Contacts of the helix formed by residues 774 - 789 (chain B) in PDB entry 1P48
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 THR 774 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B GLY 4.9 3.6 + - - -
757B LYS* 3.8 20.3 - - - +
758B TYR* 4.6 3.1 - - - -
773B LEU* 1.3 76.1 - - - +
775B GLY* 1.3 70.0 + - - +
776B PRO* 3.5 16.1 - - + +
777B GLN* 3.0 41.8 + - + +
778B LEU* 2.8 22.2 + - - +
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Residues in contact with GLY 775 (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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756B GLY 5.0 3.6 + - - -
758B TYR* 4.5 13.9 - - - -
774B THR* 1.3 81.1 + - - +
776B PRO* 1.3 66.9 - - - +
778B LEU* 3.2 3.6 + - - +
779B ALA* 3.2 17.5 + - - +
798B PHE* 3.6 19.5 - - - -
802B ASP* 5.4 0.7 - - - -
805B ALA* 5.0 9.0 - - - -
808B HIS* 6.0 0.4 - - - -
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Residues in contact with PRO 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B THR* 3.5 17.9 - - + +
775B GLY* 1.3 89.2 - - - +
777B GLN* 1.3 60.3 + - + +
779B ALA* 3.3 9.4 + - + +
780B ASP* 3.2 29.0 + - - +
808B HIS* 4.9 18.8 - - + +
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Residues in contact with GLN 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B LYS* 4.9 1.7 - - - -
772B TRP 4.1 4.3 - - - +
773B LEU* 3.6 29.9 - - + +
774B THR* 3.0 40.5 + - + +
776B PRO* 1.3 75.5 - - + +
778B LEU* 1.3 65.9 + - - +
780B ASP* 3.3 13.2 + - - +
781B LEU* 3.3 18.2 + - - +
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Residues in contact with LEU 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 6.3 0.7 - - + -
752B PHE* 4.7 4.7 - - + -
758B TYR* 3.5 40.4 - - + -
760B LEU* 4.6 12.1 - - + -
773B LEU* 4.2 15.2 - - + +
774B THR 2.8 16.1 + - - +
775B GLY 3.2 4.5 + - - +
777B GLN* 1.3 76.5 - - - +
779B ALA* 1.3 61.6 + - - +
781B LEU* 3.2 21.6 + - + +
782B TYR* 3.1 48.4 + - + +
797B PRO 3.6 21.3 - - - +
798B PHE* 4.1 5.6 - - + -
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Residues in contact with ALA 779 (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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775B GLY 3.2 12.1 + - - +
776B PRO* 3.4 13.5 - - + +
777B GLN 3.2 0.2 - - - -
778B LEU* 1.3 76.2 - - - +
780B ASP* 1.3 66.8 + - - +
782B TYR* 3.1 13.4 + - - +
783B HIS* 3.0 32.7 + - + +
798B PHE* 4.2 6.2 - - + -
808B HIS* 4.6 16.2 - - + +
809B PHE* 3.8 19.7 - - + -
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Residues in contact with ASP 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B PRO* 3.2 17.6 + - - +
777B GLN* 3.6 15.3 - - - +
778B LEU 3.3 0.4 - - - -
779B ALA* 1.3 76.9 - - - +
781B LEU* 1.3 62.6 + - - +
783B HIS* 3.5 10.9 + - - +
784B SER* 3.1 23.0 + - - -
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Residues in contact with LEU 781 (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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666B LEU* 6.5 1.1 - - + -
721B ALA* 6.5 0.2 - - + -
722B GLU* 4.1 21.1 - - - +
760B LEU* 3.8 30.5 - - + -
773B LEU* 4.3 6.7 - - + -
777B GLN 3.3 8.5 + - - +
778B LEU* 3.2 24.0 + - + +
779B ALA 3.2 0.4 - - - -
780B ASP* 1.3 80.2 - - - +
782B TYR* 1.3 65.9 + - + +
784B SER* 3.1 14.6 + - - +
785B LEU* 3.0 35.3 + - + +
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Residues in contact with TYR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 4.8 10.7 - - + +
745B LEU* 6.0 1.6 - - + -
747B CYS* 3.3 36.7 - - - +
749B SER* 4.6 1.7 - - - -
752B PHE* 4.9 1.2 - - - -
778B LEU* 3.1 48.9 + - + +
779B ALA* 3.1 9.1 + - - +
781B LEU* 1.3 77.7 - - + +
783B HIS* 1.3 65.8 + - - +
785B LEU* 3.0 21.6 + - + +
786B MET* 2.9 28.2 + - - +
794B ILE* 4.4 13.7 - - + -
797B PRO* 2.9 41.0 + - + +
798B PHE* 4.1 5.2 - + - -
809B PHE* 3.6 27.6 - + + -
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Residues in contact with HIS 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B ALA* 3.0 31.5 + - + +
780B ASP* 3.8 10.5 - - - +
782B TYR* 1.3 75.0 - - - +
784B SER* 1.3 63.0 + - - +
786B MET* 3.4 13.6 + - - +
787B LYS* 3.1 25.3 + - - +
809B PHE* 3.6 23.9 - + - -
812B THR* 3.2 46.8 + - - -
813B ALA* 4.3 4.6 + - - -
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Residues in contact with SER 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B GLU* 5.2 2.9 + - - -
780B ASP 3.1 14.8 + - - -
781B LEU* 3.1 18.8 - - - +
782B TYR 3.0 0.6 - - - -
783B HIS* 1.3 78.4 - - - +
785B LEU* 1.3 65.4 + - - +
787B LYS* 3.3 31.6 - - - +
788B ARG* 3.3 12.5 + - - +
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Residues in contact with LEU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 4.9 3.8 - - + -
721B ALA* 4.3 17.7 - - + -
722B GLU* 3.9 27.1 - - + +
725B LEU* 3.8 11.0 - - + -
745B LEU* 4.8 11.0 - - + -
781B LEU* 3.0 31.5 + - + +
782B TYR* 3.0 21.1 + - + +
784B SER* 1.3 78.5 - - - +
786B MET* 1.3 58.8 + - + +
788B ARG* 3.2 2.0 + - - +
789B TYR* 2.8 60.0 + - + +
791B ILE* 3.7 14.8 - - + +
794B ILE* 6.3 1.1 - - + -
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Residues in contact with MET 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B TYR 2.9 24.8 + - - +
783B HIS* 3.6 15.3 - - - +
784B SER 3.3 0.2 - - - -
785B LEU* 1.3 77.2 - - + +
787B LYS* 1.3 57.8 + - - +
789B TYR 3.0 20.4 - - - +
791B ILE* 4.5 14.4 + - + +
794B ILE* 3.9 26.9 - - + -
809B PHE* 4.1 13.0 - - - -
813B ALA* 2.8 30.3 - - - +
815B ILE* 3.3 35.7 - - + -
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Residues in contact with LYS 787 (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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783B HIS 3.1 13.4 + - - +
784B SER* 3.3 22.7 - - - +
786B MET* 1.3 78.3 - - - +
788B ARG* 1.3 67.6 + - - +
789B TYR 4.7 0.4 - - - -
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Residues in contact with ARG 788 (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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722B GLU* 3.7 22.4 - - - +
726B ASP* 3.1 30.3 + - - -
784B SER* 3.3 15.7 + - - +
785B LEU* 3.2 4.4 + - - +
787B LYS* 1.3 87.7 - - + +
789B TYR* 1.3 92.1 + - + +
790B PRO* 4.6 1.0 - - - +
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Residues in contact with TYR 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B GLU* 3.0 17.7 + - - -
725B LEU* 3.4 45.8 - - + -
726B ASP* 2.9 32.1 + - - -
729B VAL* 4.0 16.8 - - + -
743B ILE* 4.6 4.3 - - + -
785B LEU* 2.8 40.6 + - + +
786B MET 3.0 18.9 - - - +
787B LYS 4.7 0.4 - - - -
788B ARG* 1.3 116.1 + - + +
790B PRO* 1.3 62.1 - - + +
791B ILE* 2.8 28.1 + - + -
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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