Contacts of the helix formed by residues 721 - 740 (chain B) in PDB entry 5J3V
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 PHE 721 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B PRO* 4.4 19.3 - - + -
684B ARG* 3.4 35.7 - - - -
718B ASN* 3.3 9.7 + - + +
719B PRO 3.1 1.7 - - - -
720B GLU* 1.3 104.7 - - + +
722B ILE* 1.3 54.1 + - - +
723B SER 3.5 2.0 - - - -
724B VAL* 3.2 20.7 + - + -
725B CYS* 2.7 36.6 + - - +
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Residues in contact with ILE 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B PRO 3.5 17.3 - - - +
720B GLU* 3.5 5.7 + - - +
721B PHE* 1.3 69.8 - - - +
723B SER* 1.3 56.3 + - - +
725B CYS* 3.2 5.3 + - - +
726B ASN* 2.7 40.8 + - + +
764B PRO* 3.7 39.7 - - + -
766B THR* 5.5 3.8 - - - +
767B LEU* 4.6 15.6 - - + +
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Residues in contact with SER 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B GLN* 3.3 35.8 + - - +
721B PHE 3.5 0.4 - - - -
722B ILE* 1.3 80.3 - - - +
724B VAL* 1.3 63.0 + - - +
726B ASN* 3.8 4.9 - - - +
727B ASN* 3.2 31.2 + - - +
15D ALA* 4.5 11.7 - - - +
16D PRO 5.6 0.3 + - - -
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Residues in contact with VAL 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B PRO* 3.2 39.9 - - + +
684B ARG* 3.4 24.9 - - + +
685B GLN* 4.1 11.0 - - + +
688B PHE* 3.8 27.0 - - + -
716B ASN* 3.9 9.2 - - + +
721B PHE* 3.2 23.1 + - + +
722B ILE 3.2 0.4 - - - -
723B SER* 1.3 76.3 - - - +
725B CYS* 1.3 61.7 + - - +
727B ASN* 3.5 1.7 + - - -
728B ALA* 3.0 27.5 + - - +
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Residues in contact with CYS 725 (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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716B ASN 3.6 10.3 + - - +
717B LEU* 3.7 17.9 - - - -
718B ASN 3.5 15.5 - - - +
719B PRO* 4.2 7.0 - - + -
721B PHE 2.7 21.1 + - - +
722B ILE* 3.7 4.3 - - - +
724B VAL* 1.3 74.3 - - - +
726B ASN* 1.3 58.6 + - - +
728B ALA* 3.3 0.7 + - - +
729B THR* 3.0 39.3 + - - +
757B ILE* 3.6 30.1 - - - -
767B LEU* 4.2 14.8 - - + -
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Residues in contact with ASN 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ILE* 2.7 26.4 + - + +
723B SER* 3.8 7.0 - - - +
725B CYS* 1.3 75.3 - - - +
727B ASN* 1.3 60.5 + - - +
729B THR* 2.9 17.2 + - - -
730B TRP* 3.1 10.4 + - - +
766B THR* 3.1 27.3 + - - -
767B LEU* 3.5 22.9 - - + +
770B ASN* 2.9 27.9 + - - +
13D GLY 3.5 11.6 - - - +
15D ALA* 3.6 21.1 + - + +
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Residues in contact with ASN 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B GLN* 2.8 38.0 + - + +
688B PHE* 3.9 18.7 - - + +
689B ALA* 3.4 21.7 - - - +
723B SER 3.2 17.0 + - - +
724B VAL 4.0 2.2 - - - +
726B ASN* 1.3 77.5 - - - +
728B ALA* 1.3 57.7 + - - +
730B TRP* 3.9 10.4 - - - +
731B ALA* 3.0 29.3 + - - +
14D LYS* 3.9 5.1 - - - +
15D ALA* 3.0 31.8 + - - +
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Residues in contact with ALA 728 (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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688B PHE* 4.2 15.0 - - + +
713B LEU* 4.0 18.6 - - + +
716B ASN 3.6 17.7 - - - +
717B LEU* 3.9 9.9 - - + -
724B VAL 3.0 18.4 + - - +
725B CYS 3.4 5.4 - - - +
726B ASN 3.2 0.2 - - - -
727B ASN* 1.3 74.3 - - - +
729B THR* 1.3 66.0 + - - +
731B ALA* 3.2 4.3 + - - +
732B ILE* 3.1 28.6 + - - +
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Residues in contact with THR 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B LEU* 3.7 9.9 - - + -
725B CYS* 3.0 22.4 + - - +
726B ASN* 2.9 16.1 + - - -
728B ALA* 1.3 75.7 - - - +
730B TRP* 1.3 57.9 + - - +
732B ILE* 3.3 8.1 + - - -
733B GLY 3.1 12.0 + - - -
754B LEU* 3.7 27.8 - - + -
757B ILE* 4.9 1.6 - - + -
767B LEU* 4.4 2.1 - - + +
770B ASN* 3.7 18.6 - - - +
771B THR* 4.3 12.9 + - - +
774B THR* 2.5 31.2 + - - +
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Residues in contact with TRP 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B PHE 4.7 0.9 - - - -
689B ALA* 3.7 11.7 - - - -
692B GLY* 3.5 30.7 - - - -
693B ASP* 3.5 24.7 - - - -
696B LYS* 4.8 8.7 - - - -
726B ASN 3.1 14.4 + - - +
727B ASN* 3.9 10.8 - - - +
729B THR* 1.3 79.1 + - - +
731B ALA* 1.3 76.1 + - + +
733B GLY* 3.5 1.8 + - - -
734B GLU* 3.2 54.1 + - + +
770B ASN* 4.1 12.1 - - - +
773B ILE* 6.3 0.7 - - + -
774B THR* 4.1 4.0 - - - -
777B ARG* 4.9 7.1 + - - -
809B GLU* 4.8 4.9 + - - -
13D GLY* 3.3 44.6 - - - +
14D LYS* 3.6 29.8 - - + -
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Residues in contact with ALA 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B PHE 4.1 17.0 - - - +
691B LEU* 4.4 11.4 - - + -
692B GLY* 4.5 10.4 - - - +
713B LEU* 4.1 16.4 - - + -
727B ASN 3.0 18.2 + - - +
728B ALA 3.2 5.1 + - - +
730B TRP* 1.3 81.0 - - + +
732B ILE* 1.3 65.9 + - - +
734B GLU* 3.2 3.5 + - - +
735B ILE* 3.0 29.9 + - + +
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Residues in contact with ILE 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B MET* 4.6 12.8 - - + -
713B LEU* 3.9 25.4 - - + -
717B LEU* 3.9 22.4 - - + -
728B ALA 3.1 16.0 + - - +
729B THR* 3.5 9.4 - - - +
731B ALA* 1.3 76.3 - - - +
733B GLY* 1.3 59.7 + - - +
735B ILE* 3.2 11.7 + - - +
736B SER* 2.9 26.0 + - - -
743B MET* 4.8 2.5 - - - +
750B VAL* 3.6 42.2 - - + -
754B LEU* 5.1 1.3 - - + -
774B THR* 3.9 12.8 - - + -
778B LEU* 4.3 12.8 - - + -
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Residues in contact with GLY 733 (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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729B THR 3.1 8.3 + - - -
730B TRP 3.5 3.1 + - - -
732B ILE* 1.3 78.2 - - - +
734B GLU* 1.3 61.1 + - - +
736B SER* 3.4 13.0 - - - -
737B ILE* 3.6 2.3 - - - +
774B THR* 3.5 27.3 - - - +
777B ARG* 3.3 35.0 + - - +
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Residues in contact with GLU 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B GLY* 4.6 6.7 - - - +
695B THR* 3.8 16.7 - - + +
696B LYS* 3.2 38.8 + - + +
730B TRP* 3.2 44.4 + - + +
731B ALA* 3.2 11.1 + - - +
733B GLY* 1.3 74.9 - - - +
735B ILE* 1.3 65.4 + - - +
737B ILE* 3.4 31.7 + - - +
738B GLN* 3.6 6.6 + - - +
777B ARG* 3.4 20.9 + - - +
809B GLU* 4.6 4.5 - - - +
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Residues in contact with ILE 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LEU* 4.5 13.2 - - + -
695B THR* 3.8 25.8 - - + +
699B PHE* 4.0 3.6 - - + -
706B ILE* 3.7 31.2 - - + -
709B PHE* 5.6 0.7 - - + -
710B MET* 4.4 7.9 - - + -
713B LEU* 3.8 27.4 - - + -
731B ALA* 3.0 17.0 + - + +
732B ILE* 3.6 6.3 - - - +
734B GLU* 1.3 74.2 - - - +
736B SER* 1.3 55.4 + - - +
738B GLN* 3.2 1.8 + - - +
739B MET* 2.8 53.6 + - + +
743B MET* 3.6 9.9 - - + -
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Residues in contact with SER 736 (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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732B ILE 2.9 16.9 + - - -
733B GLY* 3.4 11.5 + - - -
735B ILE* 1.3 77.3 - - - +
737B ILE* 1.3 61.5 + - - +
740B GLY 3.1 18.9 + - - -
743B MET* 3.7 16.4 - - - +
777B ARG* 3.9 22.0 - - - -
778B LEU* 3.2 26.1 - - - +
781B VAL* 3.3 18.9 - - - +
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Residues in contact with ILE 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B GLY 3.6 12.1 - - - +
734B GLU* 3.6 23.8 - - - +
735B ILE 3.2 0.4 - - - -
736B SER* 1.3 78.1 - - - +
738B GLN* 1.3 69.9 + - + +
740B GLY* 4.0 5.0 + - - -
777B ARG* 3.6 43.7 - - + +
781B VAL* 4.8 4.4 - - - +
812B SER* 5.9 0.9 - - - -
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Residues in contact with GLN 738 (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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695B THR* 3.4 35.0 + - + +
696B LYS* 4.5 14.2 + - + +
699B PHE* 3.6 38.9 - - + +
703B LYS* 5.6 0.5 + - - -
734B GLU 3.6 5.1 + - - +
735B ILE 3.2 5.8 + - - +
737B ILE* 1.3 85.6 - - + +
739B MET* 1.3 65.1 + - - +
740B GLY 3.7 0.2 + - - -
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Residues in contact with MET 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B PHE* 3.5 22.2 - - + -
703B LYS* 3.5 25.4 + - - +
706B ILE* 4.3 14.1 - - + -
735B ILE* 2.8 35.8 + - + +
736B SER 4.3 0.2 - - - +
738B GLN* 1.3 75.9 - - - +
740B GLY* 1.3 65.3 + - - +
741B ILE* 3.8 0.3 + - - +
742B GLU* 3.3 62.2 - - + +
743B MET* 3.7 15.9 - - + +
746B TYR* 3.9 20.6 - - + +
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Residues in contact with GLY 740 (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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736B SER 3.1 15.2 + - - -
737B ILE 4.0 5.1 + - - -
738B GLN 3.4 2.4 - - - -
739B MET* 1.3 72.8 - - - +
741B ILE* 1.3 55.0 + - - -
742B GLU 2.8 17.6 + - - -
743B MET* 2.9 13.2 + - - +
781B VAL* 3.1 21.5 - - - +
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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