Contacts of the helix formed by residues 783 - 797 (chain A) in PDB entry 5XJY
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 783 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A PHE* 3.9 16.5 - - - -
728A VAL* 3.3 34.4 - - - +
729A THR* 4.8 0.9 + - - -
732A GLN* 4.0 25.2 - - - +
757A LEU* 5.5 0.2 - - - -
781A LEU 4.4 0.4 + - - -
782A LEU* 1.3 71.9 - - - +
784A PRO* 1.3 70.8 - - - +
785A VAL 3.2 2.2 - - - -
786A ALA* 2.9 23.8 + - - +
787A PHE* 3.3 8.5 + - - +
828A MET* 5.9 1.5 - - - +
831A ASP* 4.9 6.0 - - - +
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Residues in contact with PRO 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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641A PRO* 4.8 5.3 - - + +
645A THR* 5.4 2.0 - - - +
725A PHE* 4.1 22.7 - - + -
754A TYR* 5.4 4.9 - - + -
757A LEU* 3.6 44.4 - - + +
758A TYR* 3.9 30.8 - - + +
761A TYR* 4.9 0.7 - - - +
782A LEU* 3.7 6.5 - - + -
783A SER* 1.3 92.3 - - - +
785A VAL* 1.3 57.0 + - - +
787A PHE* 3.3 5.5 + - - +
788A GLY* 2.9 23.0 + - - -
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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
----------------------------------------------------------
758A TYR 4.5 2.5 - - - +
760A PRO* 4.0 4.7 - - + +
761A TYR* 3.5 40.6 - - + +
764A CYS* 5.7 0.7 - - + -
778A PHE 3.2 28.0 - - - +
779A ALA* 4.4 2.9 - - - -
782A LEU* 3.7 33.7 - - + +
784A PRO* 1.3 76.3 - - - +
786A ALA* 1.3 60.8 + - - +
788A GLY 4.2 0.4 - - - +
789A PHE* 3.0 55.8 + - + -
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Residues in contact with ALA 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A PHE* 4.4 0.7 - - - -
775A LEU* 6.3 0.4 - - - -
779A ALA* 4.6 5.6 - - + -
782A LEU 4.2 8.7 - - - +
783A SER* 2.9 12.5 + - - +
785A VAL* 1.3 81.5 - - - +
787A PHE* 1.3 59.5 + - - +
789A PHE* 4.1 7.7 - - - +
790A GLY 3.6 4.5 + - - -
824A SER* 3.5 36.1 - - - +
827A MET* 4.0 28.0 - - + -
828A MET* 4.4 9.2 - - + +
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Residues in contact with PHE 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A MET* 4.4 9.6 - - + -
641A PRO* 3.6 37.9 - - + -
644A MET* 4.1 19.7 - - + -
721A PHE* 3.4 35.2 - + - -
722A LEU* 3.8 29.6 - - + -
725A PHE* 3.5 51.1 - + + -
783A SER 3.3 3.6 + - - +
784A PRO 3.3 7.3 + - - +
785A VAL 3.2 0.6 - - - -
786A ALA* 1.3 76.8 - - - +
788A GLY* 1.3 58.3 + - - +
789A PHE 3.3 0.4 - - - -
790A GLY* 3.5 1.4 + - - -
791A CYS* 3.0 29.7 + - + +
794A PHE* 6.1 0.4 - + - -
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Residues in contact with GLY 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PRO* 4.2 13.7 - - - -
761A TYR* 3.2 38.5 + - - -
784A PRO 2.9 14.3 + - - -
785A VAL 3.2 1.5 + - - -
787A PHE* 1.3 77.8 - - - +
789A PHE* 1.3 55.8 + - - +
791A CYS* 3.3 5.5 + - - +
792A GLU* 2.9 22.7 + - - +
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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
----------------------------------------------------------
761A TYR* 3.5 27.1 - + - -
764A CYS* 4.1 29.2 - - + -
775A LEU* 3.6 51.4 - - + -
778A PHE* 5.6 2.7 - - + -
779A ALA* 5.5 0.7 - - + -
785A VAL* 3.0 36.4 + - + +
786A ALA* 4.4 6.7 - - - +
788A GLY* 1.3 74.6 - - - +
790A GLY* 1.3 61.0 + - - +
792A GLU* 3.0 14.3 + - + +
793A TYR* 3.0 23.4 + - - +
819A PHE 6.1 0.7 - - - +
824A SER* 5.6 2.0 - - - -
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Residues in contact with GLY 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A PHE* 4.3 10.3 - - - -
786A ALA 3.6 6.4 + - - -
787A PHE 3.5 4.8 + - - -
788A GLY 3.5 0.2 - - - -
789A PHE* 1.3 78.3 - - - +
791A CYS* 1.3 57.4 + - - +
793A TYR* 3.2 12.7 + - - +
794A PHE* 3.1 29.1 + - - -
820A ASN 5.5 0.9 - - - -
821A LEU* 5.1 4.6 - - - +
824A SER* 3.7 24.2 - - - -
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Residues in contact with CYS 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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637A SER* 3.7 12.6 - - - +
640A MET* 3.5 46.9 - - + -
641A PRO* 5.2 2.2 - - + -
721A PHE* 4.5 3.5 - - + -
787A PHE* 3.0 23.3 + - + +
788A GLY* 3.7 7.0 - - - +
790A GLY* 1.3 75.6 - - - +
792A GLU* 1.3 61.6 + - - +
794A PHE* 3.1 24.3 + - + +
795A ALA* 2.9 26.0 + - - +
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Residues in contact with GLU 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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638A ARG* 2.9 50.6 + - - +
761A TYR* 2.8 22.4 + - + +
765A VAL* 5.4 6.2 - - - +
788A GLY 2.9 18.8 + - - +
789A PHE* 3.0 17.0 + - + +
791A CYS* 1.3 74.9 - - - +
793A TYR* 1.3 59.5 + - - +
795A ALA* 3.2 2.9 + - - +
796A LEU* 2.9 41.8 + - + +
1524A LYS* 5.3 5.4 - - + +
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Residues in contact with TYR 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 PHE 3.0 9.3 + - - +
790A GLY* 3.2 14.4 - - - +
792A GLU* 1.3 76.9 - - - +
794A PHE* 1.3 72.9 + + - +
796A LEU* 4.6 3.8 - - + +
797A PHE* 3.0 67.2 + + + +
819A PHE 4.4 7.2 - - - +
820A ASN* 3.9 23.5 - - + +
821A LEU* 3.7 35.7 - - + +
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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
----------------------------------------------------------
637A SER* 4.4 3.1 - - - +
640A MET* 5.6 1.1 - - + -
710A LEU* 5.2 10.5 - - + -
713A SER* 4.8 17.5 - - - -
717A VAL* 4.5 10.5 - - + -
718A VAL* 3.9 30.5 - - + -
721A PHE* 3.7 39.5 - + + -
722A LEU* 6.4 0.4 - - + -
787A PHE* 6.1 0.7 - + - -
790A GLY 3.1 17.3 + - - -
791A CYS* 3.1 28.4 + - - +
793A TYR* 1.3 90.1 - + - +
795A ALA* 1.3 56.8 + - - +
797A PHE* 3.4 2.3 - - - -
798A GLU* 2.8 39.5 + - - +
821A LEU* 5.6 5.2 - - + -
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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
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633A LEU* 5.4 1.1 - - + +
634A ARG* 5.1 1.3 - - - +
637A SER* 3.3 27.1 + - - +
638A ARG* 3.6 33.9 + - - +
791A CYS 2.9 12.2 + - - +
792A GLU* 3.2 6.9 + - - +
794A PHE* 1.3 77.4 - - - +
796A LEU* 1.3 64.4 + - + +
798A GLU* 3.3 16.1 - - - +
799A GLU* 3.4 15.8 - - - +
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Residues in contact with LEU 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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638A ARG* 4.4 15.7 - - - +
792A GLU* 2.9 28.6 + - + +
793A TYR* 4.1 4.5 - - + +
794A PHE 3.3 0.2 - - - -
795A ALA* 1.3 78.7 - - - +
797A PHE* 1.3 67.9 + - + +
798A GLU 3.1 7.6 + - - -
799A GLU* 3.9 3.9 - - - +
800A GLN* 3.4 25.4 + - - +
1521A LEU* 3.3 50.9 - - + +
1522A LYS* 5.0 9.3 + - + +
1524A LYS* 3.7 34.5 - - + +
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Residues in contact with PHE 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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712A TYR 4.4 12.0 - - - +
713A SER* 4.8 6.4 - - - -
793A TYR* 3.0 63.5 + + + +
794A PHE* 3.4 4.3 - - - -
796A LEU* 1.3 82.2 - - + +
798A GLU* 1.3 59.4 + - - +
799A GLU 3.8 0.4 - - - -
800A GLN* 4.4 17.6 - - - +
801A GLY* 5.2 0.2 - - - -
1522A LYS* 3.6 48.7 - - + -
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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
------------------------------------------------------------
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