Contacts of the helix formed by residues 766 - 782 (chain C) in PDB entry 4PE5
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 766 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C HIS* 4.1 3.1 - - - -
215C GLU* 4.8 6.8 + - - -
762C MET* 3.8 19.6 - - - +
763C ARG 4.1 11.4 - - - -
764C LYS 3.4 3.8 + - - -
765C ASP* 1.3 75.1 - - - +
767C PRO* 1.3 72.0 - - - +
768C TRP* 3.3 23.4 + - - +
769C LYS* 3.0 27.6 + - - +
770C GLN* 3.8 1.9 + - - +
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Residues in contact with PRO 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C HIS* 4.6 12.6 - - + +
215C GLU* 5.8 2.2 - - - +
392C TYR* 6.0 6.5 - - + -
765C ASP 4.6 2.0 - - - +
766C SER* 1.3 86.3 - - - +
768C TRP* 1.3 69.0 + - + +
770C GLN* 3.1 12.3 + - + +
771C GLN* 2.9 35.2 + - + +
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Residues in contact with TRP 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLU* 4.0 13.3 + - - -
394C MET* 3.6 33.2 - - + +
395C SER 4.3 13.2 - - - +
396C THR* 6.2 0.2 - - - -
398C LEU* 5.5 10.8 - - + -
470C MET* 4.3 23.6 - - + -
471C GLN 5.3 2.9 - - - -
472C PHE* 4.4 23.1 - - + -
512C MET* 4.9 12.1 - - + -
762C MET* 3.6 19.7 - - + -
766C SER* 3.1 18.5 - - - -
767C PRO* 1.3 87.2 - - + +
769C LYS* 1.3 56.6 + - - +
771C GLN* 3.7 13.0 - - + +
772C VAL* 2.9 37.4 + - + +
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Residues in contact with LYS 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C GLU* 4.8 11.0 - - + -
529C PHE 5.5 6.1 - - - +
530C SER* 4.4 4.3 - - - -
762C MET* 3.4 35.6 - - + +
766C SER 3.0 17.7 + - - +
768C TRP* 1.3 78.5 - - - +
770C GLN* 1.3 58.0 + - - +
772C VAL* 4.0 2.4 - - - +
773C SER* 2.9 31.5 + - - -
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Residues in contact with GLN 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766C SER 3.8 1.3 + - - +
767C PRO* 3.1 15.0 + - + +
769C LYS* 1.3 76.4 - - - +
771C GLN* 1.3 62.5 + - + +
773C SER* 3.8 4.9 - - - -
774C LEU* 2.9 30.8 + - - +
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Residues in contact with GLN 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C MET* 5.6 7.6 - - + -
767C PRO* 2.9 25.1 + - + +
768C TRP* 3.7 17.7 - - + +
770C GLN* 1.3 77.2 - - + +
772C VAL* 1.3 58.4 + - + +
774C LEU* 3.3 7.6 + - - +
775C SER* 2.9 29.2 + - - -
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Residues in contact with VAL 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C LEU* 4.0 22.4 - - + -
512C MET* 4.0 25.1 - - + -
530C SER* 4.0 6.7 - - - +
760C ILE* 3.8 42.0 - - + -
762C MET* 5.0 0.4 - - - -
768C TRP* 2.9 25.0 + - + +
769C LYS* 4.0 4.3 - - - +
771C GLN* 1.3 77.1 - - + +
773C SER* 1.3 57.9 + - - +
775C SER* 3.1 8.1 + - - -
776C ILE* 2.9 29.1 + - + +
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Residues in contact with SER 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C SER* 3.9 13.2 - - - -
531C LYS* 3.4 29.3 + - - +
769C LYS 2.9 19.5 + - - -
770C GLN* 3.8 6.1 - - - -
772C VAL* 1.3 76.6 - - - +
774C LEU* 1.3 58.4 + - - +
776C ILE* 3.3 4.2 + - - +
777C LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B GLU* 4.5 5.6 - - + +
520B SER* 5.6 5.6 - - - +
770C GLN 2.9 18.8 + - - +
771C GLN* 3.6 8.1 - - - +
773C SER* 1.3 76.0 - - - +
775C SER* 1.3 57.5 + - - +
777C LEU* 3.4 7.0 + - - +
778C LYS* 2.9 29.6 + - - +
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Residues in contact with SER 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LYS* 5.4 0.7 - - - +
466C LEU* 3.3 24.5 - - - +
469C THR* 3.7 29.8 + - - +
771C GLN 2.9 14.1 + - - -
772C VAL* 3.1 9.8 + - - -
774C LEU* 1.3 76.2 - - - +
776C ILE* 1.3 54.4 + - - +
778C LYS* 3.4 6.8 + - - +
779C SER* 2.5 39.1 + - - -
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Residues in contact with ILE 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LEU* 3.7 31.4 - - + -
466C LEU* 4.1 12.8 - - + -
530C SER* 4.6 0.4 - - - +
531C LYS* 3.6 26.0 - - + +
532C PRO 4.4 0.9 - - - +
533C PHE* 3.8 7.9 - - + +
760C ILE* 4.1 25.1 - - + -
772C VAL* 2.9 23.7 + - + +
773C SER* 3.3 6.5 + - - +
775C SER* 1.3 73.9 - - - +
777C LEU* 1.3 60.8 + - - +
779C SER* 3.1 4.5 + - - +
780C HIS* 2.9 58.2 + - + +
785C MET* 4.0 5.8 - - + -
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Residues in contact with LEU 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ILE* 5.8 4.7 - - + +
516B ASN* 4.3 8.2 - - - -
517B GLU* 4.0 26.4 + - - +
520B SER* 4.8 4.0 - - - +
531C LYS* 5.1 7.5 - - + +
773C SER* 2.9 18.1 + - - +
774C LEU* 3.6 7.9 - - - +
776C ILE* 1.3 77.4 - - - +
778C LYS* 1.3 56.9 + - - +
780C HIS* 3.4 7.6 + - - +
781C GLU* 2.9 27.0 + - - +
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Residues in contact with LYS 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B GLU* 4.0 12.3 - - + +
774C LEU 2.9 17.6 + - - +
775C SER* 3.7 7.9 - - - +
777C LEU* 1.3 75.0 - - - +
779C SER* 1.3 52.3 + - - +
781C GLU* 3.3 16.3 - - + +
782C ASN* 2.7 29.5 + - - -
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Residues in contact with SER 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LEU* 5.2 2.6 - - - +
466C LEU* 5.7 0.5 - - - +
775C SER* 2.5 24.4 + - - -
776C ILE* 3.3 11.7 - - - +
778C LYS* 1.3 78.2 - - - +
780C HIS* 1.3 60.9 + - - +
781C GLU 3.5 0.3 + - - -
782C ASN* 3.5 16.7 + - - +
784C PHE* 3.5 34.4 + - - +
785C MET* 3.7 29.1 + - - +
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Residues in contact with HIS 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ALA* 3.3 21.4 - - - +
759B SER* 2.6 49.4 + - - +
760B THR* 5.4 3.4 - - - -
531C LYS* 6.2 0.4 - - + -
532C PRO 3.4 7.8 + - - -
533C PHE* 3.3 40.5 + - - -
534C LYS* 5.4 0.2 - - - -
535C TYR* 4.4 3.1 - + - -
776C ILE* 2.9 39.1 + - + +
777C LEU* 3.9 6.1 - - - +
779C SER* 1.3 73.5 - - - +
781C GLU* 1.3 64.0 + - - +
782C ASN 3.2 10.7 - - - +
785C MET* 3.6 25.1 - - + +
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Residues in contact with GLU 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ASN* 5.9 4.7 - - + -
517B GLU* 5.1 8.5 - - + +
694B ASN* 4.3 26.5 - - + +
697B ASN* 5.6 1.9 - - - +
698B ASN* 4.6 3.1 - - - +
758B ALA* 4.7 4.9 - - - +
777C LEU 2.9 14.6 + - - +
778C LYS* 3.3 18.2 - - - +
779C SER 3.2 0.4 - - - -
780C HIS* 1.3 78.7 - - - +
782C ASN* 1.3 58.1 + - + +
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Residues in contact with ASN 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B ASN 5.4 4.5 - - - +
698B ASN* 4.7 16.2 - - + -
758B ALA* 4.6 8.7 + - - +
778C LYS 2.7 30.3 + - - -
779C SER* 3.5 11.3 + - - +
780C HIS* 3.2 13.9 - - - +
781C GLU* 1.3 76.7 - - + +
783C GLY* 1.3 60.0 + - - +
784C PHE* 2.8 36.5 + - - +
785C MET* 4.9 1.0 + - - +
786C GLU* 5.3 1.0 + - - +
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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