Contacts of the helix formed by residues 534 - 543 (chain A) in PDB entry 5I4E
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 LEU 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A GLU* 3.2 52.3 - - + +
503A GLN* 3.8 24.7 - - + -
504A GLN* 2.8 19.6 + - - +
507A ASN* 4.1 7.6 - - - +
533A ASP* 1.3 77.0 + - - +
535A GLN* 1.3 63.6 + - - +
536A PRO* 3.3 4.2 - - - -
537A CYS* 3.4 5.1 + - + +
538A ILE* 3.0 38.8 + - + +
599A TYR* 3.5 18.8 - - + -
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Residues in contact with GLN 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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504A GLN* 4.6 1.7 + - - -
533A ASP* 3.2 30.7 + - - +
534A LEU* 1.3 77.0 - - - +
536A PRO* 1.3 82.8 - - + +
538A ILE* 4.5 5.6 - - - -
539A ASP* 2.8 37.6 + - + +
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Residues in contact with PRO 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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533A ASP* 3.9 10.5 - - + +
534A LEU* 3.4 4.0 - - - -
535A GLN* 1.3 108.3 - - + +
537A CYS* 1.3 54.3 + - - +
539A ASP* 4.0 2.7 - - + +
540A LEU 3.2 13.2 + - - -
579A HIS* 2.6 36.3 + - + -
580A PRO* 4.9 6.1 - - + -
581A LYS* 3.8 26.5 - - + -
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Residues in contact with CYS 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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500A GLU* 3.6 35.7 - - - +
534A LEU* 3.4 5.8 + - + +
535A GLN 3.3 0.4 - - - -
536A PRO* 1.3 77.3 - - - +
538A ILE* 1.3 66.7 + - - +
540A LEU* 3.2 4.2 + - - +
541A ILE* 3.1 30.0 + - - +
581A LYS* 3.9 14.9 - - + +
596A VAL* 3.8 28.7 - - - -
597A LEU 3.9 15.7 - - - +
598A HIS* 4.1 4.9 - - - -
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Residues in contact with ILE 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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497A TYR* 4.4 3.0 - - + -
500A GLU* 3.6 29.2 - - + +
501A LYS* 3.6 32.1 - - + +
504A GLN* 3.5 37.2 - - + -
534A LEU* 3.0 25.8 + - + +
535A GLN* 4.2 4.7 - - - +
537A CYS* 1.3 74.0 - - - +
539A ASP* 1.3 57.1 + - - +
541A ILE* 3.5 6.1 + - - +
542A GLU* 2.9 49.5 + - - +
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Residues in contact with ASP 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 GLN* 2.8 22.2 + - + +
536A PRO* 4.0 4.3 - - + +
538A ILE* 1.3 75.3 - - - +
540A LEU* 1.3 65.7 + - - +
541A ILE 3.2 0.2 - - - -
542A GLU* 4.5 3.1 - - - +
543A ARG* 2.9 78.5 + - - +
547A PRO* 5.9 0.5 - - - +
549A GLY* 4.4 0.5 - - - -
579A HIS* 5.6 3.9 - - + -
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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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536A PRO 3.2 5.5 + - - +
537A CYS 3.2 6.3 + - - +
539A ASP* 1.3 78.1 + - - +
541A ILE* 1.3 58.6 + - + +
549A GLY* 3.0 9.6 - - - -
550A LEU* 2.9 39.6 + - + -
576A GLN* 3.1 42.2 - - + +
579A HIS* 3.3 39.5 - - + +
581A LYS* 3.8 24.9 - - + +
582A PHE* 3.9 14.1 - - + +
596A VAL* 4.3 16.6 - - + -
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Residues in contact with ILE 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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493A LEU* 4.4 18.4 - - + -
497A TYR* 3.6 48.0 - - + -
500A GLU* 5.7 1.6 - - + -
537A CYS* 3.1 34.1 + - - +
538A ILE* 3.7 3.8 - - - +
540A LEU* 1.3 80.7 - - + +
542A GLU* 1.3 60.0 + - - +
543A ARG 3.7 0.2 - - - -
549A GLY 4.1 0.5 - - - -
550A LEU* 3.7 22.0 + - + +
551A LEU* 3.3 45.4 + - + +
596A VAL* 4.6 2.7 - - + -
598A HIS* 4.4 8.5 - - + +
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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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497A TYR* 2.4 45.4 + - + +
501A LYS* 3.3 22.6 + - - -
538A ILE* 2.9 39.1 + - - +
539A ASP* 4.5 2.5 - - - +
541A ILE* 1.3 74.5 - - - +
543A ARG* 1.3 69.0 + - - +
544A PRO* 3.1 8.9 - - + +
551A LEU* 4.7 0.9 - - - -
552A ALA 6.0 0.2 - - - -
675A LYS* 3.6 30.9 - - + +
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Residues in contact with ARG 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 ASP* 2.9 54.9 + - - +
541A ILE 3.7 1.0 - - - -
542A GLU* 1.3 79.7 - - - +
544A PRO* 1.3 71.1 - - + +
545A ALA 3.3 20.4 + - - +
546A ASN* 4.4 14.8 - - - +
547A PRO* 3.2 32.8 - - - +
549A GLY* 2.7 31.2 + - - +
552A ALA* 3.7 4.7 - - - +
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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