Contacts of the helix formed by residues 595 - 600 (chain A) in PDB entry 3I5H
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 GLY 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A SER* 5.5 0.2 + - - -
547A ASP* 4.3 0.2 - - - -
593A ILE 3.0 0.8 + - - -
594A ALA* 1.3 79.8 - - - +
596A TRP* 1.3 57.0 + - - +
597A LEU 3.1 3.6 - - - -
598A ASP* 2.5 42.9 + - - +
599A LYS* 2.9 27.4 + - - +
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Residues in contact with TRP 596 (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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474A SER* 3.4 14.0 + - - -
475A PHE* 3.1 59.9 - + + +
478A LEU* 3.5 36.8 - - + -
532A ILE* 4.5 10.8 - - + -
533A LEU* 5.4 0.4 - - + -
536A LEU* 3.7 27.1 - - + -
550A PHE* 4.3 2.5 - + + -
580A PHE* 4.2 10.1 - + - -
591A TYR* 4.2 10.3 - - + -
592A SER 2.5 25.6 + - - -
593A ILE* 2.7 52.2 + - + +
595A GLY* 1.3 76.1 - - - +
597A LEU* 1.3 66.4 + - - +
598A ASP 3.0 1.0 + - - -
599A LYS* 4.6 6.5 - - - +
600A ASN* 3.0 26.7 + - - +
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Residues in contact with LEU 597 (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 LEU* 4.3 8.1 - - + +
539A GLU* 3.2 30.1 - - + +
540A CYS* 3.6 25.9 - - - -
545A ALA* 3.4 42.2 - - + +
546A SER* 3.7 18.8 - - - +
547A ASP* 4.1 13.3 + - - +
550A PHE* 4.8 9.0 - - + -
593A ILE* 4.8 1.0 + - + +
595A GLY 3.1 0.6 - - - -
596A TRP* 1.3 78.7 - - - +
598A ASP* 1.3 68.3 + - - +
600A ASN 4.1 1.7 + - - -
601A LYS* 3.9 21.5 + - - +
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Residues in contact with ASP 598 (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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424A ASN* 4.7 6.9 + - - +
547A ASP* 4.9 4.7 - - - +
595A GLY* 2.5 26.3 + - - +
597A LEU* 1.3 75.7 - - - +
599A LYS* 1.3 69.9 + - + +
600A ASN 3.0 0.9 + - - -
601A LYS* 3.1 19.3 + - - +
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Residues in contact with LYS 599 (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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275A SER* 5.5 7.0 - - - +
279A TYR* 3.8 35.1 + - + -
281A GLN* 4.6 1.4 - - - +
431A LYS* 3.9 9.6 + - - +
472A PHE* 5.8 1.0 - - - -
474A SER* 2.7 30.3 + - - -
475A PHE* 4.3 20.9 - - + -
476A GLU* 2.8 34.6 + - - +
594A ALA* 6.3 0.2 - - - -
595A GLY* 2.9 28.4 + - - +
596A TRP* 4.1 3.1 - - - +
598A ASP* 1.3 76.1 - - + +
600A ASN* 1.3 62.1 + - - +
601A LYS 3.1 7.1 + - - +
647A ILE* 3.3 20.5 - - + +
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Residues in contact with ASN 600 (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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475A PHE* 4.2 8.2 - - + -
536A LEU* 3.6 25.7 - - + +
537A GLU* 4.5 3.5 - - - -
540A CYS* 3.8 14.7 - - - -
596A TRP 3.0 17.4 + - - +
597A LEU 4.5 0.2 - - - +
599A LYS* 1.3 77.1 - - - +
601A LYS* 1.3 56.9 + - - +
646A THR* 2.9 29.5 - - - +
647A ILE* 2.8 34.4 + - - +
648A SER* 3.0 25.8 + - - +
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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