Contacts of the helix formed by residues 539 - 547 (chain H) in PDB entry 4D1Q
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 LYS 539 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537H ASP* 3.1 22.2 + - - +
538H PHE* 1.3 82.7 - - - +
540H VAL* 1.3 66.5 + - - +
541H MET* 4.9 2.9 - - + +
542H GLU* 3.2 54.0 + - + +
543H TRP* 3.4 4.2 + - - +
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Residues in contact with VAL 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380H PRO* 4.5 10.8 - - + +
383H CYS* 5.1 1.6 - - - -
384H PHE* 6.2 0.9 - - + -
435H PHE 4.2 1.3 - - - +
436H TYR* 3.3 48.4 - - + -
437H PRO* 4.5 1.3 - - + -
538H PHE* 3.5 20.6 + - + -
539H LYS* 1.3 69.6 - - - +
541H MET* 1.3 64.1 + - + +
543H TRP* 2.8 22.0 + - - +
544H TRP* 3.2 15.7 + - + -
562H LEU* 3.2 44.0 - - + -
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Residues in contact with MET 541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H HIS* 4.1 20.9 - - - -
202H ASN* 4.2 20.6 - - - +
204H LEU* 4.2 29.4 - - + +
378H SER 5.1 2.2 - - - +
379H SER* 4.7 4.9 - - - -
380H PRO* 3.8 37.8 - - + +
539H LYS* 3.5 2.8 - - + +
540H VAL* 1.3 83.0 - - + +
542H GLU* 1.3 62.4 + - - +
544H TRP* 4.9 0.2 - - - -
545H ASN* 3.0 33.5 + - - +
559H LEU* 3.8 25.4 - - + +
562H LEU* 4.7 5.4 - - + -
563H SER 5.8 0.2 - - - -
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Residues in contact with GLU 542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H ASN* 4.3 16.1 - - - +
537H ASP 5.3 0.2 - - - +
539H LYS* 3.2 50.3 + - + +
540H VAL 3.1 0.6 - - - -
541H MET* 1.3 77.3 - - - +
543H TRP* 1.3 55.8 + - - +
545H ASN* 4.1 1.4 - - - +
546H LEU* 3.2 28.1 + - + +
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Residues in contact with TRP 543 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H PRO* 3.7 14.4 - - + -
527H TYR* 3.6 23.3 - + - -
530H GLU* 3.7 28.6 + - + -
532H VAL* 3.2 28.0 - - + +
538H PHE* 4.0 24.5 - + + -
539H LYS 3.4 0.6 + - - +
540H VAL 2.8 10.3 + - - +
542H GLU* 1.3 75.7 - - - +
544H TRP* 1.3 131.7 + + - +
545H ASN 3.2 1.1 - - - -
546H LEU* 3.0 4.5 + - + +
547H ASN* 2.9 52.3 + - + +
551H TYR* 4.2 12.8 - + - -
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Residues in contact with TRP 544 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H PHE* 3.0 49.9 + + - -
437H PRO* 3.9 2.5 - - + +
527H TYR* 3.5 31.0 - + - -
540H VAL* 3.2 14.2 + - + -
541H MET 3.5 0.6 + - - +
543H TRP* 1.3 106.3 - + - +
545H ASN* 1.3 63.6 + - - +
547H ASN* 3.1 3.9 + - + -
548H SER* 3.0 21.8 + - - -
551H TYR* 4.3 9.9 - + + -
554H LEU* 3.9 17.5 - - + -
555H SER* 3.5 41.6 - - - -
558H ALA* 3.4 12.6 - - + -
559H LEU* 3.6 25.1 - - + -
562H LEU* 3.6 21.1 - - + +
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Residues in contact with ASN 545 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H HIS* 3.0 34.1 + - - -
201H ASN* 5.2 3.8 - - - +
202H ASN* 3.6 30.8 - - - +
541H MET 3.0 21.7 + - - +
542H GLU 4.3 0.4 - - - +
544H TRP* 1.3 76.6 - - - +
546H LEU* 1.3 62.5 + - - +
548H SER* 2.9 25.9 + - - -
559H LEU* 3.6 17.8 - - - +
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Residues in contact with LEU 546 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542H GLU* 3.2 19.7 + - + +
543H TRP* 3.0 7.6 + - - +
545H ASN* 1.3 77.8 - - - +
547H ASN* 1.3 74.3 + - - +
548H SER* 3.3 5.5 + - - -
549H LYS* 4.3 7.6 + - - +
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Residues in contact with ASN 547 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530H GLU* 4.9 1.9 - - - +
543H TRP* 2.9 65.1 + - + +
544H TRP* 3.1 4.5 + - + +
546H LEU* 1.3 90.0 - - - +
548H SER* 1.3 62.2 + - - +
549H LYS* 2.9 5.9 + - - -
550H LYS* 3.0 23.3 + - + +
551H TYR* 3.0 31.3 + - + -
555H SER* 4.8 1.6 - - - -
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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