Contacts of the helix formed by residues 606 - 618 (chain B) in PDB entry 2XER
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 THR 606 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604B LEU 3.9 1.2 + - - -
605B SER* 1.3 72.6 + - - +
607B GLU* 1.3 65.5 + - - +
609B ALA* 3.1 6.6 + - - +
610B ALA* 2.8 23.9 + - - +
643B LEU* 3.9 10.3 - - + +
646B HIS* 5.4 7.6 - - + +
647B LEU* 3.6 27.8 - - + -
606C THR* 3.1 25.6 + - - +
646C HIS* 5.1 2.0 - - - +
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Residues in contact with GLU 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* 3.3 9.0 + - - +
606B THR* 1.3 79.0 - - - +
608B GLN* 1.3 66.9 + - + +
610B ALA* 3.5 5.6 + - - +
611B ASP* 3.1 22.2 + - + +
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Residues in contact with GLN 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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562B ILE* 4.6 2.3 - - - +
563B CYS* 4.7 17.6 - - - +
566B TYR* 3.4 56.7 - - + +
604B LEU* 3.7 14.7 - - + +
605B SER* 3.0 38.6 + - - +
607B GLU* 1.3 81.8 - - + +
609B ALA* 1.3 63.2 + - - +
611B ASP* 2.9 15.1 + - - +
612B ILE* 3.1 15.8 + - - +
646C HIS* 4.3 6.0 + - - -
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Residues in contact with ALA 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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601B LEU* 4.1 28.6 - - + +
604B LEU* 4.3 9.8 - - + +
605B SER 2.7 21.4 + - - +
606B THR 3.6 3.4 - - - +
608B GLN* 1.3 71.3 - - - +
610B ALA* 1.3 58.1 + - - +
612B ILE* 3.0 7.7 + - - +
613B LEU* 3.0 26.3 + - - +
640B PHE* 4.6 0.3 - - - -
643B LEU* 3.8 24.9 - - + +
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Residues in contact with ALA 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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606B THR 2.8 16.6 + - - +
607B GLU* 3.8 7.0 - - - +
609B ALA* 1.3 77.5 - - - +
611B ASP* 1.3 57.3 + - - +
613B LEU* 3.8 3.3 - - - +
614B MET* 2.8 34.7 + - + +
643B LEU* 3.9 9.8 - - + +
647B LEU* 4.4 26.9 - - + -
651B SER* 6.0 2.7 - - - -
655B LEU* 4.5 4.4 - - + +
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Residues in contact with ASP 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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566B TYR* 2.6 26.0 + - - +
570B ARG* 3.3 27.4 + - - +
607B GLU* 3.1 14.2 + - + +
608B GLN 2.9 12.7 + - - +
610B ALA* 1.3 79.1 - - - +
612B ILE* 1.3 54.4 + - - +
614B MET* 3.6 6.2 - - - +
615B THR* 2.8 41.6 + - - -
618B ARG* 5.3 2.9 + - - -
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Residues in contact with ILE 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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566B TYR* 4.0 8.7 - - + -
569B LEU* 4.5 9.4 - - + -
570B ARG* 3.5 37.7 - - + -
584B PHE* 3.5 29.4 - - + -
597B VAL* 4.1 17.7 - - + -
601B LEU* 4.2 9.4 - - + -
604B LEU* 4.1 19.1 - - + -
608B GLN 3.4 12.1 - - - +
609B ALA 3.0 7.4 + - - +
611B ASP* 1.3 77.2 - - - +
613B LEU* 1.3 52.1 + - - +
615B THR* 3.5 4.7 + - - -
616B THR* 2.7 38.9 + - - +
640B PHE* 4.5 4.9 - - + -
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Residues in contact with LEU 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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609B ALA 3.0 11.1 + - - +
610B ALA* 3.8 7.0 - - - +
611B ASP 3.3 0.2 - - - -
612B ILE* 1.3 75.8 - - - +
614B MET* 1.3 60.6 + - - +
616B THR* 3.1 6.0 + - + -
617B ALA* 2.8 32.7 + - + +
640B PHE* 3.6 48.0 - - + -
643B LEU* 4.0 10.8 - - + -
644B LEU* 3.6 35.9 - - + -
655B LEU* 4.0 16.4 - - + -
688B LEU* 4.2 23.8 - - + -
692B LEU* 5.7 1.6 - - + -
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Residues in contact with MET 614 (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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610B ALA* 2.8 18.7 + - + +
611B ASP* 3.6 8.5 - - - +
613B LEU* 1.3 76.6 - - - +
615B THR* 1.3 57.9 + - - +
617B ALA* 4.0 1.3 - - - +
618B ARG* 2.9 67.7 + - - +
654B SER* 4.5 13.5 - - - +
655B LEU* 3.5 27.1 - - + +
658B GLN* 3.7 41.7 - - + +
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Residues in contact with THR 615 (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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570B ARG* 3.2 31.6 + - - +
581B ASP* 3.9 23.6 - - + +
584B PHE* 3.6 28.3 - - + -
585B VAL* 4.9 2.1 - - + +
611B ASP* 2.8 23.7 + - - -
612B ILE 3.9 3.6 - - - -
614B MET* 1.3 75.7 - - - +
616B THR* 1.3 60.4 + - - +
618B ARG* 4.1 12.7 + - - +
619B ASN* 2.7 33.3 + - - +
623B LEU* 5.1 0.2 - - - +
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Residues in contact with THR 616 (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 PHE* 3.6 16.5 - - - -
588B MET* 4.1 10.9 - - + +
612B ILE 2.7 22.8 + - - -
613B LEU* 3.1 12.8 + - + -
615B THR* 1.3 74.9 - - - +
617B ALA* 1.3 62.5 + - - +
619B ASN 2.9 6.1 + - - -
620B LEU* 2.8 42.0 + - + -
623B LEU* 3.9 22.5 - - + +
633B LEU* 5.6 0.9 - - + -
636B LEU* 5.5 1.1 - - + -
640B PHE* 4.1 17.4 - - + -
684B PHE* 4.9 8.5 - - + -
688B LEU* 5.7 1.1 - - + -
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Residues in contact with ALA 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 2.8 25.8 + - + +
614B MET* 4.0 3.8 - - - +
616B THR* 1.3 74.7 - - - +
618B ARG* 1.3 62.4 + - - +
619B ASN 3.1 0.7 + - - -
620B LEU* 3.2 22.1 + - - +
655B LEU* 4.6 8.3 - - + +
658B GLN* 3.8 6.9 - - + +
659B LEU* 4.0 34.5 - - + +
675B HIS* 3.5 14.7 + - - -
688B LEU* 5.0 4.3 - - + -
692B LEU* 6.2 1.1 - - + -
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Residues in contact with ARG 618 (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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570B ARG* 5.0 1.6 - - - +
581B ASP* 3.0 39.8 + - - -
611B ASP* 5.3 3.0 + - - -
614B MET* 2.9 47.1 + - - +
615B THR* 4.1 15.9 + - - +
617B ALA* 1.3 77.8 - - - +
619B ASN* 1.3 65.1 + - - +
621B PRO* 4.7 0.2 - - - +
658B GLN* 3.2 41.1 - - - +
675B HIS* 3.8 12.6 + - - -
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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