Contacts of the helix formed by residues 773 - 784 (chain H) in PDB entry 6V3O
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 ARG 773 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294H ASP* 3.4 29.4 + - - -
295H GLY* 3.0 35.9 + - - +
458H GLU* 5.3 2.0 + - - -
606H LYS* 3.9 2.2 - - - -
759H ARG* 3.9 31.3 - - - +
760H PRO 4.3 13.5 + - - -
761H ALA 4.0 11.1 + - - +
762H LYS 4.7 2.8 + - - -
763H ARG* 3.0 47.1 - - + +
771H THR 4.7 0.2 - - - +
772H LEU* 1.3 85.0 - - - +
774H ALA* 1.3 66.9 + - - +
775H ILE* 3.4 1.3 - - + +
776H PRO* 3.2 19.0 - - + +
777H TRP* 3.1 23.0 + - - +
1003H SO4 5.3 1.0 + - - +
1004H SO4 3.6 15.2 + - - +
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Residues in contact with ALA 774 (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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602H SER* 4.2 24.7 - - - +
603H ASP* 3.8 16.6 - - - +
606H LYS* 3.8 11.6 - - - +
641H ARG* 6.2 0.7 - - + -
773H ARG* 1.3 71.2 - - - +
775H ILE* 1.3 67.7 + - - +
777H TRP* 3.2 4.8 + - - +
778H ILE* 3.0 28.9 + - - +
1003H SO4 4.1 11.6 + - - +
1004H SO4 3.0 19.4 + - - +
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Residues in contact with ILE 775 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H PRO* 4.9 17.0 - - + -
641H ARG* 4.4 28.9 - - + +
751H TYR* 3.6 20.4 - - + +
757H GLY* 5.8 5.2 - - - +
759H ARG* 4.0 22.0 - - - +
773H ARG* 4.5 0.6 - - + +
774H ALA* 1.3 76.2 - - + +
776H PRO* 1.3 63.9 - - + +
778H ILE* 3.9 4.1 - - - +
779H PHE* 2.8 36.5 + - + +
1003H SO4 3.2 24.0 + - - +
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Residues in contact with PRO 776 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742H PHE* 4.5 0.2 - - - -
748H GLU* 4.1 21.9 - - + +
751H TYR* 4.0 27.4 - - + +
761H ALA* 4.1 15.9 - - - +
772H LEU* 4.2 8.1 - - + -
773H ARG* 3.2 31.9 - - + +
775H ILE* 1.3 94.8 - - + +
777H TRP* 1.3 59.8 + - - +
779H PHE* 4.3 6.1 - - + -
780H SER* 3.0 30.9 + - - +
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Residues in contact with TRP 777 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602H SER 5.3 2.0 - - - -
605H GLY 5.2 0.2 + - - -
606H LYS* 3.3 39.4 - - + +
728H TYR* 3.5 20.6 + + - -
732H VAL* 4.2 5.8 - - + -
738H PHE* 3.7 25.8 - + - -
742H PHE* 4.0 8.5 - + - -
769H ILE* 3.7 26.2 - - + -
772H LEU* 3.7 20.5 - - + +
773H ARG 3.1 20.0 + - - +
774H ALA* 3.2 5.8 + - - +
776H PRO* 1.3 78.9 - - - +
778H ILE* 1.3 66.9 + - + +
780H SER* 4.8 0.2 - - - -
781H TRP* 3.3 53.8 + - - -
788H LEU* 4.0 17.0 - - + -
789H PRO* 3.2 30.9 - - + +
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Residues in contact with ILE 778 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602H SER* 3.0 39.3 - - - +
641H ARG* 5.5 5.4 - - + +
774H ALA 3.0 14.8 + - - +
775H ILE* 4.0 2.9 - - - +
777H TRP* 1.3 85.0 - - + +
779H PHE* 1.3 68.6 + - - +
780H SER 3.4 0.2 + - - -
781H TRP* 3.4 1.4 + - - -
782H THR* 3.0 33.5 + - + +
789H PRO* 4.6 13.0 - - + -
790H VAL* 5.6 2.0 - - + -
969H THR* 3.6 23.6 - - - +
970H GLY* 3.3 19.5 - - - +
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Residues in contact with PHE 779 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H PRO* 4.8 17.5 - - + -
179H THR* 4.6 14.8 - - - -
747H PRO* 5.6 1.3 - - + -
751H TYR* 3.4 40.2 - + + -
756H ILE* 4.8 3.4 - - + -
775H ILE* 2.8 28.2 + - + +
776H PRO* 4.0 4.9 - - + +
778H ILE* 1.3 73.8 - - - +
780H SER* 1.3 68.3 + - - +
782H THR* 3.0 20.9 + - - -
783H GLN* 3.1 53.4 + - + +
959H MET* 4.5 23.1 - - + -
963H ALA* 4.1 16.2 - - + -
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Residues in contact with SER 780 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742H PHE* 4.0 4.9 - - - -
746H THR* 3.4 35.9 - - - -
747H PRO* 4.4 2.7 - - - +
748H GLU* 3.3 31.8 + - - +
751H TYR* 4.6 3.6 - - - +
776H PRO* 3.0 20.6 + - - +
779H PHE* 1.3 86.8 - - - +
781H TRP* 1.3 61.1 + - - +
783H GLN* 3.7 9.5 + - - +
784H THR* 3.6 11.3 - - - +
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Residues in contact with TRP 781 (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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738H PHE* 4.2 14.1 - + - -
741H TYR* 3.8 28.0 - + - -
742H PHE* 3.3 40.9 - + + -
745H ALA* 4.7 5.8 - - + -
746H THR* 3.6 21.5 - - + -
777H TRP* 3.3 41.0 + + - +
778H ILE 3.4 2.6 + - - +
779H PHE 3.3 0.6 - - - -
780H SER* 1.3 77.7 - - - +
782H THR* 1.3 60.4 + - + +
783H GLN 3.4 0.2 - - - -
784H THR* 3.4 15.9 + - - -
786H PHE* 3.3 41.1 + + + -
787H HIS* 3.1 19.3 + - - +
788H LEU* 4.1 20.7 - - + +
789H PRO* 3.4 35.2 - - + -
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Residues in contact with THR 782 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778H ILE* 3.0 20.2 + - + +
779H PHE* 3.0 17.0 + - - -
781H TRP* 1.3 77.4 - - + +
783H GLN* 1.3 66.9 + - - +
784H THR 3.2 0.4 - - - -
785H ARG 3.2 9.2 + - - -
787H HIS* 3.2 31.9 - - + +
789H PRO* 6.0 0.9 - - + -
790H VAL* 5.5 2.2 - - + -
962H ILE* 4.2 4.4 - - - +
966H MET* 3.7 21.5 - - - +
969H THR* 3.2 33.4 - - + +
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Residues in contact with GLN 783 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747H PRO* 4.0 13.5 - - + -
779H PHE* 3.1 55.7 + - + +
780H SER 3.8 7.9 - - - +
781H TRP 3.4 0.4 - - - -
782H THR* 1.3 80.4 + - - +
784H THR* 1.3 50.9 + - - +
785H ARG* 3.3 0.7 + - - +
844H TYR* 3.6 2.4 + - - -
902H ASN* 2.7 32.4 + - - -
905H GLN* 2.8 38.7 + - - +
959H MET* 3.2 30.5 + - - +
962H ILE* 3.7 15.9 - - - +
963H ALA* 3.7 14.6 - - - +
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Residues in contact with THR 784 (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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745H ALA 3.3 25.1 + - - +
746H THR* 3.8 11.4 - - + -
747H PRO* 4.0 6.3 - - + -
780H SER 3.6 15.0 - - - +
781H TRP* 3.4 17.9 + - - -
782H THR 3.2 0.4 - - - -
783H GLN* 1.3 75.3 - - - +
785H ARG* 1.3 68.9 + - - +
786H PHE* 3.1 14.6 + - - +
840H ILE* 4.1 1.9 - - - +
841H ALA* 3.6 23.1 + - - +
844H TYR* 3.8 29.4 - - + -
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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