Contacts of the helix formed by residues 792 - 808 (chain A) in PDB entry 5IXC
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 792 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A GLU* 4.0 3.1 - - - +
713A CYS* 3.4 27.2 - - - +
730A PHE* 3.9 18.0 - - - -
788A ASN 2.7 20.5 + - - -
789A VAL 3.0 11.9 + - - -
791A THR* 1.3 79.9 - - - +
793A GLN* 1.3 66.5 + - - +
794A GLY 3.1 3.7 + - - -
795A ALA* 3.3 7.4 + - - +
796A ILE* 3.1 21.2 + - - +
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Residues in contact with GLN 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.6 43.2 + - + +
350A LEU* 4.7 3.5 - - + +
789A VAL 3.6 2.8 + - - -
790A GLN 3.1 15.2 + - - +
791A THR 3.4 1.8 - - - -
792A SER* 1.3 76.9 - - - +
794A GLY* 1.3 57.0 + - - +
796A ILE* 3.2 10.3 + - - +
797A LEU* 2.9 53.1 + - + +
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Residues in contact with GLY 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A THR 5.2 0.8 + - - -
792A SER 3.2 1.0 - - - -
793A GLN* 1.3 79.3 - - - +
795A ALA* 1.3 51.8 + - - +
797A LEU* 3.2 8.6 + - - +
798A GLN* 2.7 43.4 + - - +
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Residues in contact with ALA 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A CYS* 4.3 23.3 - - + -
715A LEU* 6.4 1.3 - - + -
728A LEU* 3.8 9.0 - - + +
792A SER* 3.3 11.7 + - - +
794A GLY* 1.3 73.7 - - - +
796A ILE* 1.3 59.2 + - - +
798A GLN* 3.3 9.5 - - - +
799A ALA* 2.8 30.5 + - - +
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Residues in contact with ILE 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.5 7.0 - - + -
348A LEU* 4.8 0.7 - - + -
350A LEU* 3.9 30.3 - - + -
668A LEU* 4.6 1.3 - - + +
670A LEU* 4.6 19.1 - - + -
728A LEU* 3.6 19.1 - - + -
730A PHE* 4.2 15.7 - - + -
789A VAL* 4.1 31.9 - - + +
792A SER* 3.1 17.0 + - - +
793A GLN* 3.5 7.2 - - - +
795A ALA* 1.3 76.5 - - - +
797A LEU* 1.3 51.6 + - - +
799A ALA* 3.2 2.9 + - - +
800A LEU* 2.7 45.5 + - + +
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Residues in contact with LEU 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 4.0 15.5 - - + +
309A LEU* 3.7 25.9 - - + +
350A LEU* 3.8 27.8 - - + -
793A GLN* 2.9 47.2 + - + +
794A GLY* 3.7 6.3 - - - +
796A ILE* 1.3 71.7 - - - +
798A GLN* 1.3 60.2 + - - +
800A LEU* 3.2 5.2 + - + +
801A ARG* 2.8 38.2 + - + +
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Residues in contact with GLN 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A GLY 2.7 25.8 + - - +
795A ALA* 3.3 9.6 - - - +
797A LEU* 1.3 73.8 - - - +
799A ALA* 1.3 53.0 + - - +
801A ARG* 3.3 12.1 + - - +
802A THR* 2.7 39.8 + - - -
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Residues in contact with ALA 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A LEU* 3.9 18.9 - - + +
715A LEU* 5.1 2.5 - - + -
726A ILE* 4.0 14.9 - - + +
728A LEU* 3.8 21.5 - - + -
795A ALA 2.8 20.4 + - - +
796A ILE 3.7 4.3 - - - +
798A GLN* 1.3 71.2 - - - +
800A LEU* 1.3 62.0 + - - +
802A THR* 3.3 7.7 + - - -
803A ALA* 2.8 30.1 + - - +
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Residues in contact with LEU 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 4.2 23.8 - - + +
308A ALA* 5.6 0.2 - - + -
309A LEU* 4.3 13.5 - - + -
321A PRO* 4.8 6.4 - - + +
323A VAL* 4.0 20.9 - - + -
350A LEU* 3.6 30.7 - - + -
353A CYS* 4.6 8.7 - - + -
668A LEU* 3.8 19.9 - - + +
796A ILE* 2.7 32.0 + - + +
797A LEU* 3.2 15.0 + - + +
799A ALA* 1.3 70.1 - - - +
801A ARG* 1.3 64.8 + - - +
803A ALA* 3.3 6.5 + - + +
804A LEU* 3.3 21.5 + - - +
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Residues in contact with ARG 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 2.7 53.4 + - + +
310A GLN 4.6 2.6 + - - -
311A LEU* 3.9 19.8 - - - +
797A LEU* 2.8 24.9 + - - +
798A GLN* 3.6 11.4 - - - +
800A LEU* 1.3 72.2 - - - +
802A THR* 1.3 57.8 + - - +
804A LEU* 2.9 18.0 - - - +
805A LYS* 2.8 38.0 - - - +
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Residues in contact with THR 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ILE* 4.3 21.1 - - + -
798A GLN* 2.7 28.8 + - - +
799A ALA* 3.6 8.3 - - - -
800A LEU 3.2 0.2 - - - -
801A ARG* 1.3 72.1 - - - +
803A ALA* 1.3 61.0 + - - +
804A LEU 3.0 5.6 + - - -
805A LYS* 3.4 12.0 + - + +
806A HIS* 3.2 23.9 + - + +
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Residues in contact with ALA 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO* 3.6 21.7 - - + +
323A VAL* 5.8 0.2 - - + -
667A ASP* 4.3 10.4 - - + +
668A LEU* 4.2 20.9 - - + -
726A ILE* 4.8 3.1 - - + +
799A ALA 2.8 17.2 + - - +
800A LEU* 3.3 9.2 + - + +
802A THR* 1.3 76.2 - - - +
804A LEU* 1.3 55.9 + - - +
806A HIS* 4.0 12.4 - - - +
807A ARG* 3.1 29.5 + - - +
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Residues in contact with LEU 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 5.1 2.7 - - + -
309A LEU* 3.8 29.4 - - + -
311A LEU* 4.4 20.0 - - + -
315A LEU* 4.3 18.2 - - + -
319A GLU* 3.4 25.8 - - + +
321A PRO* 3.8 17.7 - - + +
800A LEU 3.3 6.3 + - - +
801A ARG* 2.9 19.2 + - - +
802A THR 3.0 0.2 - - - -
803A ALA* 1.3 75.5 - - - +
805A LYS* 1.3 68.5 + - + +
807A ARG* 3.3 4.2 + - - +
808A THR* 3.2 29.3 + - + +
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Residues in contact with LYS 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A ARG* 2.8 51.7 - - - +
802A THR* 3.4 8.7 + - + +
804A LEU* 1.3 79.8 - - + +
806A HIS* 1.3 61.7 + - - +
808A THR* 2.9 28.6 + - - +
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Residues in contact with HIS 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A LEU 4.7 0.8 + - - -
667A ASP* 3.1 50.2 + - - -
722A PRO 5.2 4.4 + - - -
723A GLU* 4.3 23.3 + - + +
724A ALA 3.5 22.4 + - - -
725A PRO* 4.2 2.0 - - + -
726A ILE* 4.2 14.5 - - + +
802A THR* 3.2 18.7 + - + +
803A ALA* 4.3 5.4 - - - +
805A LYS* 1.3 78.1 - - - +
807A ARG* 1.3 66.3 + - - +
808A THR 3.4 6.6 - - - +
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Residues in contact with ARG 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LYS* 4.0 17.2 - - - +
317A GLU 4.1 0.2 + - - -
318A ASP* 3.4 38.8 + - - +
319A GLU 3.8 22.4 - - - +
320A VAL 3.0 23.5 + - - +
321A PRO* 4.3 2.5 - - + -
322A VAL* 4.9 4.6 - - - +
665A ARG* 3.4 34.2 + - - +
667A ASP* 3.3 27.1 - - - +
803A ALA 3.1 20.6 + - - +
804A LEU 3.5 5.4 - - - +
805A LYS 3.3 0.2 - - - -
806A HIS* 1.3 78.1 - - - +
808A THR* 1.3 65.4 + - - +
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Residues in contact with THR 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ASP 5.3 3.1 - - - +
319A GLU* 4.5 33.2 - - + +
804A LEU* 3.2 17.0 - - + +
805A LYS* 2.9 24.7 + - - +
806A HIS 3.4 8.8 - - - +
807A ARG* 1.3 81.7 - - - +
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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
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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