Contacts of the helix formed by residues 750 - 765 (chain B) in PDB entry 3K23
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 PRO 750 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B ASN* 3.4 23.3 - - + +
565B MET* 3.7 24.7 - - + +
568B GLY* 4.0 11.9 - - - -
748B GLU 4.1 0.2 - - - -
749B PHE* 1.3 83.6 - - - +
751B GLU* 1.3 56.9 + - - +
752B MET* 3.1 3.8 + - + +
753B LEU* 3.1 31.4 + - + +
754B ALA* 2.7 33.8 + - - +
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Residues in contact with GLU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A GLU* 5.0 0.2 - - - +
655A ARG* 3.6 24.0 + - - -
749B PHE 3.8 0.4 + - - -
750B PRO* 1.3 72.0 - - - +
752B MET* 1.3 53.5 + - - +
754B ALA* 3.3 6.4 - - - +
755B GLU* 2.7 39.2 + - + +
743E ALA* 5.4 1.0 - - - +
744E LEU* 3.4 19.0 + - + +
747E TYR* 3.1 38.8 + - - -
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Residues in contact with MET 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLY* 4.7 15.5 - - - +
571B VAL* 3.0 38.4 - - + +
572B ILE* 3.9 16.6 - - + -
575B VAL* 5.4 1.8 - - - -
750B PRO* 3.1 3.4 + - + +
751B GLU* 1.3 78.3 - - - +
753B LEU* 1.3 58.6 + - + +
755B GLU* 3.1 3.0 + - - +
756B ILE* 2.8 61.3 + - + +
744E LEU* 4.2 14.6 - - + +
745E LEU* 3.8 22.7 - - + -
748E LEU* 3.8 31.4 - - + -
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Residues in contact with LEU 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B JZN 3.5 22.2 - - - -
564B ASN* 3.1 32.1 - - + +
567B GLY 4.1 3.6 - - - +
568B GLY* 3.6 11.0 - - - +
571B VAL* 4.1 17.9 - - + -
600B TRP* 3.5 37.7 - - + -
749B PHE* 4.4 2.9 - - + -
750B PRO* 3.1 23.6 + - + +
752B MET* 1.3 79.0 - - + +
754B ALA* 1.3 63.0 + - - +
756B ILE* 4.6 4.5 - - + +
757B ILE* 3.0 40.1 + - + +
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Residues in contact with ALA 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B PHE* 4.0 21.1 - - + -
749B PHE* 3.9 15.3 - - + +
750B PRO 2.7 25.1 + - - +
751B GLU* 3.3 8.5 - - - +
753B LEU* 1.3 76.2 - - - +
755B GLU* 1.3 54.8 + - - +
758B THR* 2.7 31.5 + - - -
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Residues in contact with GLU 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B GLU* 2.7 21.5 + - + +
752B MET* 3.7 3.6 - - - +
754B ALA* 1.3 71.8 - - - +
756B ILE* 1.3 67.9 - - + +
758B THR* 3.5 6.5 - - - -
759B ASN* 3.3 28.1 + - - +
742E ASN 5.6 5.4 - - - +
743E ALA 6.0 0.2 - - - +
744E LEU* 4.0 22.7 - - + +
745E LEU* 5.5 2.0 - - + +
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Residues in contact with ILE 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B VAL* 3.9 12.6 - - + -
596B LEU* 4.9 2.5 - - + +
597B GLN* 4.5 23.7 - - + +
600B TRP* 3.2 45.5 - - + +
752B MET* 2.8 47.8 + - + +
753B LEU* 4.1 4.7 - - + +
755B GLU* 1.3 74.6 - - + +
757B ILE* 1.3 76.2 + - - +
759B ASN* 2.8 15.3 + - - +
760B GLN* 2.9 10.8 + - + -
745E LEU* 4.0 19.3 - - + -
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Residues in contact with ILE 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B JZN 5.3 0.2 - - - -
600B TRP* 4.0 22.2 - - + -
736B CYS* 3.8 16.6 - - - -
737B PHE* 3.7 28.0 - - + -
740B PHE* 3.5 29.2 - - + -
749B PHE* 3.6 35.9 - - + -
753B LEU* 3.0 25.4 + - + +
754B ALA 4.2 2.0 - - - +
756B ILE* 1.3 83.6 - - - +
758B THR* 1.3 66.8 + - - +
759B ASN 2.8 0.5 + - - -
760B GLN* 2.8 12.1 + - - +
761B ILE* 3.1 16.6 + - + +
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Residues in contact with THR 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B PHE* 3.8 17.6 - - - -
754B ALA 2.7 18.8 + - - -
755B GLU* 3.5 12.5 - - - -
757B ILE* 1.3 79.6 - - - +
759B ASN* 1.3 61.3 + - - +
761B ILE* 4.2 5.9 - - - +
762B PRO* 3.1 23.8 - - - +
528C LEU* 5.5 4.0 - - + +
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Residues in contact with ASN 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B GLN* 3.3 28.3 - - - +
755B GLU* 3.3 16.0 + - - +
756B ILE* 2.8 11.3 + - - +
757B ILE 2.8 4.2 + - - -
758B THR* 1.3 78.8 - - - +
760B GLN* 1.3 64.4 + - - +
762B PRO* 3.4 7.7 - - - +
763B LYS* 3.4 30.3 + - - +
742E ASN* 3.9 23.2 - - - +
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Residues in contact with GLN 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B GLN* 4.3 24.1 + - + +
598B TYR* 5.9 3.8 - - + -
600B TRP* 4.9 4.9 - - - +
733B LEU* 5.7 2.0 - - + -
737B PHE* 4.1 17.5 - - + -
756B ILE 2.9 9.8 + - - +
757B ILE* 2.8 13.9 + - - +
759B ASN* 1.3 70.0 - - - +
761B ILE* 1.3 52.4 + - - +
763B LYS* 2.6 19.2 + - - -
764B TYR* 2.6 36.3 + - + +
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Residues in contact with ILE 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B PHE* 3.6 52.5 - - + -
740B PHE* 4.7 3.4 - - + -
741B LEU* 4.0 28.7 - - + -
757B ILE* 3.1 21.9 + - + +
758B THR* 4.2 5.4 - - - +
760B GLN* 1.3 76.2 - - - +
762B PRO* 1.3 75.1 - - + +
764B TYR* 3.6 3.0 + - - +
765B SER* 3.6 12.5 + - - -
528C LEU* 3.8 21.3 - - + -
529C THR* 4.6 8.4 - - + +
538C VAL* 4.4 22.0 - - + +
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Residues in contact with PRO 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B THR 3.1 22.2 - - - +
759B ASN* 3.4 6.3 - - - +
760B GLN 3.4 3.6 - - - -
761B ILE* 1.3 95.2 - - + +
763B LYS* 1.3 61.0 + - + +
765B SER* 2.9 32.3 + - - -
768B ASN* 3.4 2.7 + - - -
528C LEU* 4.3 23.1 - - + +
529C THR* 6.0 0.4 - - - -
530C PRO* 5.4 7.5 - - + +
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Residues in contact with LYS 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B THR* 4.6 16.1 + - + +
597B GLN* 4.0 21.6 + - - +
598B TYR* 4.0 34.1 - - + +
759B ASN* 3.4 26.9 + - - +
760B GLN* 2.6 13.1 + - - +
762B PRO* 1.3 78.8 - - + +
764B TYR* 1.3 60.6 + - - +
765B SER 3.3 3.8 - - - +
768B ASN* 3.0 25.4 + - + +
769B ILE* 3.5 15.4 + - - +
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Residues in contact with TYR 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B TYR* 5.6 0.2 - - - -
602B TYR* 6.0 1.1 - - - -
729B VAL* 5.9 0.4 - - + -
730B GLU* 3.1 35.3 - - - +
733B LEU* 3.5 28.5 - - + -
734B ASN* 3.3 31.3 + - - -
737B PHE* 3.5 25.1 - + + -
760B GLN* 2.6 26.8 + - + +
761B ILE 3.8 6.7 - - - +
763B LYS* 1.3 68.5 - - - +
765B SER* 1.3 69.8 + - - +
766B ASN* 3.6 0.5 + - - -
769B ILE* 3.5 28.0 - - + +
771B LYS* 4.6 18.4 + - - -
537C GLU* 4.9 0.5 - - - +
538C VAL* 5.7 4.0 - - + -
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Residues in contact with SER 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B ILE 3.6 5.2 + - - -
762B PRO* 2.9 21.7 + - - -
763B LYS 3.3 6.9 - - - +
764B TYR* 1.3 84.2 - - - +
766B ASN* 1.3 72.4 + - - +
767B GLY 3.4 1.9 + - - -
768B ASN* 2.9 18.9 + - - -
769B ILE* 3.4 7.4 - - - +
530C PRO* 6.2 1.1 - - - -
534C SER* 4.2 25.8 - - - -
537C GLU* 3.8 7.9 - - - -
538C VAL* 6.5 0.9 - - - -
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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
------------------------------------------------------------
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