 - - - +
537A VAL* 3.9 23.6 - - + -
557A ARG* 3.9 16.2 - - + +
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Residues in contact with ILE 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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516A GLU* 2.9 23.3 + - + +
517A VAL* 3.2 12.3 + - + +
519A LEU* 1.3 80.8 - - + +
521A ASN* 1.3 59.4 + - - +
523A SER* 3.3 5.8 - - - -
524A MET* 2.9 30.0 + - + +
557A ARG* 3.7 37.5 - - - +
1636A LEU* 3.9 17.0 - - + -
1637A ASN* 4.4 9.6 - - - +
1C NAG 4.0 38.4 - - + +
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Residues in contact with ASN 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 VAL 3.0 16.9 + - - +
518A TRP* 4.1 2.2 - - - +
520A ILE* 1.3 75.2 - - - +
522A LYS* 1.3 60.6 + - - +
524A MET* 3.0 22.6 + - - +
525A GLU* 3.0 13.7 + - - +
2304A NAG 1.4 79.0 + - - +
1C NAG 4.6 16.4 - - + +
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Residues in contact with LYS 522 (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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384A LEU* 5.3 1.8 - - + -
513A ILE* 4.8 13.7 - - + -
518A TRP* 2.9 20.6 + - + +
519A LEU* 4.4 2.7 - - - +
521A ASN* 1.3 73.9 - - - +
523A SER* 1.3 59.3 + - - +
525A GLU* 3.4 26.3 + - - +
526A LEU* 2.9 60.1 + - + +
529A GLU* 5.8 0.4 + - - -
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Residues in contact with SER 523 (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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384A LEU* 4.8 4.4 - - - +
519A LEU* 2.6 27.0 + - - -
520A ILE* 3.3 10.8 - - - -
522A LYS* 1.3 77.2 - - - +
524A MET* 1.3 56.2 + - - +
526A LEU* 3.5 1.9 + - - +
527A LEU* 2.9 30.4 + - - +
532A PHE* 3.2 39.5 - - - -
557A ARG* 5.6 0.6 - - - +
1636A LEU* 3.3 17.8 - - - +
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Residues in contact with MET 524 (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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520A ILE* 2.9 23.4 + - + +
521A ASN* 3.0 13.2 + - - +
523A SER* 1.3 77.3 - - - +
525A GLU* 1.3 61.2 + - - +
527A LEU* 3.3 9.3 + - + +
528A ASP* 3.0 36.5 + - - +
1636A LEU* 3.7 17.7 - - + -
1637A ASN* 3.5 24.0 - - + +
1638A LEU 3.3 21.5 - - - +
1639A THR* 3.8 20.9 - - - +
1640A LYS* 6.6 0.2 - - - -
1837A GLU* 6.1 0.7 - - - +
1C NAG 5.1 8.3 - - + -
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Residues in contact with GLU 525 (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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521A ASN 3.0 12.0 + - - +
522A LYS* 3.8 31.2 + - + +
523A SER 3.3 0.2 - - - -
524A MET* 1.3 77.2 - - - +
526A LEU* 1.3 58.2 + - + +
528A ASP* 3.2 10.0 + - + +
529A GLU* 2.9 33.2 + - + +
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Residues in contact with LEU 526 (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 LYS* 4.8 22.2 - - + -
384A LEU* 3.7 28.3 - - + -
511A GLU* 6.3 0.4 - - - -
522A LYS* 2.9 48.2 + - + +
523A SER 4.0 2.9 - - - +
525A GLU* 1.3 77.0 - - + +
527A LEU* 1.3 58.7 + - - +
529A GLU* 2.9 45.9 + - + +
530A ARG 3.4 0.7 + - - -
531A LYS* 3.3 32.4 + - + +
532A PHE* 4.4 6.7 - - + -
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Residues in contact with LEU 527 (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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523A SER 2.9 19.0 + - - +
524A MET* 3.6 15.3 - - + +
525A GLU 3.2 0.2 - - - -
526A LEU* 1.3 77.6 - - - +
528A ASP* 1.3 64.2 + - - +
529A GLU 3.3 0.5 + - - -
530A ARG* 3.4 13.2 + - - -
531A LYS 5.2 0.4 - - - +
532A PHE* 4.1 23.1 - - + +
559A ASP* 3.5 32.1 - - + +
1636A LEU* 3.8 26.7 - - + -
1637A ASN 5.2 0.7 - - - +
1639A THR* 5.3 10.3 - - + +
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Residues in contact with ASP 528 (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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524A MET* 3.0 24.7 + - - +
525A GLU* 3.2 10.2 + - - +
527A LEU* 1.3 80.9 - - - +
529A GLU* 1.3 55.4 + - - +
530A ARG* 3.3 4.2 + - - +
1639A THR* 3.7 22.4 + - - -
1640A LYS* 6.0 1.2 - - - +
1641A GLN* 5.5 2.4 + - - -
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Residues in contact with GLU 529 (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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522A LYS* 5.8 0.7 + - - -
525A GLU* 2.9 18.1 + - + +
526A LEU* 2.9 35.9 + - + +
528A ASP* 1.3 76.7 - - - +
530A ARG* 1.3 61.1 + - - +
531A LYS* 2.9 30.6 + - + +
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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