Contacts of the helix formed by residues 606 - 613 (chain B) in PDB entry 1XMI
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 LYS 606 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580B VAL* 5.9 4.4 - - + +
583B GLU* 3.6 37.2 + - - +
604B THR* 3.1 11.4 + - - +
605B SER* 1.3 90.7 + - - +
607B MET* 1.3 65.0 + - - +
608B GLU* 4.4 4.9 - - + +
609B HIS* 3.1 27.4 + - + +
610B LEU* 3.3 16.7 + - - +
648B ASP* 2.7 34.5 + - - +
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Residues in contact with MET 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B SER 3.7 4.0 + - - -
606B LYS* 1.3 71.6 - - - +
608B GLU* 1.3 63.0 + - - +
610B LEU* 3.2 8.7 + - - +
611B LYS* 3.0 42.1 + - - +
630B PHE* 3.7 34.3 - - + -
634B GLN* 4.4 13.2 - - + +
640B PHE* 4.6 31.2 - - + -
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B LYS* 3.4 41.4 + - + +
587B PHE* 4.4 6.4 - - + -
606B LYS* 3.2 3.3 - - + +
607B MET* 1.3 78.8 - - - +
609B HIS* 1.3 72.7 + - + +
611B LYS* 3.4 18.4 - - + +
612B LYS* 3.3 26.2 + - + +
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Residues in contact with HIS 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 4.7 1.4 - - - +
455B ALA* 4.6 2.3 - - - +
575B PHE* 3.8 22.2 - + - -
583B GLU* 3.4 31.3 + - - +
584B LYS* 5.5 2.8 - - - +
587B PHE* 3.5 51.1 - + + +
602B LEU* 3.9 7.0 - - + +
604B THR* 2.8 36.8 + - + -
606B LYS* 3.1 19.3 + - + +
608B GLU* 1.3 80.9 - - + +
610B LEU* 1.3 64.0 + - - +
612B LYS* 3.2 3.6 + - - +
613B ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B ALA* 4.2 6.3 - - + +
457B ALA* 4.5 5.6 - - + -
604B THR* 3.8 29.2 - - + +
605B SER 4.6 3.1 - - - +
606B LYS 3.3 24.4 + - - +
607B MET* 3.2 9.3 + - - +
609B HIS* 1.3 76.4 - - - +
611B LYS* 1.3 65.0 + - - +
612B LYS 3.4 0.5 + - - -
613B ALA* 3.4 10.4 + - - +
616B ILE* 3.7 47.9 - - + +
618B ILE* 4.0 17.7 - - + -
630B PHE* 3.5 25.0 - - + +
633B LEU* 4.6 6.3 - - + -
645B MET* 4.4 13.7 - - - -
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Residues in contact with LYS 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B MET* 3.0 42.5 + - - +
608B GLU* 3.4 20.2 - - + +
610B LEU* 1.3 77.6 - - - +
612B LYS* 1.3 62.4 + - + +
613B ALA 4.1 4.3 - - - +
630B PHE* 3.6 37.5 - - + +
634B GLN* 6.1 0.6 - - - +
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Residues in contact with LYS 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 4.5 5.8 - - + +
587B PHE* 3.9 16.6 - - + -
588B GLU* 3.8 25.4 + - - -
592B CYS* 3.9 23.5 - - - +
608B GLU* 3.3 14.5 + - + +
609B HIS 3.2 5.5 + - - +
610B LEU 3.2 0.6 - - - -
611B LYS* 1.3 79.3 - - + +
613B ALA* 1.3 65.5 + - - +
614B ASP* 3.7 4.2 + - - +
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Residues in contact with ALA 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 3.7 20.4 - - + +
455B ALA* 3.8 17.9 - - + +
609B HIS 3.1 14.8 + - - +
610B LEU 3.7 13.7 - - - +
611B LYS 3.4 4.8 - - - +
612B LYS* 1.3 80.1 - - - +
614B ASP* 1.3 63.8 + - - +
615B LYS 3.5 19.7 - - - +
616B ILE* 4.1 2.5 - - + +
629B THR* 5.9 1.4 - - - -
630B PHE* 5.6 2.8 + - - +
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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