Contacts of the helix formed by residues 612 - 630 (chain N) in PDB entry 5KHU
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 PRO 612 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611N VAL* 3.8 28.9 - - - -
613N GLU* 3.8 29.4 - - - -
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Residues in contact with GLU 613 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612N PRO* 3.8 28.9 - - - -
614N ASP* 3.8 25.8 - - - +
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Residues in contact with ASP 614 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613N GLU* 3.8 25.6 - - - +
615N ILE* 3.8 30.1 - - - +
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Residues in contact with ILE 615 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614N ASP* 3.8 28.7 - - - +
616N ARG* 3.8 25.8 - - - +
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Residues in contact with ARG 616 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615N ILE* 3.8 26.0 - - - +
617N ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 617 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616N ARG* 3.8 29.6 - - - +
618N ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 618 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617N ALA* 3.8 27.4 - - - +
619N LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 619 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618N ALA* 3.8 28.9 - - - +
620N GLU* 3.8 26.9 - - - +
622N TYR* 4.4 19.5 - - - +
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Residues in contact with GLU 620 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619N LEU* 3.8 24.5 - - - +
621N ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 621 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620N GLU* 3.8 29.4 - - - +
622N TYR* 3.8 25.6 - - - +
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Residues in contact with TYR 622 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619N LEU* 4.4 15.7 - - - +
621N ALA* 3.8 28.3 - - - +
623N CYS* 3.8 27.8 - - - +
625N LYS* 4.5 18.4 - - - +
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Residues in contact with CYS 623 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622N TYR* 3.8 24.2 - - - +
624N LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 624 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623N CYS* 3.8 28.7 - - - +
625N LYS* 3.8 25.8 - - - +
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Residues in contact with LYS 625 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622N TYR* 4.5 17.0 - - - +
624N LYS* 3.8 26.2 - - - +
626N TYR* 3.8 29.4 - - - +
628N GLN* 4.7 14.4 - - - +
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Residues in contact with TYR 626 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625N LYS* 3.8 25.6 - - - +
627N GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 627 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626N TYR* 3.8 29.6 - - - +
628N GLN* 3.8 24.9 - - - +
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Residues in contact with GLN 628 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625N LYS* 4.7 14.4 - - - +
627N GLU* 3.8 26.0 - - - +
629N LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 629 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628N GLN* 3.8 28.5 - - - +
630N LYS* 3.8 28.9 - - - +
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Residues in contact with LYS 630 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629N LEU* 3.8 28.3 - - - +
631N ALA* 3.8 29.8 - - - +
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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