Contacts of the helix formed by residues 752 - 769 (chain B) in PDB entry 2JIU
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 752 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B GLU* 5.7 0.3 - - - +
750B ALA* 3.2 7.3 + - - -
751B THR* 1.3 79.1 + - - +
753B PRO* 1.4 76.0 - - - +
754B LYS* 4.0 5.9 + - - +
755B ALA* 3.2 24.3 + - - +
756B ASN* 2.9 28.4 + - - +
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Residues in contact with PRO 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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752B SER* 1.4 87.0 - - - +
754B LYS* 1.3 53.6 + - - +
756B ASN* 3.2 5.3 + - + +
757B LYS* 2.6 38.1 + - - +
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Residues in contact with LYS 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B SER* 4.3 6.1 - - - +
753B PRO* 1.3 78.4 - - - +
755B ALA* 1.3 64.8 + - - +
757B LYS* 3.2 9.5 + - + +
758B GLU* 3.1 52.8 + - + +
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Residues in contact with ALA 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B LEU* 3.4 29.4 - - + +
749B GLU* 4.2 14.4 - - + +
750B ALA 4.2 10.3 - - - +
751B THR* 5.5 0.9 - - - -
752B SER* 3.2 22.4 + - - +
754B LYS* 1.3 80.1 - - - +
756B ASN* 1.3 65.8 + - - +
758B GLU* 3.2 8.9 + - - +
759B ILE 3.0 18.2 + - - -
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Residues in contact with ASN 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B LEU* 5.7 1.0 - - - +
751B THR* 4.2 14.6 + - - +
752B SER 2.9 27.4 + - - +
753B PRO* 3.6 4.9 - - + +
755B ALA* 1.3 72.2 - - - +
757B LYS* 1.3 69.9 + - - +
759B ILE* 3.1 23.2 - - + +
760B LEU* 3.1 18.5 + - + +
784B SER 4.8 7.6 + - - +
785B THR* 5.2 1.8 - - - +
786B VAL* 4.1 27.5 - - - +
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Residues in contact with LYS 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B PRO 2.6 19.2 + - - +
754B LYS* 3.3 12.8 - - - +
756B ASN* 1.3 72.8 - - - +
758B GLU* 1.3 66.8 + - + +
760B LEU* 3.2 5.6 + - - +
761B ASP* 3.0 50.6 + - - +
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Residues in contact with GLU 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B LEU* 5.2 4.8 - - + +
754B LYS* 3.1 44.2 + - + +
755B ALA* 3.2 9.8 + - - +
757B LYS* 1.3 78.7 - - + +
759B ILE* 1.3 64.6 + - - +
761B ASP* 3.1 14.7 + - - +
762B GLU* 3.0 26.8 + - + +
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Residues in contact with ILE 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B LYS* 4.6 9.9 - - - -
746B GLU* 4.7 2.9 - - - -
747B LEU* 3.7 35.9 - - + +
755B ALA 3.0 10.9 + - - +
756B ASN* 3.1 29.6 - - - +
758B GLU* 1.3 76.9 - - - +
760B LEU* 1.3 63.0 + - + +
762B GLU* 3.6 8.8 - - - +
763B ALA* 3.5 17.7 + - - +
786B VAL* 3.7 47.1 - - + +
788B LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 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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704B LEU* 6.2 0.7 - - + -
756B ASN* 3.1 32.5 + - + +
757B LYS* 3.8 4.3 - - - +
759B ILE* 1.3 79.9 - - + +
761B ASP* 1.3 65.7 + - - +
763B ALA* 3.2 7.7 + - + +
764B TYR* 3.0 21.3 + - - +
780B ILE* 4.3 20.0 - - + -
782B LEU* 4.5 9.6 - - + -
786B VAL* 4.1 29.4 - - + -
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Residues in contact with ASP 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B LYS* 3.0 47.7 + - - +
758B GLU* 3.2 18.1 - - - +
760B LEU* 1.3 73.5 - - - +
762B GLU* 1.3 65.6 + - + +
764B TYR* 3.2 11.0 + - - +
765B VAL* 3.2 25.7 + - + +
861B LEU* 5.7 3.8 - - + +
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Residues in contact with GLU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B LYS* 3.0 31.0 + - - +
747B LEU* 5.6 1.9 - - - +
758B GLU 3.0 11.9 + - - +
759B ILE* 3.6 14.4 - - - +
761B ASP* 1.3 77.8 - - - +
763B ALA* 1.3 57.4 + - - +
765B VAL* 3.1 9.3 + - - +
766B MET* 2.9 53.7 + - + +
788B LEU* 4.1 6.7 - - + +
857B GLY* 3.4 26.4 + - - -
858B LEU* 4.4 6.4 + - + +
859B ALA* 5.4 10.2 - - + +
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Residues in contact with ALA 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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704B LEU* 4.7 9.1 - - + +
759B ILE 3.5 5.7 + - - +
760B LEU* 3.2 12.7 + - + +
761B ASP 3.2 0.6 - - - -
762B GLU* 1.3 76.3 - - - +
764B TYR* 1.3 59.9 + - - +
766B MET* 4.5 0.9 - - - -
767B ALA* 3.0 32.9 + - - +
777B LEU* 3.5 7.7 - - + +
780B ILE* 4.0 20.4 - - + -
788B LEU* 3.5 28.9 - - + +
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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
----------------------------------------------------------
700B ASN* 3.5 25.1 + - - +
760B LEU 3.0 12.9 + - - +
761B ASP* 3.2 13.9 + - - +
763B ALA* 1.3 77.0 - - - +
765B VAL* 1.3 60.6 + - + +
767B ALA* 4.1 3.6 - - - +
768B SER* 2.4 41.7 + - - -
861B LEU* 6.2 2.0 - - + -
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Residues in contact with VAL 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 ASP 3.4 15.0 - - - +
762B GLU* 3.1 10.0 + - - +
764B TYR* 1.3 82.3 - - + +
766B MET* 1.3 61.1 + - + +
768B SER* 3.0 21.8 + - - -
769B VAL* 3.0 12.7 + - + +
831B ARG* 4.2 1.5 + - - +
833B LEU* 3.6 36.1 - - + -
858B LEU* 4.2 17.5 - - + +
861B LEU* 3.9 33.9 - - + -
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Residues in contact with MET 766 (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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762B GLU* 2.9 46.7 + - + +
765B VAL* 1.3 78.1 - - + +
767B ALA* 1.3 60.3 + - - +
768B SER 3.2 0.2 - - - -
769B VAL* 3.5 23.4 + - - +
776B ARG* 5.1 0.3 - - - +
777B LEU* 3.9 36.5 + - + +
788B LEU* 3.7 28.3 - - + -
790B MET* 4.5 3.1 - - - -
855B ASP* 3.4 45.9 - - + +
856B PHE* 3.8 18.4 - - + -
858B LEU* 4.7 7.4 - - + -
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Residues in contact with ALA 767 (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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702B ALA* 3.5 21.2 - - + +
703B LEU 4.2 19.1 + - - +
704B LEU* 4.6 8.7 - - + -
763B ALA 3.0 18.6 + - - +
764B TYR* 4.1 5.2 - - - +
766B MET* 1.3 76.3 - - - +
768B SER* 1.3 60.7 + - - +
769B VAL 3.3 4.1 - - - +
777B LEU* 3.6 18.5 - - + +
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Residues in contact with SER 768 (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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700B ASN* 3.4 26.1 + - - -
702B ALA* 4.3 8.3 - - - +
764B TYR* 2.4 31.0 + - - -
765B VAL* 3.0 8.4 + - - -
767B ALA* 1.3 76.4 - - - +
769B VAL* 1.3 63.8 + - - +
770B ASP* 3.2 9.8 + - - +
827B TYR* 3.8 1.6 + - - -
831B ARG* 2.9 32.0 + - - -
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Residues in contact with VAL 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B VAL 3.0 19.3 + - - +
766B MET* 3.5 18.1 - - - +
767B ALA 3.3 4.4 - - - +
768B SER* 1.3 75.2 - - - +
770B ASP* 1.3 62.9 + - - +
771B ASN 4.8 0.9 - - - +
774B VAL* 3.4 35.0 - - + +
775B CYS 4.0 6.3 - - - +
776B ARG* 4.8 11.4 - - - +
827B TYR* 3.7 6.7 - - + -
828B LEU* 4.3 9.2 - - + -
831B ARG* 3.3 11.7 - - - +
833B LEU* 4.3 18.2 - - + -
855B ASP* 3.6 15.5 - - - +
858B LEU* 4.4 3.6 - - + -
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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