Contacts of the helix formed by residues 529 - 538 (chain A) in PDB entry 5UNJ
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 ASN 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLY 5.0 0.8 + - - -
346A CYS* 3.9 26.2 - - - +
347A LYS* 2.5 40.7 + - - +
350A ASP* 3.4 28.7 - - + +
526A VAL* 4.7 0.6 - - - +
527A PRO* 2.9 31.7 + - - +
528A TYR* 1.3 75.7 + - - +
530A ASN* 1.3 67.5 + - - +
531A LEU 3.2 3.0 + - - -
532A LEU* 3.2 11.1 + - + -
533A ILE* 2.9 29.4 + - + +
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Residues in contact with ASN 530 (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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350A ASP* 4.2 1.4 + - - -
528A TYR* 3.1 49.3 + - + +
529A ASN* 1.3 73.7 + - - +
531A LEU* 1.3 57.8 + - - +
533A ILE* 4.0 4.2 - - - +
534A GLU* 2.9 33.1 + - - +
744C LEU* 4.2 16.8 - - + +
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Residues in contact with LEU 531 (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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350A ASP* 3.4 10.2 + - - +
353A LEU* 3.9 17.3 - - + +
354A PHE* 3.8 54.5 - - + +
357A VAL* 4.6 4.0 - - + -
529A ASN 3.3 0.6 - - - -
530A ASN* 1.3 77.0 - - - +
532A LEU* 1.3 66.0 + - - +
534A GLU* 3.3 5.0 + - + +
535A MET* 3.0 49.2 + - + +
744C LEU* 3.9 21.6 - - + +
745C LEU* 4.6 16.8 - - + +
748C LEU* 4.1 14.1 - - + -
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Residues in contact with LEU 532 (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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346A CYS* 3.8 40.6 - - + +
349A ALA* 4.8 12.6 - - + -
350A ASP* 2.8 23.8 + - + +
353A LEU* 3.9 15.0 - - + +
382A TRP* 3.8 29.2 - - + -
386A LEU* 5.6 0.4 - - + -
517A LEU* 4.7 14.6 - - + -
526A VAL* 4.4 15.0 - - + -
529A ASN* 3.2 9.4 + - + +
531A LEU* 1.3 72.0 - - - +
533A ILE* 1.3 63.7 + - + +
535A MET* 3.3 2.6 + - - +
536A LEU* 3.1 30.0 + - + +
601A RJW 5.0 3.1 - - + -
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Residues in contact with ILE 533 (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 HIS* 3.4 51.1 - - + +
526A VAL* 3.6 26.5 - - + +
527A PRO 4.8 1.6 - - - +
528A TYR* 5.9 0.4 - - - -
529A ASN 2.9 26.2 + - - +
530A ASN* 4.0 4.0 - - - +
532A LEU* 1.3 76.5 - - + +
534A GLU* 1.3 63.9 + - - +
536A LEU* 3.1 15.6 + - + +
537A HIS* 3.0 33.7 + - + +
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Residues in contact with GLU 534 (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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375A MET* 5.2 0.5 - - - +
379A GLN* 5.6 4.1 + - - +
530A ASN* 2.9 18.8 + - - +
531A LEU* 3.3 6.7 + - + +
533A ILE* 1.3 77.9 - - - +
535A MET* 1.3 63.4 + - - +
537A HIS* 3.2 16.3 + - - +
538A ALA* 3.2 12.5 + - - +
743C SER* 2.8 28.3 + - - -
744C LEU* 2.8 31.3 + - - +
745C LEU* 3.0 23.8 + - - +
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Residues in contact with MET 535 (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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353A LEU* 4.4 11.7 - - + -
357A VAL* 5.9 3.1 - - + -
378A LEU* 3.4 32.3 - - + +
379A GLN* 3.7 14.6 - - - +
382A TRP* 3.3 51.4 + - + -
514A GLU* 4.7 1.2 - - - +
531A LEU* 3.0 39.8 + - + +
532A LEU 3.8 3.6 - - - +
534A GLU* 1.3 79.3 - - - +
536A LEU* 1.3 62.1 + - - +
538A ALA* 3.3 17.9 + - - +
745C LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 536 (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 TRP* 3.8 24.9 - - + -
514A GLU* 3.7 38.1 - - + +
517A LEU* 4.2 29.4 - - + +
518A TYR* 3.6 32.2 - - + +
521A HIS* 4.8 2.7 - - + -
526A VAL* 5.6 1.1 - - + -
532A LEU* 3.1 25.7 + - + +
533A ILE* 3.1 27.3 + - + +
535A MET* 1.3 78.7 - - - +
537A HIS* 1.3 59.8 + - + +
538A ALA 3.5 4.5 + - - +
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Residues in contact with HIS 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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518A TYR* 3.9 26.9 + + - -
521A HIS* 3.8 33.0 - + - -
522A LEU* 5.7 3.2 - - + +
533A ILE* 3.0 27.3 + - + +
534A GLU* 3.2 10.9 + - - +
536A LEU* 1.3 77.2 - - - +
538A ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 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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379A GLN* 3.7 50.1 - - + +
534A GLU 3.2 10.5 + - - +
535A MET* 3.4 16.9 - - - +
536A LEU 3.2 6.4 - - - +
537A HIS* 1.3 82.1 - - - +
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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