Contacts of the helix formed by residues 606 - 613 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A VAL* 5.0 12.3 - - + +
583A GLU* 3.3 39.9 + - - +
604A THR* 3.0 3.9 + - - +
605A SER* 1.3 88.2 - - - +
607A MET* 1.3 60.7 + - - +
608A GLU* 3.1 4.7 - - + +
609A HIS* 2.9 48.6 + - + +
610A LEU* 3.2 15.6 + - - +
648A ASP* 5.7 3.4 + - - -
653A PHE* 6.3 0.6 - - - -
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Residues in contact with MET 607 (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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605A SER 3.5 5.8 + - - -
606A LYS* 1.3 70.9 - - - +
608A GLU* 1.3 56.1 + - - +
610A LEU* 3.2 13.4 + - + +
611A LYS* 2.9 43.6 + - - +
630A PHE* 3.5 36.6 - - + -
634A GLN* 3.7 9.0 - - - +
641A SER* 3.5 39.0 - - - +
644A LEU* 5.7 6.1 - - + -
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Residues in contact with GLU 608 (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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584A LYS* 5.9 9.9 - - + -
587A PHE* 4.5 2.9 - - + -
606A LYS* 3.1 4.2 - - + -
607A MET* 1.3 79.8 - - - +
609A HIS* 1.3 70.0 + - + +
611A LYS* 3.3 14.9 + - - +
612A LYS* 3.1 24.3 + - - +
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Residues in contact with HIS 609 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A LEU* 4.6 1.2 - - - +
455A ALA* 4.3 3.4 - - - +
575A PHE* 3.8 20.0 - + - -
583A GLU* 3.2 35.3 - - - +
584A LYS* 5.3 3.6 - - - +
587A PHE* 3.5 52.0 - + + +
602A LEU* 4.1 6.3 - - + +
604A THR* 2.8 35.9 + - + +
606A LYS* 2.9 21.0 + - + +
608A GLU* 1.3 82.0 - - + +
610A LEU* 1.3 57.2 + - - +
612A LYS* 3.5 2.3 + - - +
613A ALA* 3.1 27.5 + - - +
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Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A ALA* 4.4 5.6 - - + +
457A ALA* 4.4 15.5 - - + -
604A THR* 3.9 22.2 - - + +
605A SER 4.7 1.8 - - - -
606A LYS 3.2 26.5 + - - +
607A MET* 3.4 12.3 - - + +
609A HIS* 1.3 74.8 - - - +
611A LYS* 1.3 63.9 + - - +
613A ALA* 3.3 16.9 + - - +
616A ILE* 3.6 28.8 - - + +
618A ILE* 4.2 23.1 - - + -
630A PHE* 3.5 35.5 + - + +
640A PHE* 4.4 12.8 - - + -
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Residues in contact with LYS 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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607A MET* 2.9 32.5 + - - +
608A GLU* 3.4 15.0 - - - +
610A LEU* 1.3 77.8 - - - +
612A LYS* 1.3 59.0 + - + +
613A ALA 3.6 3.6 + - - +
630A PHE* 3.5 43.7 - - + +
634A GLN* 5.3 2.4 - - - +
518C ARG* 5.9 0.7 + - - -
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Residues in contact with LYS 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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453A LEU* 4.4 6.1 - - + +
587A PHE* 3.9 19.1 - - + -
588A GLU* 3.3 34.7 + - - -
592A CYS* 3.8 22.5 - - - +
608A GLU 3.1 15.1 + - - +
609A HIS 4.0 0.2 - - - +
611A LYS* 1.3 75.4 - - + +
613A ALA* 1.3 65.4 + - - +
614A ASP* 3.7 4.0 + - - +
518C ARG* 5.0 5.1 + - - -
522C LYS* 3.2 35.5 + - - +
527C GLU* 4.7 6.3 + - - -
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Residues in contact with ALA 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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453A LEU* 3.9 17.5 - - + +
455A ALA* 3.7 17.5 - - + +
609A HIS 3.1 16.7 + - - +
610A LEU 3.3 14.7 + - - +
611A LYS 4.1 4.0 - - - +
612A LYS* 1.3 82.0 - - - +
614A ASP* 1.3 64.3 + - - +
615A LYS* 3.6 19.0 - - - +
616A ILE* 4.0 2.9 - - + +
629A THR* 5.8 2.1 - - - -
630A PHE 5.6 2.4 + - - -
518C ARG* 4.5 6.1 + - - -
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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