Contacts of the helix formed by residues 606 - 613 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B GLU* 4.6 13.0 - - + +
580E VAL* 5.5 7.5 - - - +
583E GLU* 3.6 37.2 + - - +
604E THR* 3.1 3.4 + - - +
605E SER* 1.3 99.0 - - - +
607E MET* 1.3 65.8 + - - +
608E GLU* 4.3 3.1 - - + +
609E HIS* 3.0 44.7 + - + +
610E LEU* 3.3 14.5 + - - +
648E ASP* 3.9 15.7 + - - +
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Residues in contact with MET 607 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B GLU* 4.1 20.0 + - + +
404B GLY* 3.9 23.6 - - - +
407B GLU* 3.7 31.4 - - + -
408B LEU* 6.5 0.2 - - + -
605E SER 3.5 5.1 + - - -
606E LYS* 1.3 70.5 - - - +
608E GLU* 1.3 62.2 + - - +
610E LEU* 3.2 15.3 + - + +
611E LYS* 3.1 39.5 + - - +
630E PHE* 3.7 32.1 - - + -
634E GLN* 4.9 11.0 - - + +
640E PHE* 4.9 16.8 - - + -
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Residues in contact with GLU 608 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B GLU* 3.0 34.5 + - - +
584E LYS* 3.7 30.7 + - + +
587E PHE* 4.4 5.7 - - + -
606E LYS* 3.2 2.0 - - + -
607E MET* 1.3 78.6 - - - +
609E HIS* 1.3 72.3 + - + +
611E LYS* 3.5 19.9 + - + +
612E LYS* 3.4 21.9 + - + +
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Residues in contact with HIS 609 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E LEU* 4.7 1.4 - - - +
455E ALA* 4.3 2.2 - - - +
575E PHE* 4.0 18.4 - + - -
583E GLU* 3.5 30.5 + - + +
584E LYS* 5.5 3.4 - - + +
587E PHE* 3.5 52.9 - + + +
602E LEU* 4.0 7.0 - - + +
604E THR* 2.8 33.5 + - + +
606E LYS* 3.0 24.6 + - + +
608E GLU* 1.3 81.5 - - + +
610E LEU* 1.3 65.9 + - - +
612E LYS* 3.4 2.8 + - - +
613E ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 610 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E ALA* 3.8 11.9 - - + -
457E ALA* 4.5 14.4 - - + -
604E THR* 3.8 26.2 - - + +
605E SER 5.4 2.7 - - - +
606E LYS 3.3 11.4 + - - +
607E MET* 3.2 16.1 + - + +
609E HIS* 1.3 80.2 - - - +
611E LYS* 1.3 61.3 + - - +
613E ALA* 3.4 11.9 + - - +
616E ILE* 3.6 45.7 - - + +
618E ILE* 4.7 2.9 - - + -
630E PHE* 3.6 20.6 - - + +
633E LEU* 4.5 12.8 - - + -
640E PHE* 6.4 1.1 - - + -
645E MET* 4.5 17.5 - - + -
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Residues in contact with LYS 611 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B GLU* 5.5 4.8 - - - +
607E MET* 3.1 34.7 + - - +
608E GLU* 3.7 19.5 - - + +
609E HIS 3.3 0.4 - - - -
610E LEU* 1.3 77.7 - - - +
612E LYS* 1.3 61.3 + - + +
613E ALA 3.7 4.5 + - - +
630E PHE* 3.5 49.0 - - + +
634E GLN* 5.7 0.6 - - - +
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Residues in contact with LYS 612 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E LEU* 4.3 6.0 - - - +
587E PHE* 3.9 25.8 - - + -
588E GLU* 3.6 33.0 + - - +
592E CYS* 3.7 22.3 - - - +
593E LYS* 5.8 1.0 - - - +
608E GLU* 3.4 6.1 + - + +
609E HIS 3.4 0.8 + - - -
610E LEU 3.3 0.4 - - - -
611E LYS* 1.3 78.6 - - + +
613E ALA* 1.3 65.2 + - - +
614E ASP* 3.8 4.5 + - - +
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Residues in contact with ALA 613 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E LEU* 3.7 19.3 - - + +
455E ALA* 3.7 16.2 - - + +
609E HIS 3.2 16.3 + - - +
610E LEU 3.6 13.7 - - - +
611E LYS 3.4 5.3 - - - +
612E LYS* 1.3 80.5 - - - +
614E ASP* 1.3 62.5 + - - +
615E LYS 3.4 20.8 - - - +
616E ILE* 4.0 2.1 - - + +
629E THR* 5.9 1.4 - - - -
630E PHE* 5.6 2.4 + - - +
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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