Contacts of the helix formed by residues 668 - 699 (chain H) 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 SER 668 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667H GLN* 3.8 29.6 - - - +
669H SER* 3.7 29.8 - - - +
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Residues in contact with SER 669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668H SER* 3.7 30.1 - - - +
670H VAL* 3.7 26.0 - - - +
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Residues in contact with VAL 670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669H SER* 3.7 29.4 - - - +
671H LEU* 3.8 25.8 - - - +
673H CYS* 4.4 17.5 - - - +
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Residues in contact with LEU 671 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670H VAL* 3.8 26.7 - - - +
672H LEU* 3.7 29.4 - - - +
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Residues in contact with LEU 672 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671H LEU* 3.7 30.7 - - - +
673H CYS* 3.8 25.4 - - - +
675H ILE* 3.9 24.0 - - - +
----------------------------------------------------------
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Residues in contact with CYS 673 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670H VAL* 4.4 19.5 - - - +
672H LEU* 3.8 24.0 - - - +
674H HIS* 3.7 29.8 - - - +
----------------------------------------------------------
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Residues in contact with HIS 674 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673H CYS* 3.7 29.6 - - - +
675H ILE* 3.8 27.4 - - - +
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Residues in contact with ILE 675 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672H LEU* 3.9 20.2 - - - +
674H HIS* 3.8 26.2 - - - +
676H GLY* 3.7 29.8 - - - +
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Residues in contact with GLY 676 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675H ILE* 3.7 29.4 - - - +
677H VAL* 3.8 26.5 - - - +
679H GLN* 4.6 16.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 677 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676H GLY* 3.8 23.3 - - - +
678H VAL* 3.7 30.3 - - - +
680H HIS* 4.7 13.9 - - - +
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Residues in contact with VAL 678 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677H VAL* 3.7 29.6 - - - +
679H GLN* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with GLN 679 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676H GLY* 4.6 13.2 - - - +
678H VAL* 3.8 29.4 - - - +
680H HIS* 3.8 24.9 - - - +
682H LEU* 4.4 19.1 - - - +
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Residues in contact with HIS 680 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677H VAL* 4.7 17.0 - - - +
679H GLN* 3.8 25.4 - - - +
681H ALA* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 681 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680H HIS* 3.8 29.6 - - - +
682H LEU* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 682 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679H GLN* 4.4 18.8 - - - +
681H ALA* 3.8 25.1 - - - +
683H LYS* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 683 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682H LEU* 3.8 29.4 - - - +
684H LYS* 3.8 23.8 - - - +
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Residues in contact with LYS 684 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683H LYS* 3.8 24.9 - - - +
685H SER* 3.8 29.8 - - - +
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Residues in contact with SER 685 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684H LYS* 3.8 24.9 - - - +
686H GLU* 3.8 29.4 - - - +
688H ALA* 4.4 18.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 686 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685H SER* 3.8 28.7 - - - +
687H LYS* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 687 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686H GLU* 3.8 29.8 - - - +
688H ALA* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 688 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685H SER* 4.4 16.8 - - - +
687H LYS* 3.8 29.6 - - - +
689H LEU* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 689 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688H ALA* 3.8 25.4 - - - +
690H ASP* 3.8 30.1 - - - +
692H LEU* 4.4 18.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 690 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689H LEU* 3.8 24.5 - - - +
691H THR* 3.7 29.6 - - - +
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Residues in contact with THR 691 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690H ASP* 3.7 29.8 - - - +
692H LEU* 3.8 26.2 - - - +
694H LYS* 4.3 20.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 692 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689H LEU* 4.4 17.7 - - - +
691H THR* 3.8 23.8 - - - +
693H ASN* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ASN 693 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692H LEU* 3.8 29.6 - - - +
694H LYS* 3.8 25.4 - - - +
696H ILE* 4.3 19.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 694 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691H THR* 4.3 17.7 - - - +
693H ASN* 3.8 23.6 - - - +
695H ALA* 3.8 29.8 - - - +
697H VAL* 4.6 13.5 - - - +
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Residues in contact with ALA 695 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694H LYS* 3.8 28.9 - - - +
696H ILE* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 696 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693H ASN* 4.3 16.4 - - - +
695H ALA* 3.8 23.8 - - - +
697H VAL* 3.8 29.6 - - - +
700H PRO* 4.5 19.5 - - - -
----------------------------------------------------------
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Residues in contact with VAL 697 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694H LYS* 4.6 16.8 - - - +
696H ILE* 3.8 28.9 - - - +
698H ILE* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with ILE 698 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697H VAL* 3.8 28.7 - - - +
699H ASP* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with ASP 699 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698H ILE* 3.8 28.7 - - - +
700H PRO* 3.7 30.1 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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