Contacts of the helix formed by residues 736 - 753 (chain B) in PDB entry 1J1C
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 736 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B HIS* 3.2 47.6 + - - +
676B GLY* 4.4 8.0 + - - -
677B ILE 4.2 3.6 + - - -
678B CYS* 3.7 26.3 + - - +
707B LEU* 3.7 5.7 - - - +
735B THR* 1.3 70.9 - - - +
737B SER* 1.3 56.2 + - - +
738B ILE 2.9 6.3 - - - -
739B ASP* 2.9 19.6 + - - +
740B VAL 3.8 0.3 + - - -
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Residues in contact with SER 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B GLU* 4.2 2.1 + - - -
735B THR* 2.8 21.5 + - - -
736B SER* 1.3 78.5 - - - +
738B ILE* 1.3 60.9 + - - +
739B ASP 3.1 0.7 - - - -
740B VAL* 3.2 24.0 + - - +
741B TRP 3.2 6.8 + - - -
825B PRO* 3.6 37.2 - - - +
826B THR* 5.8 0.4 - - - -
828B ARG* 3.2 19.9 + - - -
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Residues in contact with ILE 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B CYS* 3.6 22.4 - - - -
680B ARG* 4.2 17.9 - - + -
717B ILE* 4.2 2.2 - - + -
718B CYS* 5.7 2.5 - - + -
724B ALA* 4.0 17.9 + - + +
726B GLU* 3.2 26.0 - - + +
727B LEU* 4.1 20.6 - - + -
734B TYR* 3.8 37.7 - - + -
735B THR 3.3 16.8 + - - +
736B SER 2.9 1.6 - - - -
737B SER* 1.3 79.4 - - - +
739B ASP* 1.3 64.4 + - - +
741B TRP* 3.4 4.0 + - - +
742B SER* 3.0 26.8 + - - -
828B ARG* 4.2 0.4 - - - +
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Residues in contact with ASP 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LEU* 3.9 14.7 - - + +
673B HIS* 2.9 26.0 + - + +
678B CYS* 3.4 12.6 - - - -
679B HIS* 2.9 26.2 + - - +
680B ARG* 3.0 25.2 + - - -
681B ASP 4.4 0.2 + - - -
682B ILE* 3.8 17.2 + - + +
736B SER 2.9 8.5 + - - +
738B ILE* 1.3 79.9 - - - +
740B VAL* 1.3 58.7 + - - +
742B SER* 3.4 7.6 + - - -
743B ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B PHE* 4.8 3.6 - - + -
669B LEU* 4.8 3.1 - - + -
673B HIS* 4.6 2.2 - - + -
736B SER 4.5 3.1 - - - +
737B SER* 3.2 21.0 + - - +
738B ILE 3.2 0.4 - - - -
739B ASP* 1.3 77.1 - - - +
741B TRP* 1.3 65.0 + - - +
743B ALA* 3.3 6.5 + - - +
744B GLY* 3.0 19.4 + - - -
820B LEU* 3.6 27.4 - - + +
828B ARG* 4.2 13.2 - - + -
829B LEU 3.3 28.5 - - - +
830B THR* 4.7 0.7 - - - -
831B PRO* 4.0 29.6 - - + -
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Residues in contact with TRP 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B TYR 5.0 0.4 + - - -
722B TYR 3.6 7.2 - - - -
723B ARG 3.2 13.4 + - - -
724B ALA* 3.4 29.6 - - + -
725B PRO* 3.5 30.3 - - + -
737B SER 3.2 3.2 + - - -
738B ILE 3.6 7.4 - - - +
739B ASP 3.3 0.2 - - - -
740B VAL* 1.3 79.1 - - - +
742B SER* 1.3 64.4 + - - +
744B GLY 3.0 10.6 + - - -
745B CYS* 3.0 23.1 + - - -
757B PHE* 3.6 25.9 - + - -
769B ILE* 3.8 21.3 - - + +
773B LEU* 4.0 16.6 - - + -
820B LEU 4.1 8.5 + - - -
821B LEU* 3.3 43.1 - - + +
822B GLU 3.6 21.5 - - - -
828B ARG* 3.8 12.1 - - - +
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Residues in contact with SER 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B ILE* 3.6 30.9 + - - -
718B CYS* 3.8 13.7 - - - -
722B TYR* 2.8 28.1 + - - -
724B ALA 5.1 0.2 + - - -
738B ILE* 3.0 12.9 + - - +
739B ASP* 3.5 10.8 + - - -
740B VAL 3.3 0.2 - - - -
741B TRP* 1.3 80.4 - - - +
743B ALA* 1.3 61.2 + - - +
745B CYS* 3.2 7.4 + - - +
746B VAL* 3.1 24.1 + - - +
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Residues in contact with ALA 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B MET* 3.1 12.8 - - + +
665B LEU* 3.8 27.1 - - + -
666B PHE* 3.6 30.1 - - + -
669B LEU* 4.2 6.3 - - + -
682B ILE* 4.2 3.5 - - + +
739B ASP 2.9 17.1 + - - +
740B VAL 3.7 2.0 - - - +
742B SER* 1.3 76.8 - - - +
744B GLY* 1.3 62.2 + - - +
746B VAL* 3.1 2.9 + - - +
747B LEU 3.0 19.2 + - - -
820B LEU* 4.8 0.7 - - - -
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Residues in contact with GLY 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B VAL 3.0 12.7 + - - -
741B TRP 3.0 5.3 + - - -
743B ALA* 1.3 77.0 - - - +
745B CYS* 1.3 55.1 + - - +
747B LEU* 3.4 2.8 + - - +
748B ALA* 3.0 30.0 + - - +
817B CYS* 4.6 2.4 - - - -
820B LEU* 3.7 25.5 - - - +
821B LEU* 3.8 18.5 - - - +
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Residues in contact with CYS 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B TYR 3.7 17.5 - - - +
722B TYR* 3.6 21.1 - - + -
741B TRP* 3.0 44.4 + - - -
742B SER 3.2 8.7 + - - +
744B GLY* 1.3 73.2 - - - +
746B VAL* 1.3 60.1 + - - +
748B ALA* 3.9 1.0 - - - +
749B GLU* 2.9 31.5 + - - +
756B ILE* 4.3 13.9 + - + +
757B PHE* 4.0 17.0 - - - -
821B LEU* 4.1 3.1 - - - -
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Residues in contact with VAL 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B VAL* 4.7 7.0 - - + -
662B MET* 3.9 17.0 - - + -
665B LEU* 4.9 0.9 - - + -
682B ILE* 4.5 3.1 - - + -
683B LYS* 4.4 5.4 - - - -
684B PRO* 4.1 29.8 - - + -
687B LEU* 4.1 24.2 - - + -
722B TYR* 4.3 7.0 - - + -
742B SER 3.1 15.0 + - - +
743B ALA* 3.1 12.1 + - - +
745B CYS* 1.3 74.7 - - - +
747B LEU* 1.3 60.6 + - - +
749B GLU* 3.2 6.5 + - - +
750B LEU* 2.9 41.3 + - + +
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Residues in contact with LEU 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B VAL* 3.6 26.7 - - + -
662B MET* 3.6 30.7 - - + -
743B ALA 3.0 7.6 + - - +
744B GLY* 3.6 6.7 - - - +
745B CYS 3.3 0.2 - - - -
746B VAL* 1.3 77.3 - - - +
748B ALA* 1.3 63.8 + - - +
750B LEU* 3.1 5.3 + - - +
751B LEU* 3.0 30.3 + - + +
813B ALA 4.3 4.3 - - - +
816B LEU* 3.7 34.8 - - + -
817B CYS* 3.6 23.6 - - - +
820B LEU* 4.0 9.6 - - + -
839B PHE* 4.2 11.2 - - + -
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Residues in contact with ALA 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B GLY 3.0 17.0 + - - +
745B CYS 3.9 4.0 - - - +
747B LEU* 1.3 77.0 - - - +
749B GLU* 1.3 57.6 + - - +
751B LEU* 3.3 2.3 + - - +
752B LEU* 2.8 35.8 + - - +
756B ILE* 3.9 35.4 - - + -
805B PHE* 4.1 11.2 - - + -
817B CYS* 4.1 13.9 - - - -
821B LEU* 4.6 3.6 - - + -
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Residues in contact with GLU 749 (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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640B TYR* 5.9 1.6 - - - -
643B ALA* 5.7 7.7 - - + +
684B PRO* 4.3 11.5 - - - +
722B TYR* 2.5 40.4 + - - -
745B CYS 2.9 17.2 + - - +
746B VAL* 3.5 4.9 - - - +
748B ALA* 1.3 74.5 - - - +
750B LEU* 1.3 63.8 + - + +
753B GLY* 2.8 29.6 + - - -
754B GLN* 3.5 24.9 - - - +
755B PRO* 3.7 28.0 - - + +
756B ILE 4.7 1.1 - - - +
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Residues in contact with LEU 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B VAL* 3.9 26.7 - - + -
643B ALA* 3.9 21.5 - - + -
652B THR* 4.1 10.0 + - - +
653B LEU* 4.5 30.7 + - + +
658B VAL* 4.1 30.2 - - + +
661B TYR* 4.9 9.4 - - + -
662B MET* 4.2 19.3 - - + -
684B PRO* 6.4 0.7 - - + -
746B VAL* 2.9 34.4 + - + +
747B LEU 3.6 4.3 - - - +
749B GLU* 1.3 80.4 - - + +
751B LEU* 1.3 61.0 + - - +
753B GLY* 4.2 2.4 + - - -
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Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B THR* 3.7 5.9 + - - -
655B VAL* 4.9 14.6 - - + -
658B VAL* 4.3 20.9 - - + -
747B LEU* 3.0 29.2 + - + +
748B ALA 3.6 5.4 - - - +
750B LEU* 1.3 79.4 - - - +
752B LEU* 1.3 61.7 + - - +
805B PHE* 4.0 27.7 - - + -
806B ARG* 3.3 30.7 + - - +
809B THR* 4.5 14.6 - - + -
810B PRO* 5.1 0.4 - - + -
813B ALA* 3.8 32.5 - - + +
817B CYS* 4.2 11.4 - - - -
839B PHE* 5.1 1.6 - - + -
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Residues in contact with LEU 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B THR* 4.9 1.9 + - - -
748B ALA 2.8 19.3 + - - +
751B LEU* 1.3 78.8 - - - +
753B GLY* 1.3 58.0 + - - +
754B GLN* 3.2 30.7 + - + +
755B PRO 4.9 0.2 - - - +
756B ILE* 3.8 41.1 - - + -
804B VAL* 3.3 30.1 - - + +
805B PHE* 3.6 21.8 - - + -
806B ARG 5.0 2.2 - - - +
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Residues in contact with GLY 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B ALA 6.1 0.2 - - - -
647B SER* 2.7 30.3 + - - -
651B GLN 5.6 4.5 - - - -
652B THR* 4.8 6.7 - - - -
749B GLU* 2.8 17.4 + - - -
750B LEU 4.2 3.7 + - - -
751B LEU 3.6 1.6 - - - -
752B LEU* 1.3 73.7 - - - +
754B GLN* 1.3 60.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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