Contacts of the helix formed by residues 606 - 613 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A GLU* 4.2 17.3 - - - +
580D VAL* 5.3 10.2 - - + +
583D GLU* 3.4 39.0 + - - +
604D THR* 2.9 10.2 + - - +
605D SER* 1.3 90.8 - - - +
607D MET* 1.3 65.6 + - - +
608D GLU* 4.5 1.6 - - + +
609D HIS* 3.1 25.9 + - + +
610D LEU* 3.1 24.8 + - - +
648D ASP 5.7 2.7 + - - -
653D PHE* 6.3 1.4 - - - -
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Residues in contact with MET 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A GLU* 4.1 35.1 + - + +
404A GLY* 3.8 10.1 - - - +
407A GLU* 5.2 8.1 - - + -
605D SER 3.7 4.0 + - - -
606D LYS* 1.3 70.7 - - - +
608D GLU* 1.3 56.2 - - - +
610D LEU* 3.3 6.2 + - - +
611D LYS* 2.8 56.8 + - - +
630D PHE* 3.6 23.2 - - + -
634D GLN* 4.1 5.4 - - - +
641D SER* 3.2 40.4 - - - +
644D LEU* 4.0 20.8 - - + +
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Residues in contact with GLU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A GLU* 4.0 19.4 + - - +
584D LYS* 3.4 43.1 - - - +
587D PHE* 3.9 17.8 - - + -
588D GLU* 5.5 3.1 - - - +
606D LYS* 3.3 1.7 - - + +
607D MET* 1.3 80.1 - - - +
609D HIS* 1.3 71.4 + - + +
611D LYS* 3.2 16.7 + - + +
612D LYS* 3.0 30.2 + - + +
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Residues in contact with HIS 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D LEU* 4.7 1.4 - - - +
455D ALA* 4.4 2.3 - - - +
575D PHE* 3.9 22.0 - + - -
583D GLU* 3.5 31.7 + - - +
584D LYS* 5.4 0.4 - - - -
587D PHE* 3.6 50.1 - + + +
602D LEU* 4.0 6.9 - - + +
604D THR* 2.9 33.6 + - + +
606D LYS* 3.1 21.3 + - + +
608D GLU* 1.3 87.6 + - - +
610D LEU* 1.3 63.3 + - - +
612D LYS* 3.3 3.3 + - - +
613D ALA* 3.0 24.1 + - - +
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Residues in contact with LEU 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D ALA* 4.1 8.1 - - + -
457D ALA* 4.3 7.2 - - + -
604D THR* 3.8 30.3 - - + +
605D SER 4.8 1.6 - - - -
606D LYS 3.1 21.0 + - - +
607D MET 3.5 8.3 - - - +
609D HIS* 1.3 76.1 - - - +
611D LYS* 1.3 61.2 + - - +
613D ALA* 3.5 9.2 + - - +
616D ILE* 3.4 34.3 - - + +
618D ILE* 4.2 14.4 - - + -
630D PHE* 3.6 36.5 + - + +
640D PHE* 4.2 13.5 - - + -
644D LEU* 4.1 17.9 - - + -
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Residues in contact with LYS 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A GLU* 6.0 2.2 - - - +
607D MET* 2.8 48.0 + - - +
608D GLU* 3.2 16.6 + - + +
610D LEU* 1.3 77.6 - - - +
612D LYS* 1.3 61.3 + - - +
613D ALA 3.4 0.9 + - - +
630D PHE* 3.5 33.8 - - + +
634D GLN* 4.7 4.8 + - - +
534E ALA* 4.5 28.7 - - + +
536E LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D LEU* 4.5 5.7 - - + +
587D PHE* 3.9 16.2 - - + -
588D GLU* 3.4 33.3 + - - -
592D CYS* 3.8 27.5 - - - +
608D GLU* 3.0 18.1 + - + +
609D HIS 3.9 3.6 - - - +
611D LYS* 1.3 75.6 - - - +
613D ALA* 1.3 65.5 + - - +
614D ASP* 3.6 3.5 + - - +
531E SER* 3.1 39.1 + - - +
533E PHE 5.7 1.8 - - - +
534E ALA* 6.1 3.4 - - - -
536E LYS* 3.1 22.5 + - + +
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Residues in contact with ALA 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D LEU* 3.7 21.3 - - + +
455D ALA* 3.7 17.7 - - + +
609D HIS 3.0 15.8 + - - +
610D LEU 3.6 11.6 - - - +
611D LYS 3.3 3.5 - - - +
612D LYS* 1.3 76.8 - - - +
614D ASP* 1.3 64.7 + - - +
615D LYS* 3.4 19.4 - - - +
616D ILE* 4.1 1.4 - - + +
629D THR* 5.7 1.2 - - - -
630D PHE 5.6 2.8 + - - -
536E LYS* 2.9 15.3 + - - -
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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