Contacts of the helix formed by residues 609 - 616 (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 GLU 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ARG* 4.7 16.2 + - - -
438A PHE* 3.7 31.8 - - + -
565A ASP* 3.1 20.9 + - - +
607A ALA 3.3 0.2 + - - -
608A ASN* 1.4 78.9 - - + +
610A TRP* 1.3 59.9 + - - +
611A LEU 3.4 2.2 - - - -
612A MET* 3.6 13.1 + - + +
613A LYS* 3.0 44.0 + - + +
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Residues in contact with TRP 610 (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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489A SER* 3.1 42.9 + - - -
490A PHE* 3.1 24.2 - + + +
493A LEU* 3.6 31.4 - - + -
550A LEU* 6.2 0.9 - - + -
554A LEU* 4.0 17.4 - - + +
565A ASP* 3.3 3.7 + - - +
568A PHE* 3.7 26.7 - + + -
594A PHE* 3.4 33.4 - + - -
605A TYR* 4.0 12.3 - - + -
606A LYS 3.1 17.4 + - - -
607A ALA* 3.5 27.3 + - + +
608A ASN 3.6 8.1 - - - -
609A GLU* 1.3 74.9 - - - +
611A LEU* 1.4 64.3 + - - +
613A LYS* 4.1 4.4 - - + +
614A ASN* 3.1 27.5 + - - +
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Residues in contact with LEU 611 (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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554A LEU* 3.7 21.3 - - + -
557A GLU* 3.7 22.4 - - + -
558A CYS* 4.0 23.3 - - + +
563A ALA* 3.7 28.3 - - + +
564A THR* 3.6 25.4 - - - +
565A ASP* 3.3 17.3 + - - +
568A PHE* 4.0 10.1 - - + -
610A TRP* 1.4 77.1 - - - +
612A MET* 1.3 71.5 + - + +
614A ASN* 4.1 0.4 - - - +
615A MET* 3.1 30.3 + - - +
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Residues in contact with MET 612 (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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438A PHE* 5.8 13.0 - - + -
558A CYS* 5.8 0.7 - - + +
565A ASP* 5.9 0.4 - - - +
609A GLU* 3.6 16.3 + - + +
610A TRP 3.2 0.4 - - - -
611A LEU* 1.3 87.3 - - + +
613A LYS* 1.4 55.3 + - - +
614A ASN 3.2 1.3 - - - -
615A MET* 3.7 30.5 - - + -
616A ASP* 2.7 31.0 + - - -
617A PRO* 3.2 27.6 - - + +
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Residues in contact with LYS 613 (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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289A SER* 4.8 10.6 + - - -
445A LYS* 5.3 13.0 - - - +
489A SER* 3.2 17.2 + - - +
490A PHE* 4.3 24.5 - - + -
491A GLU* 2.9 42.8 + - - +
608A ASN 4.5 6.9 + - - +
609A GLU* 3.0 36.2 + - + +
610A TRP* 4.1 3.8 - - + +
612A MET* 1.4 74.2 - - + +
614A ASN* 1.4 56.3 + - - +
616A ASP* 4.1 8.1 + - - +
670A VAL* 3.3 24.3 - - - +
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Residues in contact with ASN 614 (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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490A PHE* 3.9 8.0 - - + -
551A LEU* 5.2 0.5 - - - +
554A LEU* 3.7 27.2 - - + +
555A ASP* 3.0 29.2 + - - +
558A CYS* 3.9 6.9 - - - -
610A TRP 3.1 18.9 + - - +
611A LEU 4.1 2.7 - - - +
613A LYS* 1.4 74.6 - - - +
615A MET* 1.3 63.8 + - - +
616A ASP* 3.3 1.1 - - - +
669A THR* 3.4 19.2 + - - +
670A VAL* 2.8 33.1 + - - +
671A GLY* 3.0 33.6 + - - -
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Residues in contact with MET 615 (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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558A CYS* 3.5 34.8 - - + +
559A TRP* 3.7 49.4 - - + -
611A LEU 3.1 18.4 + - - +
612A MET* 3.7 24.9 - - + +
614A ASN* 1.3 76.0 - - - +
616A ASP* 1.4 65.4 + - - +
617A PRO* 4.6 11.7 - - + -
644A ILE* 3.6 26.6 - - + +
668A ARG 5.4 2.3 - - - +
669A THR* 4.7 8.6 - - - +
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Residues in contact with ASP 616 (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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288A LYS* 2.8 39.1 + - - -
445A LYS* 5.2 5.2 + - - -
449A GLU* 4.7 2.9 - - - +
612A MET 2.7 18.1 + - - +
613A LYS* 4.5 5.3 - - - +
614A ASN 3.3 0.4 - - - -
615A MET* 1.4 74.4 - - - +
617A PRO* 1.4 68.4 - - - +
618A LEU* 3.8 12.3 + - - +
644A ILE* 4.5 9.8 + - + +
670A VAL* 3.7 27.5 - - + +
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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