Contacts of the helix formed by residues 777 - 790 (chain A) in PDB entry 5EPG
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 PHE 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775A THR* 3.1 9.1 + - - +
776A GLN* 1.3 79.8 - - - +
778A PRO* 1.3 68.4 - - + +
779A LYS* 3.9 21.3 - - + -
780A TYR* 3.1 35.6 + + + +
781A ILE* 3.2 13.7 + - - +
811A VAL* 4.3 14.6 - - + -
1083A ALA 3.4 18.6 - - - -
1084A ASN* 4.0 8.5 - - - -
1085A ILE* 3.4 55.0 - - + +
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Residues in contact with PRO 778 (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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775A THR* 4.0 3.3 - - + -
776A GLN 3.8 4.9 - - - +
777A PHE* 1.3 88.3 - - + +
779A LYS* 1.3 57.6 + - - +
781A ILE* 2.9 4.9 + - + +
782A GLN* 2.8 28.6 + - - +
798A CYS* 3.8 31.7 - - + +
800A VAL* 4.2 11.9 - - + -
1043A GLY 5.0 5.2 - - - +
1045A ILE* 3.8 29.2 - - + -
1075A THR* 4.3 13.2 - - + +
1077A THR* 4.1 11.7 - - + +
1083A ALA* 6.0 3.1 - - + +
1084A ASN 5.5 2.7 - - - +
1086A SER* 5.7 0.2 - - - +
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Residues in contact with LYS 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A PHE* 3.3 16.6 - - + -
778A PRO* 1.3 78.8 - - - +
780A TYR* 1.3 56.3 + - - +
782A GLN* 3.5 17.9 + - - +
783A ASP* 3.1 51.6 + - - +
1077A THR* 4.2 6.2 - - + +
1082A ASN* 3.7 29.6 - - - +
1083A ALA* 3.1 35.6 - - + +
1084A ASN* 5.1 4.5 - - - -
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Residues in contact with TYR 780 (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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653A PHE* 3.8 31.8 - + - -
777A PHE* 3.1 38.5 + + + +
779A LYS* 1.3 78.0 - - - +
781A ILE* 1.3 72.2 + - + +
783A ASP* 3.3 8.4 + - + +
784A ILE* 3.0 38.5 + - + +
811A VAL* 3.5 35.9 - - + -
812A LEU* 3.1 37.9 + - + +
815A GLY* 3.7 13.9 - - - -
816A ILE* 4.5 1.2 - - - +
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Residues in contact with ILE 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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771A VAL* 3.8 24.2 - - + -
773A VAL* 4.1 3.8 - - + -
775A THR* 3.8 27.8 - - + +
777A PHE 3.2 12.7 + - - +
778A PRO 2.9 7.2 + - - +
780A TYR* 1.3 78.6 - - + +
782A GLN* 1.3 67.7 + - - +
784A ILE* 3.3 3.7 - - - +
785A VAL* 3.0 33.3 + - + +
798A CYS* 3.8 18.8 - - + -
814A THR* 4.2 9.2 - - + -
815A GLY* 3.3 36.1 - - - +
818A ALA* 4.3 5.6 - - + -
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Residues in contact with GLN 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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778A PRO 2.8 11.1 + - - +
779A LYS* 3.5 20.1 - - - +
781A ILE* 1.3 77.7 - - - +
783A ASP* 1.3 63.4 + - - +
786A ALA* 3.0 32.4 + - - +
793A ALA* 3.7 24.5 + - + +
796A VAL* 3.3 37.0 + - + +
797A MET* 4.0 6.3 - - - +
798A CYS* 4.5 4.7 - - + +
1077A THR* 3.1 40.7 + - + +
1082A ASN* 5.4 5.4 + - - +
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Residues in contact with ASP 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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653A PHE* 4.0 18.0 - - + -
779A LYS* 3.1 41.7 + - - +
780A TYR* 3.6 11.3 - - + +
781A ILE 3.2 0.2 - - - -
782A GLN* 1.3 87.3 - - - +
784A ILE* 1.3 58.2 + - - +
786A ALA* 3.9 2.7 - - - +
787A SER* 2.9 32.2 + - - -
793A ALA* 4.9 8.0 - - - +
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Residues in contact with ILE 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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653A PHE* 4.0 28.5 - - + -
662A PHE* 3.7 24.9 - - + -
780A TYR* 3.0 33.7 + - + +
781A ILE* 3.3 12.1 - - + +
783A ASP* 1.3 76.5 - - - +
785A VAL* 1.3 60.6 + - + +
787A SER* 3.8 0.9 - - - -
788A THR* 2.7 36.7 + - - -
815A GLY* 3.1 43.1 - - - +
816A ILE* 3.6 5.2 - - + +
819A ALA* 3.7 12.6 - - + -
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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
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769A MET* 4.9 1.6 - - + -
771A VAL* 4.3 11.4 - - + -
781A ILE* 3.0 25.6 + - + +
784A ILE* 1.3 75.7 - - + +
786A ALA* 1.3 59.5 + - - +
788A THR* 3.3 5.6 + - - -
789A LEU* 3.0 46.2 + - + +
796A VAL* 3.7 21.3 - - + -
818A ALA* 3.9 37.9 - - + +
819A ALA* 4.0 3.6 - - - +
822A ALA* 3.5 22.4 - - + -
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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
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782A GLN 3.0 20.8 + - - +
783A ASP* 3.9 3.8 - - - +
785A VAL* 1.3 73.4 - - - +
787A SER* 1.3 59.9 + - - +
789A LEU* 3.2 2.4 + - - -
790A LYS 2.8 9.7 + - - -
791A LEU* 2.8 46.3 + - - +
792A PRO 4.0 9.4 - - - +
793A ALA* 4.3 6.5 - - + -
796A VAL* 3.9 21.5 - - + +
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Residues in contact with SER 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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650A VAL* 3.5 12.9 - - - +
652A SER 5.1 3.3 + - - -
653A PHE* 3.3 31.7 - - - +
783A ASP 2.9 19.3 + - - -
784A ILE 3.8 2.9 + - - -
786A ALA* 1.3 75.7 - - - +
788A THR* 1.3 63.3 + - - +
790A LYS* 3.1 14.5 + - - +
791A LEU 5.2 0.4 - - - -
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Residues in contact with THR 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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647A LEU* 5.7 1.3 - - + -
650A VAL* 3.3 40.2 - - - +
662A PHE* 3.5 17.4 - - + -
784A ILE 2.7 22.6 + - - -
785A VAL 3.3 5.6 + - - +
787A SER* 1.3 77.4 + - - +
789A LEU* 1.3 60.4 + - + +
790A LYS* 4.4 1.9 - - - +
819A ALA* 3.4 38.5 - - - +
820A VAL* 5.5 0.2 - - - -
823A PHE* 4.0 26.5 - - + +
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Residues in contact with LEU 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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767A GLN* 4.7 4.6 + - - +
769A MET* 3.6 34.1 - - + -
785A VAL* 3.0 33.1 + - + +
786A ALA 3.9 0.7 - - - +
788A THR* 1.3 78.6 - - + +
790A LYS* 1.3 72.2 + - - +
791A LEU* 3.4 32.6 + - + +
796A VAL* 4.5 1.1 - - + -
822A ALA* 3.8 11.7 - - + +
823A PHE* 4.0 13.5 - - + -
826A ASN* 3.6 39.0 - - + +
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Residues in contact with LYS 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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649A ASP* 2.8 39.2 + - - -
650A VAL* 4.2 16.0 - - + +
786A ALA 2.8 5.2 + - - -
787A SER* 3.1 14.5 + - - +
788A THR 4.9 0.9 - - - +
789A LEU* 1.3 81.0 - - - +
791A LEU* 1.3 62.3 + - - +
792A PRO* 4.6 1.9 - - - +
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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