Contacts of the helix formed by residues 541 - 554 (chain A) in PDB entry 5C53
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 GLN 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A GLU* 2.9 48.5 + - + +
540A GLN* 1.3 79.7 + - - +
542A ASP* 1.3 64.6 + - + +
543A VAL 3.4 0.2 - - - -
544A MET* 3.2 19.8 + - + +
545A ALA* 2.9 28.1 + - - +
397B GLN* 5.2 5.7 - - - +
400B GLN* 5.8 8.5 - - + +
122C ARG* 5.0 15.8 - - - +
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Residues in contact with ASP 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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539A PHE 4.3 10.9 + - - +
541A GLN* 1.3 84.8 - - + +
543A VAL* 1.3 69.9 + - + +
544A MET 3.1 0.2 - - - -
545A ALA* 3.4 6.8 + - - +
546A ARG* 2.9 35.7 + - - +
400B GLN* 5.0 12.5 + - + +
404B ASN* 3.5 31.8 - - - +
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Residues in contact with VAL 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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539A PHE 5.7 0.7 - - - +
540A GLN* 3.2 32.7 - - + +
542A ASP* 1.3 85.6 - - + +
544A MET* 1.3 59.4 + - + +
546A ARG* 3.7 18.9 - - + +
547A ALA* 2.9 28.2 + - - +
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Residues in contact with MET 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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540A GLN* 3.5 24.0 + - - +
541A GLN* 3.3 19.5 - - + +
542A ASP 3.1 0.2 - - - -
543A VAL* 1.3 81.7 - - + +
545A ALA* 1.3 60.7 + - - +
547A ALA* 3.3 5.5 + - - +
548A CYS* 2.9 29.4 + - + +
397B GLN* 4.2 23.6 - - - +
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Residues in contact with ALA 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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541A GLN 2.9 15.8 + - - +
542A ASP 3.7 5.4 - - - +
544A MET* 1.3 76.2 - - - +
546A ARG* 1.3 57.6 + - - +
548A CYS* 3.6 8.6 + - - +
549A LEU* 2.9 29.1 + - - +
397B GLN* 3.3 38.3 + - + +
398B VAL* 4.8 0.5 - - - -
400B GLN* 4.3 11.2 - - + -
401B GLY* 4.0 14.4 - - - +
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Residues in contact with ARG 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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542A ASP* 2.9 27.9 + - - +
543A VAL* 3.7 16.2 - - - +
544A MET 3.2 0.2 - - - -
545A ALA* 1.3 73.8 - - - +
547A ALA* 1.3 62.3 + - - +
549A LEU* 3.1 12.6 + - + +
550A GLN* 2.9 35.1 + - + +
401B GLY* 4.6 5.5 - - - -
404B ASN* 3.2 23.2 - - - +
405B GLU* 5.9 3.8 - - - +
408B GLU* 2.6 42.2 + - - -
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Residues in contact with ALA 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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543A VAL 2.9 20.0 + - - +
544A MET* 3.7 6.1 - - - +
546A ARG* 1.3 77.1 - - - +
548A CYS* 1.3 58.6 + - - +
550A GLN* 3.4 6.8 + - - +
551A LYS* 2.9 44.9 + - + +
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Residues in contact with CYS 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 MET* 2.9 17.7 + - + +
545A ALA* 3.7 8.3 - - - +
547A ALA* 1.3 75.8 - - - +
549A LEU* 1.3 58.4 + - - +
551A LYS* 3.8 12.0 + - - +
552A LEU* 2.9 37.1 + - - +
395B LEU* 5.6 7.2 - - - -
397B GLN* 4.6 21.1 - - - +
398B VAL* 4.2 24.9 - - - -
448B LEU* 6.1 2.0 - - - -
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Residues in contact with LEU 549 (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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545A ALA 2.9 19.6 + - - +
546A ARG* 3.3 9.9 - - + +
548A CYS* 1.3 79.5 - - - +
550A GLN* 1.3 59.5 + - + +
552A LEU* 3.2 6.7 + - + +
553A LYS* 2.9 26.8 + - + +
398B VAL* 3.7 29.8 - - + +
401B GLY* 3.5 26.5 - - - +
402B LEU* 4.5 4.5 - - + +
405B GLU* 3.2 30.1 - - + +
468B ILE* 3.7 29.6 - - + -
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Residues in contact with GLN 550 (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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546A ARG* 2.9 23.4 + - + +
547A ALA* 4.0 6.1 - - - +
549A LEU* 1.3 78.0 - - + +
551A LYS* 1.3 62.4 + - + +
553A LYS* 3.2 17.6 + - + +
554A GLY* 3.2 12.1 + - - -
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Residues in contact with LYS 551 (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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547A ALA* 2.9 31.4 + - + +
548A CYS* 3.8 10.1 + - - +
550A GLN* 1.3 77.3 - - + +
552A LEU* 1.3 60.3 + - - +
553A LYS 3.6 0.2 + - - -
554A GLY* 4.1 1.4 + - - -
555A THR* 3.3 24.9 - - - +
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Residues in contact with LEU 552 (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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548A CYS* 2.9 22.4 + - - +
549A LEU* 3.5 7.0 - - + +
551A LYS* 1.3 75.6 - - - +
553A LYS* 1.3 64.1 + - - +
555A THR* 2.9 19.3 + - - +
556A THR* 3.4 9.7 + - - -
398B VAL* 4.9 17.7 - - + -
447B THR 4.3 10.3 - - - +
448B LEU* 3.7 46.4 - - + +
450B ASN 4.2 3.7 - - - +
451B GLY* 4.5 2.2 - - - -
468B ILE* 3.8 29.2 - - + -
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Residues in contact with LYS 553 (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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549A LEU* 2.9 14.6 + - + +
550A GLN* 3.2 16.1 + - + +
552A LEU* 1.3 77.3 - - - +
554A GLY* 1.3 59.4 + - - +
555A THR 2.9 10.5 + - - -
556A THR 3.4 4.0 + - - -
557A GLU* 4.2 7.4 + - - +
467B HIS* 3.1 68.8 + - + +
468B ILE* 4.1 8.7 - - + -
469B SER* 2.8 54.9 + - - +
470B LYS* 3.3 12.4 - - - +
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Residues in contact with GLY 554 (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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550A GLN 3.2 10.2 + - - -
551A LYS 4.1 1.3 + - - -
552A LEU 3.6 0.4 - - - -
553A LYS* 1.3 80.0 - - - +
555A THR* 1.3 63.1 + - - +
556A THR 3.7 0.9 - - - -
557A GLU* 4.7 15.9 - - - +
558A LEU* 5.6 1.0 - - - +
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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