Contacts of the helix formed by residues 534 - 546 (chain A) in PDB entry 1CWS
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 GLU 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A ASN 3.1 7.4 + - - +
533A HIS* 1.3 75.9 + - + +
535A ALA* 1.3 57.6 - - - +
537A LYS* 3.2 55.3 + - - +
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Residues in contact with ALA 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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533A HIS* 3.0 23.5 + - + -
534A GLU* 1.3 76.0 - - - +
536A PHE* 1.3 73.5 + - + +
537A LYS 3.7 0.9 - - - -
538A ASP* 6.0 0.7 - - - +
539A GLU* 4.7 3.5 - - - +
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Residues in contact with PHE 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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430A TYR* 3.6 41.5 - + + -
529A ARG* 3.4 44.9 - - - -
531A MET 5.5 0.4 - - - -
533A HIS* 2.9 52.3 + + + +
535A ALA* 1.3 87.3 - - + +
537A LYS* 1.3 55.9 + - - +
538A ASP* 3.1 4.0 - - - +
539A GLU* 2.9 20.9 + - + +
540A LEU* 2.8 34.8 + - - +
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Residues in contact with LYS 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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532A ASN 5.6 1.8 - - - +
533A HIS 3.6 4.3 + - - +
534A GLU* 3.2 56.7 + - - +
535A ALA 3.7 1.2 - - - -
536A PHE* 1.3 77.2 - - - +
538A ASP* 1.3 67.0 + - - +
540A LEU* 3.3 12.1 + - - +
541A LYS* 3.1 32.0 + - + +
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Residues in contact with ASP 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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535A ALA 5.5 0.2 - - - -
536A PHE* 3.1 0.8 - - - -
537A LYS* 1.3 82.0 - - - +
539A GLU* 1.3 70.6 + - - +
541A LYS* 3.2 12.9 + - - +
542A THR* 2.9 34.9 + - - +
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Residues in contact with GLU 539 (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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430A TYR* 3.7 26.9 - - + -
535A ALA 4.7 2.8 - - - +
536A PHE* 2.9 31.0 + - + +
538A ASP* 1.3 84.3 - - - +
540A LEU* 1.3 68.6 + - - +
542A THR* 3.4 11.1 + - - +
543A PHE* 3.0 26.2 + - - +
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Residues in contact with LEU 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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428A TYR* 4.5 10.8 - - + -
430A TYR* 3.6 19.9 - - - +
531A MET* 3.5 41.5 - - + +
532A ASN* 4.8 4.9 - - + -
536A PHE 2.8 9.8 + - - +
537A LYS* 3.4 13.9 - - - +
539A GLU* 1.3 79.0 - - - +
541A LYS* 1.3 71.7 + - + +
543A PHE* 3.4 4.0 + - - +
544A ARG* 3.1 59.1 + - + +
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Residues in contact with LYS 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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537A LYS* 3.1 19.0 + - - +
538A ASP* 3.2 13.9 + - - +
540A LEU* 1.3 89.7 - - + +
542A THR* 1.3 61.9 + - - +
543A PHE 3.4 0.2 + - - -
544A ARG* 3.4 12.6 + - - +
545A LEU* 3.4 20.7 + - + +
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Residues in contact with THR 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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538A ASP* 2.9 19.0 + - - +
539A GLU* 3.6 14.0 + - - +
541A LYS* 1.3 76.2 - - - +
543A PHE* 1.4 66.6 + - + +
545A LEU* 3.4 22.3 + - - +
546A LYS* 3.8 21.5 - - + +
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Residues in contact with PHE 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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428A TYR* 3.4 43.7 - + + -
429A PRO* 3.5 30.1 - - + -
430A TYR* 5.4 1.6 - - + -
444A PRO* 3.6 27.6 - - + -
445A LEU* 3.7 35.9 - - + -
539A GLU 3.0 18.3 + - - +
540A LEU 3.8 3.4 - - - +
541A LYS 3.2 0.2 - - - -
542A THR* 1.4 77.5 - - + +
544A ARG* 1.3 67.0 + - - +
546A LYS* 2.8 41.3 + - + +
547A THR* 3.8 4.8 + - + -
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Residues in contact with ARG 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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428A TYR* 3.2 25.9 + - + +
531A MET* 3.6 30.7 - - - +
540A LEU* 3.1 38.4 + - + +
541A LYS* 3.4 7.2 + - - +
543A PHE* 1.3 76.7 - - - +
545A LEU* 1.3 61.5 + - + +
546A LYS 3.0 3.2 + - - -
547A THR* 3.0 33.2 + - - +
550A TRP* 3.5 14.1 - - + -
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Residues in contact with LEU 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 LYS* 3.4 15.4 + - + +
542A THR* 3.4 14.8 + - - +
543A PHE 3.1 1.2 + - - -
544A ARG* 1.3 80.2 - - + +
546A LYS* 1.3 59.0 + - + +
547A THR 3.5 1.7 - - - +
550A TRP* 4.0 29.3 - - + -
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Residues in contact with LYS 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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445A LEU* 3.8 13.4 - - + +
447A ARG* 2.9 42.1 + - - +
542A THR* 3.8 26.1 - - + +
543A PHE* 2.8 34.3 + - + +
545A LEU* 1.3 79.9 - - + +
547A THR* 1.3 61.7 + - - +
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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