Contacts of the helix formed by residues 533 - 543 (chain A) in PDB entry 5W3R
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 SER 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A LEU* 1.3 80.8 - - - +
534A ARG* 1.3 64.3 + - - +
535A LEU* 3.7 7.5 + - - +
536A LYS* 3.0 26.9 + - - +
537A ALA* 3.0 23.0 + - - +
555A ARG* 3.8 0.2 - - - -
558A GLU* 3.5 30.5 + - - -
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Residues in contact with ARG 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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533A SER* 1.3 73.7 - - - +
535A LEU* 1.3 59.2 + - - +
537A ALA* 3.4 0.3 + - - +
538A ALA* 3.0 28.8 + - + +
555A ARG* 3.6 14.3 - - - +
558A GLU* 4.9 1.6 + - - +
576A HIS* 3.5 42.1 + - + +
578A ARG* 2.6 34.4 - - - +
701A PO4 3.1 29.4 + - - +
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Residues in contact with LEU 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 SER* 3.2 6.3 + - - +
534A ARG* 1.3 80.3 - - - +
536A LYS* 1.3 57.4 + - - +
538A ALA* 3.3 7.1 + - + +
539A GLN* 2.9 63.7 + - + +
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Residues in contact with LYS 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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532A LEU* 3.7 25.8 - - + -
533A SER* 3.0 18.6 + - - +
535A LEU* 1.3 77.0 - - - +
537A ALA* 1.3 57.7 + - - +
539A GLN* 3.2 13.4 + - + +
540A LEU* 2.8 60.6 + - + +
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Residues in contact with ALA 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 LEU* 4.0 15.1 - - + +
533A SER 3.0 18.4 + - - +
534A ARG 3.7 3.4 - - - +
536A LYS* 1.3 76.8 - - - +
538A ALA* 1.3 61.7 + - - +
540A LEU* 3.3 1.4 + - - +
541A VAL* 3.1 28.4 + - - +
553A LEU* 4.0 9.4 - - + -
555A ARG* 3.4 30.7 - - - +
567A THR* 3.8 13.9 - - + +
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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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534A ARG* 3.0 17.7 + - + +
535A LEU* 3.6 9.6 - - + +
537A ALA* 1.3 77.2 - - - +
539A GLN* 1.3 58.8 + - + +
541A VAL* 3.2 4.0 + - - +
542A LEU* 2.9 39.8 + - + +
567A THR* 4.1 2.6 - - - +
574A ALA* 3.5 28.9 - - + -
576A HIS* 4.2 7.0 - - - +
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Residues in contact with GLN 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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535A LEU* 2.9 50.7 + - + +
536A LYS* 3.9 14.8 + - + +
538A ALA* 1.3 75.7 - - + +
540A LEU* 1.3 56.4 + - - +
542A LEU* 3.7 6.0 - - + +
543A THR* 2.7 35.7 + - - -
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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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529A HIS* 4.5 11.7 - - + +
532A LEU* 4.2 10.1 - - + -
536A LYS* 2.8 57.4 + - + +
537A ALA 3.7 4.3 - - - +
539A GLN* 1.3 78.8 - - - +
541A VAL* 1.3 63.2 + - - +
542A LEU 3.3 0.3 + - - -
543A THR* 3.3 19.1 + - - +
544A GLY 4.9 0.3 + - - -
548A SER* 5.4 0.9 + - - -
551A VAL* 5.3 0.3 - - - +
553A LEU* 3.9 24.5 - - + -
625A VAL* 4.2 24.9 - - + +
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Residues in contact with VAL 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 ALA 3.1 15.1 + - - +
538A ALA* 3.4 14.1 - - - +
540A LEU* 1.3 77.9 - - - +
542A LEU* 1.3 61.8 + - + +
548A SER* 3.3 15.7 - - - -
551A VAL* 3.7 32.1 - - + +
552A PHE* 4.0 11.9 - - - +
553A LEU* 4.3 11.0 - - + -
567A THR* 3.9 23.6 - - + +
568A PHE 3.8 22.0 - - - +
569A ASN* 2.9 23.9 + - + +
574A ALA* 4.4 2.0 - - + -
625A VAL* 4.3 2.0 - - + -
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Residues in contact with LEU 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 ALA* 2.9 25.9 + - + +
539A GLN* 3.7 5.6 - - + +
541A VAL* 1.3 77.9 - - + +
543A THR* 1.3 63.9 + - - +
544A GLY 3.2 2.7 - - - -
545A GLY* 2.9 16.7 + - - +
569A ASN* 3.5 19.7 - - + +
572A GLY* 3.5 36.1 - - - +
573A LYS* 3.6 11.7 - - - -
574A ALA* 3.8 23.3 - - + +
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Residues in contact with THR 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 GLN 2.7 21.0 + - - -
540A LEU* 3.3 17.2 + - - +
542A LEU* 1.3 78.7 - - - +
544A GLY* 1.3 57.9 + - - +
545A GLY 3.4 2.3 + - - -
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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