Contacts of the helix formed by residues 539 - 548 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A ASP* 3.1 23.6 - - - +
538A PHE* 1.3 80.3 - - - +
540A VAL* 1.3 67.9 + - - +
541A MET* 2.9 4.3 + - + +
542A GLU* 3.1 50.0 + - + +
543A TRP* 3.3 10.2 + - - +
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Residues in contact with VAL 540 (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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380A PRO* 3.7 23.0 - - + +
383A CYS* 5.0 2.9 - - - -
435A PHE 3.0 28.5 - - - +
436A TYR* 3.7 27.0 - - + -
437A PRO* 3.6 18.2 - - + -
538A PHE* 3.2 13.8 - - + -
539A LYS* 1.3 71.3 - - - +
541A MET* 1.3 67.0 + - - +
543A TRP* 3.4 1.9 + - - +
544A TRP* 3.2 29.0 + - - +
562A LEU* 3.3 28.0 - - + -
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Residues in contact with MET 541 (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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199A HIS* 4.0 20.0 - - + -
202A ASN* 3.8 18.8 - - - +
203A GLU* 4.8 0.2 - - - -
204A LEU* 3.8 41.1 - - + +
378A SER 5.3 2.2 - - - +
379A SER* 4.9 5.2 - - - -
380A PRO* 4.0 27.6 - - + +
539A LYS* 2.9 3.6 + - + +
540A VAL* 1.3 85.3 - - + +
542A GLU* 1.3 66.1 + - + +
544A TRP* 3.3 5.2 + - - +
545A ASN* 3.2 23.2 + - - +
559A LEU* 4.1 18.1 - - + +
562A LEU* 5.2 5.6 - - + +
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Residues in contact with GLU 542 (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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202A ASN* 4.6 11.2 - - + +
539A LYS* 3.1 46.7 + - + +
541A MET* 1.3 75.6 - - + +
543A TRP* 1.3 56.7 + - - +
545A ASN* 2.7 31.7 + - - +
546A LEU* 2.9 23.8 + - + +
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Residues in contact with TRP 543 (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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437A PRO* 3.7 17.0 - - + -
527A TYR* 3.2 27.4 - + - -
530A GLU* 3.7 30.1 + - + +
532A VAL* 3.8 19.5 - - + +
538A PHE* 4.2 24.5 - + + -
539A LYS 3.3 8.8 + - - +
540A VAL* 3.9 6.5 - - - +
541A MET 3.4 0.2 - - - -
542A GLU* 1.3 77.9 - - - +
544A TRP* 1.3 104.4 + + - +
546A LEU* 3.7 5.8 - - - -
547A ASN* 3.0 38.5 + - + +
551A TYR* 4.1 10.1 - + - -
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Residues in contact with TRP 544 (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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435A PHE* 3.1 31.9 + + - -
437A PRO* 4.3 0.4 - - - +
527A TYR* 3.4 38.6 - + - -
540A VAL* 3.2 25.8 + - + +
541A MET* 3.3 6.2 + - - +
542A GLU 2.9 2.6 + - - -
543A TRP* 1.3 102.7 - + - +
545A ASN* 1.3 57.8 + - - +
546A LEU 2.9 2.4 + - - -
547A ASN 3.0 2.0 + - - +
548A SER* 2.7 35.7 + - - -
551A TYR* 4.4 11.2 - + + -
554A LEU* 3.9 25.1 - - + -
555A SER* 3.9 25.5 - - - -
558A ALA* 3.4 21.1 - - + -
559A LEU* 3.7 21.8 - - + -
562A LEU* 3.5 19.8 - - + +
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Residues in contact with ASN 545 (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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199A HIS* 3.0 37.8 + - - -
201A ASN 3.5 8.3 + - - +
202A ASN* 3.5 30.1 - - - +
541A MET 3.2 7.8 + - - +
542A GLU 2.7 12.6 + - - +
544A TRP* 1.3 75.0 - - - +
546A LEU* 1.3 59.7 + - + +
548A SER* 2.7 27.9 + - - -
559A LEU* 3.6 11.3 - - - +
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Residues in contact with LEU 546 (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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202A ASN* 5.4 2.9 - - - +
542A GLU* 2.9 26.9 + - + +
543A TRP* 3.8 7.0 - - + +
545A ASN* 1.3 83.0 - - + +
547A ASN* 1.3 73.8 + - - +
548A SER* 2.9 12.1 + - - -
549A LYS* 3.9 13.3 + - - +
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Residues in contact with ASN 547 (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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530A GLU* 3.1 24.3 - - - +
543A TRP* 3.0 41.3 + - + +
544A TRP* 3.0 6.0 + - + +
546A LEU* 1.3 87.2 - - - +
548A SER* 1.3 51.7 + - - +
549A LYS 3.0 3.1 - - - -
550A LYS* 2.9 13.6 + - + +
551A TYR* 2.6 60.1 + - + -
555A SER* 4.8 0.9 - - - -
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Residues in contact with SER 548 (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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544A TRP 2.7 14.3 + - - -
545A ASN* 2.7 32.5 + - - -
546A LEU 2.9 3.0 + - - -
547A ASN* 1.3 69.6 - - - +
549A LYS* 1.3 76.8 + - - +
551A TYR 3.0 1.7 - - - +
552A PRO* 3.0 31.9 - - - +
555A SER* 3.5 18.1 + - - -
559A LEU* 6.3 0.2 - - - -
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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