Contacts of the helix formed by residues 780 - 797 (chain A) in PDB entry 1T65
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 MET 780 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A LEU* 3.5 23.8 - - + -
704A LEU* 4.0 14.8 - - + -
764A PHE* 6.3 1.1 - - - -
770A PHE* 6.2 0.2 - - - -
775A MET 4.0 2.2 - - - -
778A SER* 3.1 17.7 - - - +
779A ARG* 1.3 79.9 - - - +
781A TYR* 1.3 64.9 + - - +
783A GLN* 3.1 31.3 - - - +
784A CYS* 3.0 30.8 + - - -
787A MET* 5.2 2.0 - - - -
873A LEU* 4.0 24.2 - - - -
876A PHE* 3.3 33.9 - - + -
931A DHT 3.7 17.0 - - + -
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Residues in contact with TYR 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLU* 3.0 36.1 + - - -
775A MET* 3.5 33.5 + - + +
776A HIS* 4.0 21.1 - - + +
779A ARG 3.6 2.2 - - - -
780A MET* 1.3 77.4 - - - +
782A SER* 1.3 67.9 + - - +
783A GLN* 3.8 0.2 + - - -
784A CYS* 3.1 4.9 + - - +
785A VAL* 2.9 49.0 + - + +
788A ARG* 5.4 0.9 + - - -
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Residues in contact with SER 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A TYR* 1.3 85.5 - - - +
783A GLN* 1.3 83.3 + - - +
785A VAL* 3.3 6.4 + - - +
786A ARG* 3.2 30.5 + - - +
872A GLU* 4.2 7.2 + - - -
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Residues in contact with GLN 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A ARG 4.8 0.6 + - - +
780A MET* 3.1 36.7 - - + +
782A SER* 1.3 88.4 + - - +
784A CYS* 1.3 63.8 + - - +
786A ARG* 3.2 9.1 + - - +
787A MET* 3.1 28.9 + - + +
869A ILE* 4.8 3.6 - - + +
872A GLU* 3.5 37.5 + - + +
873A LEU* 4.0 24.7 - - + -
876A PHE* 3.8 25.7 - - - +
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Residues in contact with CYS 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU* 3.7 21.6 - - + +
764A PHE* 4.8 2.5 - - - -
770A PHE* 4.4 9.6 - - - -
775A MET* 3.6 33.7 - - + +
778A SER* 4.2 7.6 - - - -
780A MET* 3.0 32.7 + - - +
781A TYR 3.4 7.9 - - - +
783A GLN* 1.3 78.3 - - - +
785A VAL* 1.3 61.7 + - - +
787A MET* 3.2 18.8 + - - +
788A ARG* 3.1 19.4 + - - +
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Residues in contact with VAL 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLU* 4.7 2.7 - - - +
775A MET* 4.7 3.4 - - - -
781A TYR* 2.9 55.8 + - + +
782A SER* 3.7 9.0 - - - +
783A GLN 3.3 0.4 - - - -
784A CYS* 1.3 77.4 - - - +
786A ARG* 1.3 63.6 + - + +
788A ARG* 3.2 30.3 + - - +
789A HIS* 3.1 21.5 + - + +
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Residues in contact with ARG 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A SER* 3.2 16.8 + - - +
783A GLN* 3.2 9.8 + - - +
785A VAL* 1.3 81.1 - - + +
787A MET* 1.3 60.3 + - - +
789A HIS* 3.3 9.1 + - - +
790A LEU 3.1 16.5 + - - -
865A SER* 4.7 3.4 + - - +
868A PRO* 3.7 31.9 + - - +
869A ILE* 3.7 38.2 - - + +
872A GLU* 2.5 41.9 + - - -
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Residues in contact with MET 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A VAL* 4.0 16.6 - - + -
749A MET* 3.6 27.6 - - + -
750A GLY* 4.9 3.8 - - - -
762A LEU* 4.1 11.6 - - + +
764A PHE* 4.4 10.5 - - + -
780A MET* 5.2 2.2 - - - -
783A GLN* 3.1 23.5 + - + +
784A CYS* 3.2 28.2 + - - +
786A ARG* 1.3 75.6 - - - +
788A ARG* 1.3 60.6 + - - +
790A LEU* 3.3 10.9 + - + +
791A SER* 3.0 24.8 + - - -
869A ILE* 3.8 18.4 - - + -
873A LEU* 4.0 31.6 - - + -
931A DHT 4.5 7.2 - - + -
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Residues in contact with ARG 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A SER* 3.6 26.5 - - - +
760A ARG 4.9 8.7 + - - -
761A MET* 5.6 1.3 - - - +
762A LEU* 3.9 17.2 - - + +
772A GLU* 2.7 34.7 + - - +
775A MET* 4.7 14.5 - - + +
781A TYR* 5.4 0.8 + - - -
784A CYS 3.1 12.6 + - - +
785A VAL* 3.6 31.2 + - - +
786A ARG 3.2 0.2 - - - -
787A MET* 1.3 75.1 - - - +
789A HIS* 1.3 65.7 + - - +
791A SER* 3.3 4.9 + - - -
792A GLN* 3.0 34.5 + - + +
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Residues in contact with HIS 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A VAL* 3.1 13.9 + - + +
786A ARG* 3.4 13.2 - - - +
788A ARG* 1.3 77.1 - - - +
790A LEU* 1.3 63.9 + - - +
792A GLN* 3.2 15.0 + - - +
793A GLU* 3.1 36.2 + - - +
796A TRP* 3.8 31.4 - + - -
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Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A VAL* 4.0 36.1 - - + +
747A PHE* 4.5 13.7 - - + -
750A GLY* 5.0 2.7 - - - -
786A ARG 3.1 12.9 + - - +
787A MET* 3.4 11.0 - - - +
789A HIS* 1.3 79.1 + - - +
791A SER* 1.3 63.7 + - - +
793A GLU* 3.1 21.2 + - - +
794A PHE* 3.5 20.4 + - + -
862A LEU* 3.7 28.0 - - + -
865A SER* 4.1 12.6 - - - +
866A VAL* 4.4 16.2 - - + -
869A ILE* 4.5 12.6 - - + -
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Residues in contact with SER 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A GLY* 3.1 30.3 + - - -
753A SER* 3.4 12.7 - - - -
754A PHE* 3.3 13.7 + - - +
759A SER* 2.6 28.5 + - - -
762A LEU* 5.3 0.9 - - - -
787A MET 3.0 13.2 + - - -
788A ARG* 3.5 12.6 - - - -
789A HIS 3.2 0.2 - - - -
790A LEU* 1.3 78.7 - - - +
792A GLN* 1.3 60.7 + - - +
794A PHE* 3.2 22.0 + - - +
795A GLY 4.0 1.0 + - - -
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Residues in contact with GLN 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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754A PHE* 5.6 0.9 - - - -
759A SER* 3.7 22.0 + - - -
788A ARG* 3.0 32.8 + - + +
789A HIS* 3.5 17.8 - - - +
791A SER* 1.3 76.0 - - - +
793A GLU* 1.3 58.4 + - - +
795A GLY* 3.0 17.9 + - - +
796A TRP* 3.0 56.1 + - + +
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Residues in contact with GLU 793 (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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789A HIS* 3.1 35.4 + - - +
790A LEU* 3.1 11.9 + - - +
792A GLN* 1.3 73.7 - - - +
794A PHE* 1.3 65.8 + - - +
796A TRP* 3.2 26.9 - - + +
797A LEU* 2.9 53.0 + - + +
799A ILE* 5.0 0.4 - - - -
862A LEU* 3.8 24.7 - - + +
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Residues in contact with PHE 794 (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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747A PHE* 3.5 52.7 - + - -
750A GLY* 3.6 22.0 - - - -
751A TRP* 3.4 45.3 - + + -
754A PHE* 3.8 22.9 - - + -
790A LEU* 3.5 28.2 + - + -
791A SER 3.2 8.0 + - - +
792A GLN 3.2 0.6 - - - -
793A GLU* 1.3 78.6 - - - +
795A GLY* 1.3 58.4 + - - +
798A GLN* 3.4 1.7 + - - -
799A ILE* 3.1 50.0 + - + +
804A PHE* 4.1 4.3 - + - -
862A LEU* 4.5 7.2 - - + -
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Residues in contact with GLY 795 (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 PHE* 3.3 30.5 - - - -
792A GLN 3.0 7.8 + - - -
794A PHE* 1.3 78.7 - - - +
796A TRP* 1.3 66.0 + - - +
797A LEU 3.2 0.2 - - - -
798A GLN* 3.1 19.5 + - - +
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Residues in contact with TRP 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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789A HIS* 3.8 32.8 - + - -
792A GLN* 3.0 59.2 + - + +
793A GLU* 3.2 33.0 - - + +
795A GLY* 1.3 78.0 - - - +
797A LEU* 1.3 63.0 + - + +
798A GLN* 3.5 6.6 + - - +
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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
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793A GLU* 2.9 40.7 + - - +
796A TRP* 1.3 77.5 - - + +
798A GLN* 1.3 71.8 + - - +
799A ILE* 3.8 13.9 - - + -
855A ARG* 2.9 27.7 + - - +
858A GLN* 3.9 44.2 - - + +
862A LEU* 4.2 31.6 - - + -
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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
------------------------------------------------------------
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