Contacts of the helix formed by residues 778 - 793 (chain A) in PDB entry 2DQM
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 ASN 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ASP* 3.2 25.4 + - - +
257A PHE* 3.6 22.0 - - + -
775A THR* 3.2 23.9 + - + +
776A MET 3.2 0.6 - - - -
777A SER* 1.3 80.5 + - - +
779A PRO* 1.3 66.0 - - - +
780A ASN* 2.8 39.2 + - - +
781A ARG* 3.1 29.5 + - + +
782A ILE* 3.0 25.4 + - - +
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Residues in contact with PRO 779 (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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106A LEU* 3.7 17.9 - - + -
257A PHE* 4.3 4.9 - - + -
258A PHE 3.6 24.2 - - - +
259A ASN* 3.4 25.6 - - - +
777A SER 3.6 9.0 - - - +
778A ASN* 1.3 86.0 - - - +
780A ASN* 1.3 57.7 + - - +
782A ILE* 3.6 11.3 - - + +
783A ARG* 2.9 40.9 + - - +
819A ASN* 3.9 7.6 - - - +
822A VAL* 3.9 15.5 - - + -
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Residues in contact with ASN 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP 4.6 8.0 + - - +
258A PHE 4.0 5.4 + - - +
272A ASN* 2.8 40.7 + - - -
273A SER* 5.2 0.4 + - - -
274A LYS* 2.9 36.0 - - - +
744A LEU* 3.8 8.5 - - - +
747A ASP* 3.6 4.9 - - - +
778A ASN* 2.8 17.4 + - - +
779A PRO* 1.3 73.8 - - - +
781A ARG* 1.3 70.7 + - - +
783A ARG* 3.5 7.3 + - - +
784A SER* 2.7 33.8 + - - -
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Residues in contact with ARG 781 (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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256A ASP 5.8 0.2 + - - -
743A GLY* 3.3 32.1 + - - -
744A LEU* 3.6 10.9 - - - +
747A ASP* 2.7 42.5 + - - -
750A PHE* 4.2 9.3 - - - -
773A SER 3.4 25.9 + - - +
774A PHE* 3.4 22.1 - - + -
775A THR* 3.6 20.5 - - + +
778A ASN* 3.1 41.2 + - + +
780A ASN* 1.3 86.6 - - - +
782A ILE* 1.3 64.0 + - - +
784A SER* 3.3 1.7 + - - -
785A LEU* 3.0 21.1 + - - +
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Residues in contact with ILE 782 (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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774A PHE* 4.1 7.0 - - + -
775A THR 4.2 0.9 - - - +
776A MET* 3.0 45.5 - - - +
777A SER 4.9 0.2 - - - -
778A ASN 3.0 17.8 + - - +
779A PRO* 3.6 12.1 - - + +
780A ASN 3.3 0.2 - - - -
781A ARG* 1.3 76.7 - - - +
783A ARG* 1.3 57.6 + - - +
786A ILE* 2.9 33.0 + - + +
787A GLY 3.1 5.7 + - - -
815A LEU* 3.7 25.1 - - + -
818A ARG* 5.2 0.4 - - - -
819A ASN* 5.8 2.0 - - + +
822A VAL* 3.7 18.8 - - + -
826A LEU* 3.5 27.8 - - + -
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Residues in contact with ARG 783 (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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259A ASN 3.6 22.7 + - - -
260A MET* 4.5 12.1 + - - +
272A ASN* 5.9 1.4 - - - +
779A PRO* 2.9 28.7 + - - +
780A ASN* 4.0 6.2 + - - +
782A ILE* 1.3 77.0 - - - +
784A SER* 1.3 58.4 + - - +
787A GLY* 3.3 8.7 - - - +
788A ALA* 2.9 27.5 + - - +
822A VAL* 4.5 8.5 - - + -
825A ARG* 3.0 46.3 - - - +
826A LEU* 4.4 15.5 - - + -
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Residues in contact with SER 784 (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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274A LYS* 4.6 4.2 + - - -
747A ASP* 3.1 46.9 + - - +
750A PHE* 3.4 5.9 - - - +
751A ILE* 3.3 30.5 + - - +
780A ASN 2.7 22.2 + - - -
781A ARG 3.8 2.5 - - - -
783A ARG* 1.3 77.8 - - - +
785A LEU* 1.3 58.0 + - - +
788A ALA* 3.3 16.7 - - - +
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Residues in contact with LEU 785 (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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750A PHE* 4.0 33.4 - - + +
754A ALA* 3.3 12.0 - - + +
765A VAL* 3.9 38.9 - - + +
768A LEU* 3.9 28.5 - - + +
769A LEU* 4.0 15.5 - - + -
774A PHE* 3.8 27.1 - - + -
781A ARG 3.0 14.7 + - - +
784A SER* 1.3 78.1 - - - +
786A ILE* 1.3 67.2 + - + +
788A ALA 4.1 0.2 - - - -
789A PHE* 3.2 19.6 + - - +
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Residues in contact with ILE 786 (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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765A VAL* 5.3 0.2 - - - -
769A LEU* 4.2 10.8 - - + -
774A PHE* 4.1 9.6 - - + -
776A MET* 3.9 21.3 - - + -
782A ILE* 2.9 21.4 + - + +
785A LEU* 1.3 73.9 - - + +
787A GLY* 1.3 66.8 + - - +
789A PHE* 3.2 6.0 + - - +
790A ALA* 3.1 22.3 + - - +
807A PHE* 4.3 15.0 - - + -
808A LEU* 4.2 12.8 - - + -
811A MET* 3.6 47.1 - - + -
815A LEU* 5.1 0.2 - - + -
826A LEU* 3.7 20.0 - - + -
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Residues in contact with GLY 787 (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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782A ILE 3.1 11.1 + - - -
783A ARG* 3.3 11.2 - - - -
786A ILE* 1.3 76.4 - - - +
788A ALA* 1.3 56.9 + - - +
790A ALA* 4.9 2.5 - - - -
791A GLY* 2.8 30.1 + - - -
792A SER* 5.0 0.2 + - - -
826A LEU* 4.1 23.2 - - - +
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Residues in contact with ALA 788 (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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751A ILE* 4.2 17.7 - - + -
754A ALA* 3.8 12.6 - - + -
755A THR* 3.9 9.5 - - + +
783A ARG 2.9 10.7 + - - +
784A SER 3.3 23.8 - - - +
785A LEU 3.8 0.2 + - - -
786A ILE 3.3 0.4 - - - -
787A GLY* 1.3 74.6 - - - +
789A PHE* 1.3 59.4 + - - +
792A SER* 2.8 41.2 + - - +
793A ASN 3.3 1.9 + - - -
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Residues in contact with PHE 789 (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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754A ALA* 3.6 25.7 - - + +
761A VAL* 4.4 3.8 - - + -
762A LEU* 3.8 42.0 - - + -
765A VAL* 4.1 18.2 - - + -
785A LEU 3.2 17.2 + - - +
786A ILE* 3.5 6.7 - - - +
787A GLY 3.2 0.2 - - - -
788A ALA* 1.3 79.4 - - - +
790A ALA* 1.3 67.4 + - + +
793A ASN* 3.2 28.8 + - - +
796A ALA* 3.6 39.7 - - + -
797A PHE* 3.8 16.8 - + - +
804A GLY* 4.1 12.3 - - - -
807A PHE* 4.1 19.7 - + - -
808A LEU* 6.5 0.2 - - + -
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Residues in contact with ALA 790 (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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786A ILE* 3.1 13.1 + - + +
787A GLY* 4.2 3.1 - - - +
789A PHE* 1.3 84.2 - - + +
791A GLY* 1.3 60.9 + - - +
794A PRO* 4.7 5.0 - - - +
797A PHE* 3.6 41.1 - - + +
808A LEU* 4.2 18.8 - - + -
826A LEU* 4.7 2.9 - - + +
829A PRO* 3.6 26.5 - - + +
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Residues in contact with GLY 791 (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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623A ASN* 3.2 24.3 + - - +
787A GLY 2.8 19.4 + - - -
790A ALA* 1.3 75.5 - - - +
792A SER* 1.3 61.4 + - - +
793A ASN 3.6 0.4 - - - -
794A PRO* 4.0 5.2 - - - +
829A PRO* 3.9 13.6 - - - +
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Residues in contact with SER 792 (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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622A VAL* 4.3 9.4 - - - +
623A ASN* 4.4 7.6 + - - +
751A ILE* 6.1 1.1 - - - -
755A THR* 3.7 22.7 - - - +
787A GLY 4.0 0.4 + - - -
788A ALA* 2.8 26.7 + - - +
791A GLY* 1.3 72.6 + - - -
793A ASN* 1.3 59.3 + - - +
794A PRO* 3.2 9.8 - - - +
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Residues in contact with ASN 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ALA 2.9 26.7 + - - +
755A THR* 3.5 11.4 - - - +
756A SER 3.3 24.0 + - - +
761A VAL* 4.0 3.8 - - - +
788A ALA 3.3 1.5 + - - +
789A PHE* 3.2 20.3 + - + +
790A ALA 4.9 0.2 - - - -
792A SER* 1.3 79.6 - - - +
794A PRO* 1.3 58.1 - - - +
795A ALA* 3.1 8.4 + - - +
796A ALA* 3.2 29.2 + - + +
797A PHE 2.8 23.2 + - - -
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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