Contacts of the helix formed by residues 613 - 623 (chain B) in PDB entry 5EIX
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 SER 613 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610B LYS 5.2 2.2 - - - -
611B LYS 2.6 14.0 + - - -
612B ARG* 1.3 74.7 - - - +
614B GLU* 1.3 58.1 - - - -
615B ASP 3.2 1.1 - - - -
616B ARG* 3.0 40.6 + - - +
617B ARG* 3.0 25.7 + - - +
1175B GLY* 3.8 13.9 - - - +
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Residues in contact with GLU 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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612B ARG 2.5 15.7 + - - +
613B SER* 1.3 73.4 - - - +
615B ASP* 1.3 57.0 + - - +
617B ARG* 3.0 33.4 + - - +
618B ASN* 2.9 38.4 + - - +
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Residues in contact with ASP 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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606B MET* 4.6 11.5 - - + +
612B ARG* 3.8 48.0 + - + +
613B SER 3.2 0.6 - - - -
614B GLU* 1.3 78.6 - - - +
616B ARG* 1.3 57.5 + - - +
618B ASN* 3.6 8.9 + - - +
619B TRP* 2.9 28.4 + - - +
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Residues in contact with ARG 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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606B MET* 3.1 29.0 + - - +
607B LEU* 3.2 25.4 + - + +
608B LEU* 4.8 0.8 - - - +
609B ALA 2.4 30.4 + - - +
610B LYS* 4.1 4.0 + - - +
611B LYS 2.5 21.4 + - - -
612B ARG* 4.2 1.6 - - - +
613B SER* 3.0 28.8 + - - +
615B ASP* 1.3 77.2 - - - +
617B ARG* 1.3 57.1 + - - +
619B TRP* 3.5 17.9 - - + +
620B LEU* 2.9 39.7 + - + +
1018B TYR* 4.0 18.1 + - + -
1174B VAL 5.4 1.3 - - - -
1175B GLY* 4.1 19.3 - - - +
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Residues in contact with ARG 617 (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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612B ARG 5.6 0.2 + - - -
613B SER* 3.0 13.1 + - - +
614B GLU* 3.2 32.7 - - - +
616B ARG* 1.3 76.9 - - - +
618B ASN* 1.3 61.7 + - - +
620B LEU* 3.2 11.1 + - - +
621B GLN* 2.9 30.8 + - + +
1175B GLY* 3.2 29.4 + - - +
1176B MET* 5.0 17.9 - - + +
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Residues in contact with ASN 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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614B GLU* 2.9 25.4 + - - +
615B ASP* 4.0 8.1 - - - +
617B ARG* 1.3 78.2 - - - +
619B TRP* 1.3 60.0 + - - +
621B GLN* 3.2 11.6 + - - +
622B GLU* 2.9 30.8 + - - +
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Residues in contact with TRP 619 (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 MET* 3.5 28.7 - - + +
607B LEU* 3.7 23.1 - - + -
615B ASP 2.9 19.7 + - - +
616B ARG* 3.5 13.7 - - + +
618B ASN* 1.3 77.5 - - - +
620B LEU* 1.3 91.9 + - + +
622B GLU* 4.1 4.4 - - + +
623B LYS* 3.1 32.0 + - + +
1015B GLU* 3.1 49.5 + - + -
1018B TYR* 4.1 12.1 - + - -
1019B LEU* 3.5 39.7 - - + -
1022B SER* 4.6 1.6 - - - -
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Residues in contact with LEU 620 (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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616B ARG* 2.9 25.5 + - + +
617B ARG* 3.6 7.6 - - - +
619B TRP* 1.3 101.3 - - + +
621B GLN* 1.3 63.5 + - - +
623B LYS* 3.6 13.5 - - - -
624B GLY* 3.9 2.1 + - - -
1019B LEU* 3.6 17.7 - - + -
1022B SER* 3.7 17.0 - - - -
1023B MET* 3.6 32.5 - - + +
1026B ILE* 3.6 18.4 - - + -
1174B VAL 3.4 25.8 - - - +
1175B GLY* 4.9 0.4 - - - -
1176B MET* 5.0 4.7 - - + -
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Residues in contact with GLN 621 (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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617B ARG* 2.9 15.7 + - + +
618B ASN* 3.3 17.0 - - - +
619B TRP 3.1 0.2 - - - -
620B LEU* 1.3 76.6 - - - +
622B GLU* 1.3 66.7 + - - +
623B LYS 3.4 0.2 + - - -
624B GLY 3.0 21.1 - - - +
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Residues in contact with GLU 622 (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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618B ASN 2.9 18.4 + - - +
619B TRP* 4.2 4.5 - - + +
621B GLN* 1.3 73.5 - - - +
623B LYS* 1.3 57.5 + - - +
624B GLY 3.0 8.3 + - - +
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Residues in contact with LYS 623 (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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619B TRP* 3.1 27.8 + - + +
620B LEU 3.6 8.9 - - - +
621B GLN 3.2 0.4 - - - -
622B GLU* 1.3 73.2 - - - +
624B GLY* 1.3 54.9 + - - +
1019B LEU* 4.4 33.2 - - + +
1023B MET* 4.7 4.2 - - - +
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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