Contacts of the helix formed by residues 766 - 782 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS* 4.1 3.8 - - - -
762A MET* 3.8 19.8 - - - +
763A ARG 4.1 11.9 - - - -
764A LYS 3.5 3.6 + - - -
765A ASP* 1.3 74.8 - - - +
767A PRO* 1.3 72.3 - - - +
768A TRP* 3.2 23.9 + - - +
769A LYS* 3.0 27.1 + - - +
770A GLN* 3.9 1.9 + - - +
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Residues in contact with PRO 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A HIS* 4.5 14.1 - - + +
392A TYR* 6.2 5.2 - - + +
766A SER* 1.3 87.2 - - - +
768A TRP* 1.3 68.6 + - + +
770A GLN* 3.1 11.2 + - + +
771A GLN* 2.9 35.6 + - + +
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Residues in contact with TRP 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A MET* 3.3 34.9 - - + +
395A SER 4.3 12.5 + - - +
396A THR* 6.2 0.7 - - - -
470A MET* 4.3 23.8 - - + -
471A GLN 5.0 4.5 - - - -
472A PHE* 4.5 27.8 - + + -
512A MET* 4.7 12.8 - - + -
762A MET* 3.5 20.0 - - + -
766A SER* 3.1 18.8 - - - -
767A PRO* 1.3 85.7 - - + +
769A LYS* 1.3 56.9 + - - +
770A GLN 3.3 0.2 - - - -
771A GLN* 3.8 13.6 - - + +
772A VAL* 2.9 38.5 + - + +
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Residues in contact with LYS 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLU* 4.7 12.6 - - + -
529A PHE 5.1 7.1 - - - +
530A SER* 4.2 4.8 - - - -
762A MET* 3.5 35.1 - - + +
766A SER 3.0 17.4 + - - +
768A TRP* 1.3 78.0 - - - +
770A GLN* 1.3 57.6 - - - +
772A VAL* 3.9 2.1 - - - +
773A SER* 2.9 30.5 + - - -
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Residues in contact with GLN 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER 3.9 1.2 + - - +
767A PRO* 3.1 14.1 + - + +
769A LYS* 1.3 76.2 - - - +
771A GLN* 1.3 60.3 + - + +
773A SER* 3.3 5.6 + - - -
774A LEU* 2.9 42.7 + - + +
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Residues in contact with GLN 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A MET* 5.5 7.4 - - + -
767A PRO* 2.9 25.5 + - + +
768A TRP* 3.8 19.1 - - + +
770A GLN* 1.3 77.4 - - + +
772A VAL* 1.3 57.8 + - + +
774A LEU* 3.4 11.7 + - - +
775A SER* 2.9 29.7 + - - -
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Residues in contact with VAL 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 4.1 24.5 - - + -
472A PHE* 6.5 0.7 - - + -
512A MET* 4.3 21.8 - - + -
530A SER* 3.9 6.3 - - - +
760A ILE* 3.7 42.6 - - + -
762A MET* 5.0 0.7 - - + -
768A TRP* 2.9 25.9 + - + +
769A LYS* 4.0 3.8 - - - +
771A GLN* 1.3 76.7 - - + +
773A SER* 1.3 59.0 + - - +
775A SER* 3.1 7.9 + - - -
776A ILE* 2.9 29.0 + - + +
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Residues in contact with SER 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 3.8 20.1 - - - -
531A LYS* 3.3 23.3 + - - +
769A LYS 2.9 19.0 + - - -
770A GLN* 3.6 7.2 - - - -
771A GLN 3.3 0.2 - - - -
772A VAL* 1.3 77.7 - - - +
774A LEU* 1.3 59.0 + - - +
776A ILE* 3.3 4.4 + - - +
777A LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLN* 2.9 27.7 + - + +
771A GLN* 3.8 11.9 - - - +
773A SER* 1.3 78.1 - - - +
775A SER* 1.3 57.6 + - - +
777A LEU* 3.5 5.2 + - + +
778A LYS* 2.9 29.8 + - - +
517D GLU* 4.3 9.3 - - + +
520D SER* 3.4 42.4 - - - +
521D GLU* 5.0 5.2 - - - +
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Residues in contact with SER 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LYS* 5.0 0.9 + - - +
466A LEU* 3.3 24.8 - - - +
469A THR* 3.7 30.6 + - - -
771A GLN 2.9 18.1 + - - -
772A VAL* 3.4 6.5 - - - -
774A LEU* 1.3 75.4 - - - +
776A ILE* 1.3 54.9 + - - +
778A LYS* 3.5 7.0 + - - +
779A SER* 2.6 38.9 + - - -
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Residues in contact with ILE 776 (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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462A LEU* 3.7 33.0 - - + -
466A LEU* 4.2 13.9 - - + -
530A SER* 4.7 0.7 - - - +
531A LYS* 3.7 25.1 - - + +
532A PRO 4.3 0.7 - - - +
533A PHE* 3.7 12.3 - - + +
760A ILE* 3.9 29.6 - - + -
772A VAL* 2.9 21.9 + - + +
773A SER 3.7 4.5 - - - +
775A SER* 1.3 73.8 - - - +
777A LEU* 1.3 60.5 + - - +
779A SER* 3.0 5.6 + - - +
780A HIS* 2.9 54.0 + - + +
785A MET* 4.0 2.7 - - + -
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Residues in contact with LEU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LYS* 5.0 9.1 - - + +
773A SER 2.9 17.9 + - - +
774A LEU* 3.7 8.1 - - + +
776A ILE* 1.3 77.0 - - - +
778A LYS* 1.3 56.4 + - - +
780A HIS* 3.0 9.5 + - - +
781A GLU* 2.9 28.8 + - - +
515D ILE* 5.6 6.7 - - + +
516D ASN* 4.3 9.0 - - - +
517D GLU* 4.0 24.1 + - - +
520D SER* 4.9 2.9 - - - +
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Residues in contact with LYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A LEU 2.9 19.4 + - - +
775A SER* 3.7 7.6 - - - +
777A LEU* 1.3 75.8 - - - +
779A SER* 1.3 50.5 + - - +
780A HIS 3.1 0.4 - - - -
781A GLU* 3.2 39.0 - - + +
782A ASN* 2.4 32.6 + - - +
517D GLU* 3.8 17.9 - - + +
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Residues in contact with SER 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 5.3 2.0 - - - +
465A LYS* 5.5 3.8 - - - +
466A LEU* 5.9 0.3 - - - +
775A SER* 2.6 25.8 + - - -
776A ILE* 3.0 11.5 + - - +
778A LYS* 1.3 76.6 - - - +
780A HIS* 1.3 57.6 + - - +
782A ASN* 3.7 7.1 + - - +
784A PHE* 3.3 41.1 + - - +
785A MET* 3.4 32.7 + - - +
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Residues in contact with HIS 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LYS* 6.3 0.4 - - + -
532A PRO 3.4 9.9 + - - -
533A PHE* 3.4 33.4 - - - -
535A TYR* 4.3 5.8 - + - -
776A ILE* 2.9 34.7 + - + +
777A LEU* 3.0 11.4 + - - +
779A SER* 1.3 77.7 - - - +
781A GLU* 1.3 62.3 + - - +
782A ASN 3.1 11.6 + - - +
785A MET* 3.5 24.5 - - + +
758D ALA* 3.3 21.5 - - - +
759D SER* 2.4 50.2 + - - +
760D THR* 5.2 6.0 - - - -
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Residues in contact with GLU 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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777A LEU 2.9 10.2 + - - +
778A LYS* 3.2 52.3 - - + +
780A HIS* 1.3 77.7 - - - +
782A ASN* 1.3 67.7 + - - +
516D ASN* 5.1 8.3 - - + -
517D GLU* 5.0 10.1 - - + +
693D ARG 4.8 0.5 - - - +
694D ASN* 3.9 31.7 - - + +
697D ASN* 4.0 27.2 - - - +
698D ASN* 4.8 1.0 - - - +
758D ALA* 4.6 5.9 - - - +
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Residues in contact with ASN 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 LYS* 2.4 36.6 + - - +
779A SER* 3.7 8.3 - - - +
780A HIS* 3.3 13.7 - - - +
781A GLU* 1.3 91.5 + - - +
783A GLY* 1.3 57.6 + - - +
784A PHE* 2.8 37.0 + - - +
785A MET* 4.9 1.7 + - - +
786A GLU* 5.2 1.0 + - - +
697D ASN 5.5 2.7 - - - +
698D ASN* 4.7 15.0 - - + -
758D ALA* 4.4 11.2 + - - -
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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
------------------------------------------------------------
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