Contacts of the helix formed by residues 773 - 784 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294D ASP* 2.9 49.9 + - - -
295D GLY* 4.3 6.3 + - - -
456D ARG* 3.8 12.9 - - - +
606D LYS* 4.1 2.5 - - - -
759D ARG* 3.0 48.2 - - - +
760D PRO 4.2 10.8 - - - -
761D ALA 3.2 20.7 + - - +
762D LYS 5.0 1.8 - - - -
763D ARG* 3.5 37.5 - - + +
771D THR 4.5 0.9 - - - +
772D LEU* 1.3 80.0 - - - +
774D ALA* 1.3 67.3 + - - +
775D ILE 3.4 0.7 - - - -
776D PRO* 3.2 10.7 - - + +
777D TRP* 3.2 15.6 + - - +
1002D SO4 4.1 6.2 + - - -
1004D SO4 3.3 21.1 + - - +
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Residues in contact with ALA 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D SER* 4.1 29.8 - - - +
603D ASP* 3.9 13.7 - - - +
606D LYS* 4.2 11.6 - - + +
641D ARG* 4.9 1.6 - - - -
773D ARG* 1.3 71.0 - - - +
775D ILE* 1.3 66.8 + - - +
777D TRP* 3.1 3.2 + - - +
778D ILE* 2.9 30.1 + - + +
1002D SO4 4.0 9.6 - - - +
1004D SO4 2.9 20.8 + - - +
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Residues in contact with ILE 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D PRO* 4.7 17.9 - - + -
641D ARG* 3.3 50.7 - - - +
675D GLU* 5.8 0.4 - - - +
751D TYR* 3.8 19.5 - - - +
759D ARG* 3.7 22.0 - - - +
774D ALA* 1.3 75.9 - - - +
776D PRO* 1.3 65.1 - - + +
778D ILE* 3.7 3.1 - - - +
779D PHE* 2.7 34.7 + - + +
1002D SO4 3.5 17.0 - - - +
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Residues in contact with PRO 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D GLU* 3.4 20.7 - - - +
751D TYR* 3.9 19.7 - - + -
759D ARG* 4.1 4.5 - - - +
761D ALA* 3.8 31.2 - - + +
772D LEU* 3.9 11.4 - - + -
773D ARG* 3.2 20.6 - - + +
775D ILE* 1.3 95.7 - - + +
777D TRP* 1.3 53.4 + - - +
779D PHE* 4.1 7.4 - - + -
780D SER* 2.6 35.7 + - - -
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Residues in contact with TRP 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D LYS* 3.6 31.7 - - + +
728D TYR* 3.4 26.6 + + - -
732D VAL* 4.0 11.9 - - + -
738D PHE* 3.8 26.2 - + - -
742D PHE* 4.0 13.2 - + - -
769D ILE* 3.7 31.2 - - + -
772D LEU* 4.1 8.4 - - + +
773D ARG 3.2 15.4 + - - +
774D ALA* 3.1 8.4 + - - +
776D PRO* 1.3 79.0 - - - +
778D ILE* 1.3 69.6 + - + +
780D SER* 4.5 0.7 - - - -
781D TRP* 3.3 53.5 + - - -
788D LEU* 4.0 17.3 - - + -
789D PRO* 3.3 29.6 - - + +
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Residues in contact with ILE 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D SER* 4.3 15.7 - - - +
610D ARG* 6.2 0.4 - - - +
641D ARG* 5.4 8.1 - - - +
774D ALA* 2.9 18.1 + - - +
775D ILE* 4.0 2.9 - - - +
777D TRP* 1.3 80.2 - - + +
779D PHE* 1.3 62.2 + - - +
781D TRP* 3.6 1.6 + - - +
782D THR* 2.3 35.6 + - - +
789D PRO* 3.8 28.3 - - + +
790D VAL* 5.0 5.4 - - + -
969D THR* 3.6 22.9 - - - +
970D GLY* 3.3 35.2 - - - +
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Residues in contact with PHE 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D PRO* 4.9 14.6 - - + -
179D THR* 4.5 15.0 - - - -
747D PRO* 5.4 1.8 - - + -
751D TYR* 3.4 44.6 - + + -
756D ILE* 4.9 1.6 - - + -
775D ILE* 2.7 27.5 + - + +
776D PRO* 4.0 5.6 - - + +
778D ILE* 1.3 73.1 - - - +
780D SER* 1.3 64.0 + - - +
782D THR* 3.1 7.7 + - - -
783D GLN* 3.0 66.9 + - + +
959D MET* 4.3 22.7 - - + -
963D ALA* 4.3 15.5 - - + -
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Residues in contact with SER 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D PHE* 3.5 15.4 - - - -
746D THR* 3.7 24.2 - - - -
747D PRO* 3.8 3.8 - - - +
748D GLU* 3.3 25.6 + - - -
751D TYR* 5.8 0.7 - - - -
776D PRO 2.6 22.3 + - - -
777D TRP 4.0 0.5 + - - -
779D PHE* 1.3 86.0 - - - +
781D TRP* 1.3 60.3 + - - +
783D GLN* 3.4 14.4 + - - +
784D THR* 3.4 19.1 - - - +
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Residues in contact with TRP 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D PHE* 4.2 16.8 - + - -
741D TYR* 3.8 29.6 - + - -
742D PHE* 3.2 42.8 - + + -
745D ALA* 4.8 5.4 - - + -
746D THR* 3.6 18.8 - - + -
777D TRP* 3.3 39.0 + + - +
778D ILE 3.6 1.9 + - - +
779D PHE 3.3 0.6 - - - -
780D SER* 1.3 79.3 + - - +
782D THR* 1.3 61.3 + - - +
784D THR* 3.3 16.8 + - - -
786D PHE* 3.4 41.1 + + + -
787D HIS* 3.2 19.4 + - - +
788D LEU* 4.2 17.0 - - + +
789D PRO* 3.5 33.0 - - + -
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Residues in contact with THR 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D ILE* 2.3 30.8 + - - +
779D PHE* 3.4 6.3 - - - -
781D TRP* 1.3 76.6 - - - +
783D GLN* 1.3 64.2 + - - +
785D ARG* 3.3 10.2 + - - -
787D HIS* 3.2 33.3 + - + +
962D ILE* 4.2 7.1 - - - +
966D MET* 3.8 20.2 - - + +
967D GLN 5.5 0.7 - - - +
969D THR* 3.5 31.2 + - + +
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Residues in contact with GLN 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D PRO* 4.0 10.8 - - + -
779D PHE* 3.0 60.1 + - + +
780D SER* 3.6 9.9 - - - +
781D TRP 3.3 0.8 - - - -
782D THR* 1.3 78.0 - - - +
784D THR* 1.3 59.8 + - - +
785D ARG* 3.3 1.1 + - - +
844D TYR* 3.6 2.6 + - - -
902D ASN* 2.8 26.3 + - - -
905D GLN* 2.9 38.0 + - - +
959D MET* 3.3 25.4 + - - +
962D ILE* 3.8 15.8 - - - +
963D ALA* 3.7 15.4 - - - +
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Residues in contact with THR 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745D ALA 3.3 27.0 + - - +
746D THR* 3.8 11.2 - - + -
747D PRO* 4.0 6.3 - - + -
780D SER 3.4 15.9 - - - +
781D TRP* 3.3 17.3 + - - -
782D THR 3.2 0.2 - - - -
783D GLN* 1.3 77.2 - - - +
785D ARG* 1.3 67.6 + - - +
786D PHE* 3.2 15.2 + - - +
840D ILE* 4.1 1.9 - - - +
841D ALA* 3.5 22.2 + - - +
844D TYR* 3.9 26.5 - - + -
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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