Contacts of the helix formed by residues 684 - 699 (chain H) in PDB entry 5G04
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 684 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655H GLU* 3.1 23.0 + - - +
679H GLN* 3.1 19.1 + - + +
682H LEU* 3.3 23.0 + - + +
683H LYS* 1.3 73.5 - - - +
685H SER* 1.3 57.9 + - - +
686H GLU* 3.3 3.6 - - - -
687H LYS* 3.1 42.9 + - + +
688H ALA* 3.0 23.0 + - - +
527K ILE* 5.8 6.1 - - - +
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Residues in contact with SER 685 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679H GLN 4.0 0.2 + - - -
680H HIS* 4.2 24.7 - - - +
683H LYS* 2.9 17.0 + - - +
684H LYS* 1.3 72.4 - - - +
686H GLU* 1.3 74.7 + - - +
688H ALA* 3.3 9.8 + - - +
689H LEU* 2.8 33.4 + - - +
712H VAL* 4.5 0.7 - - - -
716H ASN* 4.0 22.1 + - - -
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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
----------------------------------------------------------
683H LYS 4.8 4.5 - - - +
684H LYS* 3.3 1.4 - - - -
685H SER* 1.3 91.6 + - - +
687H LYS* 1.3 63.2 + - + +
689H LEU* 3.6 5.8 + - - +
690H ASP* 2.9 27.9 + - - +
716H ASN* 4.2 12.8 + - - +
718H LYS* 5.9 1.0 + - - -
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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
----------------------------------------------------------
679H GLN* 3.9 11.2 - - - +
684H LYS* 3.1 43.9 + - + +
686H GLU* 1.3 75.9 - - + +
688H ALA* 1.3 65.5 + - - +
690H ASP* 3.2 15.5 + - + +
691H THR* 3.1 25.7 + - - +
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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
----------------------------------------------------------
676H GLY* 3.5 24.0 - - - +
679H GLN* 3.4 12.5 + - + -
680H HIS* 3.6 21.8 - - + +
684H LYS 3.0 8.7 + - - +
685H SER* 3.3 13.5 - - - +
686H GLU 3.3 0.2 - - - -
687H LYS* 1.3 76.0 - - - +
689H LEU* 1.3 57.5 - - - +
691H THR* 3.2 5.0 + - - -
692H LEU* 2.8 34.7 + - + +
712H VAL* 4.7 4.7 - - + -
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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
----------------------------------------------------------
685H SER 2.8 27.7 + - - +
686H GLU* 3.6 6.7 + - - +
687H LYS 3.4 0.2 - - - -
688H ALA* 1.3 73.4 - - - +
690H ASP* 1.3 61.9 - - - +
692H LEU* 4.0 7.7 - - + +
693H ASN* 3.0 28.8 + - - +
709H ARG* 4.1 29.6 + - - +
712H VAL* 3.1 29.2 - - + -
713H LEU* 3.3 42.0 - - + -
716H ASN* 3.5 15.0 - - - +
718H LYS* 6.1 1.3 - - - +
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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
----------------------------------------------------------
686H GLU* 2.9 20.1 - - - +
687H LYS* 3.2 19.5 + - + +
689H LEU* 1.3 75.8 - - - +
691H THR* 1.3 63.6 + - - +
693H ASN* 3.6 6.0 + - - +
694H LYS* 3.3 23.4 + - - +
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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
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672H LEU* 3.8 42.8 - - + +
675H ILE* 4.7 7.4 - - + -
676H GLY* 4.4 4.3 - - - +
679H GLN* 3.0 34.0 + - - +
687H LYS* 3.1 7.6 + - - +
688H ALA 3.5 3.4 - - - -
690H ASP* 1.3 75.2 - - - +
692H LEU* 1.3 62.1 + - - +
694H LYS* 3.1 23.2 - - - +
695H ALA* 3.2 7.8 + - - +
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Residues in contact with LEU 692 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672H LEU 4.9 0.4 - - - +
673H CYS* 4.0 29.6 - - + +
676H GLY* 4.5 10.8 - - - -
677H VAL* 5.1 1.1 - - + -
688H ALA* 2.8 26.7 + - + +
689H LEU* 4.0 5.4 - - + +
691H THR* 1.3 70.8 - - - +
693H ASN* 1.3 63.7 + - - +
695H ALA* 3.1 16.0 + - - +
696H ILE* 3.3 12.3 + - - +
705H CYS* 3.7 16.8 - - - +
708H HIS* 3.9 20.9 - - + -
709H ARG* 3.4 38.6 - - + +
712H VAL* 3.9 24.2 - - + -
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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
----------------------------------------------------------
689H LEU 3.0 19.8 + - - +
690H ASP* 3.7 7.2 - - - +
691H THR 3.3 0.2 - - - -
692H LEU* 1.3 74.3 - - - +
694H LYS* 1.3 63.4 + - - +
696H ILE* 3.3 17.3 + - - +
697H VAL* 3.3 22.2 + - - +
709H ARG* 3.8 32.0 + - - +
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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
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662H LEU* 6.1 0.2 - - - +
666H PRO 4.9 4.6 + - - -
667H GLN* 6.1 0.2 - - - +
672H LEU* 3.7 34.2 - - + +
690H ASP 3.3 10.7 + - - +
691H THR* 3.1 15.4 + - - +
693H ASN* 1.3 78.0 - - - +
695H ALA* 1.3 57.0 + - - +
697H VAL* 3.1 10.7 + - + +
698H ILE* 3.0 47.3 + - - +
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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
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669H SER* 4.3 12.5 - - - +
672H LEU* 3.9 28.0 - - + +
673H CYS* 4.6 3.1 - - - +
691H THR 3.2 4.9 + - - +
692H LEU* 3.1 9.6 + - - +
694H LYS* 1.3 77.7 - - - +
696H ILE* 1.3 62.2 + - - +
698H ILE* 3.1 26.1 - - + +
699H ASP* 3.2 11.4 + - - +
702H ASN* 5.8 0.2 - - - +
705H CYS* 3.4 22.7 - - + -
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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
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692H LEU 3.3 1.7 + - - +
693H ASN* 3.3 13.1 + - - +
695H ALA* 1.3 77.3 - - - +
697H VAL* 1.3 63.5 + - + +
699H ASP 3.1 23.7 - - - +
700H PRO* 3.8 5.5 - - + +
705H CYS* 3.2 20.9 - - + -
706H LYS* 3.7 55.2 - - + +
709H ARG* 3.8 30.5 - - - +
725H GLU* 3.9 5.8 - - - +
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Residues in contact with VAL 697 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693H ASN* 3.3 23.9 + - - +
694H LYS* 3.1 12.8 + - - +
696H ILE* 1.3 79.3 - - + +
698H ILE* 1.3 66.2 + - + +
699H ASP 3.7 0.5 + - - -
700H PRO* 5.1 3.8 - - - +
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Residues in contact with ILE 698 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482H LYS* 4.5 7.4 + - - -
667H GLN* 3.3 45.8 + - + +
669H SER* 3.7 25.1 - - - +
672H LEU* 3.8 11.7 - - + -
694H LYS* 3.0 38.4 + - - +
695H ALA* 3.1 24.0 - - - +
697H VAL* 1.3 80.8 - - + +
699H ASP* 1.3 65.7 + - - +
700H PRO* 4.0 4.7 - - - +
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Residues in contact with ASP 699 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482H LYS* 3.6 19.2 + - - -
512H LEU* 3.8 19.3 - - - +
513H SER* 6.1 0.2 - - - -
514H GLU* 5.1 4.3 - - - +
667H GLN* 4.0 16.9 + - - +
669H SER* 3.5 34.6 + - - +
695H ALA 3.2 6.7 + - - +
696H ILE* 3.1 14.7 - - - +
698H ILE* 1.3 86.3 - - - +
700H PRO* 1.4 69.4 - - + +
701H LYS* 3.5 3.4 - - + +
702H ASN* 4.0 13.3 + - + +
706H LYS* 5.9 0.2 - - - -
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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
------------------------------------------------------------
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