Contacts of the helix formed by residues 678 - 695 (chain A) in PDB entry 3JS2
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 678 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ILE* 3.7 22.4 - - + +
670A GLU* 4.7 3.9 + - + +
676A ILE* 3.9 20.0 - - + -
677A TYR* 1.3 81.2 - - - +
679A HIS* 1.3 63.8 + - - +
680A GLN* 3.1 32.7 + - - +
681A SER* 2.7 27.6 + - - -
682A ASP 3.3 4.7 + - - -
741A PRO* 5.5 0.9 - - - +
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Residues in contact with HIS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A ALA* 3.7 39.5 + - + +
618A LYS* 4.0 12.6 + - - +
619A CYS 3.4 26.4 + - - -
620A ILE* 3.5 23.5 - - + +
678A THR* 1.3 76.2 - - - +
680A GLN* 1.3 61.3 + - + +
682A ASP* 3.2 12.2 + - - +
683A VAL* 3.0 32.4 + - + +
747A PHE* 4.0 6.4 - - + -
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Residues in contact with GLN 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU* 4.8 0.2 - - - +
678A THR* 3.1 25.3 + - - +
679A HIS* 1.3 77.1 + - + +
681A SER* 1.3 63.2 + - - +
683A VAL* 3.1 19.5 + - + +
684A TRP 3.1 6.2 + - - -
741A PRO* 3.4 42.6 + - + +
742A SER* 3.8 16.0 - - - +
744A ARG* 3.1 20.7 + - + +
745A PRO 5.9 1.3 - - - +
746A THR* 6.5 1.8 - - + -
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Residues in contact with SER 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ILE* 5.0 0.2 - - - +
668A ALA* 3.6 24.8 + - - +
670A GLU* 3.6 13.0 + - - -
671A ALA* 4.2 14.4 - - - -
676A ILE 4.3 1.8 - - - -
677A TYR* 3.6 12.0 - - - +
678A THR* 2.7 37.3 + - - -
680A GLN* 1.3 79.0 - - - +
682A ASP* 1.3 62.9 + - - +
684A TRP* 3.2 5.7 + - - +
685A SER* 3.2 22.1 + - - -
744A ARG* 3.9 0.6 - - - +
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Residues in contact with ASP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A MET* 3.5 14.9 - - + +
619A CYS 4.6 1.2 - - - +
620A ILE* 3.7 15.5 - - - +
621A HIS* 2.8 29.3 + - - +
622A ARG* 3.0 27.1 + - - -
623A ASP 4.6 0.3 + - - -
624A LEU* 3.9 6.6 - - - +
678A THR 3.3 1.5 + - - +
679A HIS* 3.2 16.4 + - - +
681A SER* 1.3 82.5 + - - +
683A VAL* 1.3 59.1 + - - +
685A SER* 3.3 9.4 + - - -
686A PHE* 2.9 26.5 + - - +
747A PHE* 3.6 16.2 - - + -
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Residues in contact with VAL 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A HIS* 3.0 21.2 + - + +
680A GLN* 3.1 12.7 + - + +
682A ASP* 1.3 74.1 - - - +
684A TRP* 1.3 66.1 + - - +
686A PHE* 3.1 3.8 + - - +
687A GLY 3.1 16.8 + - - -
736A CYS* 3.5 32.0 - - + +
744A ARG* 4.3 7.4 - - + -
745A PRO* 3.4 28.5 - - + +
746A THR* 4.5 1.8 - - - -
747A PHE* 3.6 34.1 - - + +
750A LEU* 4.1 7.4 - - + -
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Residues in contact with TRP 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LYS 5.2 1.8 + - - -
666A TRP 3.7 9.5 + - - -
667A MET 3.6 8.7 + - - -
668A ALA* 3.5 24.5 - - + -
669A PRO* 3.5 32.3 - - + -
680A GLN 3.1 5.9 + - - -
681A SER 3.2 9.8 + - - +
683A VAL* 1.3 77.5 - - - +
685A SER* 1.3 63.8 + - - +
687A GLY 3.0 10.2 + - - -
688A VAL* 3.3 17.7 + - + +
701A TYR* 5.8 1.6 - - - -
713A LEU* 4.0 18.6 - - + -
718A ARG* 3.7 31.0 - - - -
736A CYS 3.4 13.0 + - - +
737A TRP* 3.3 50.7 + + + -
738A HIS 3.7 6.3 - - - -
739A ALA* 4.9 0.7 - - - -
744A ARG* 3.5 24.5 - - - +
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Residues in contact with SER 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ARG 5.3 4.2 + - - -
623A ASP* 5.5 0.3 - - - -
624A LEU* 3.5 36.4 + - - +
666A TRP* 2.6 27.9 + - - +
667A MET* 4.6 2.1 - - - -
681A SER 3.2 10.5 + - - -
682A ASP* 3.5 12.6 + - - -
683A VAL 3.2 0.2 - - - -
684A TRP* 1.3 78.3 - - - +
686A PHE* 1.3 58.1 + - - +
688A VAL* 3.0 7.5 + - - +
689A LEU* 2.8 27.6 + - - +
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Residues in contact with PHE 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ALA* 3.7 18.4 - - - -
607A VAL* 3.9 13.9 - - + -
608A ALA* 3.7 29.6 - - + -
611A MET* 5.0 0.2 - - + -
624A LEU* 3.8 17.7 - - + +
682A ASP 2.9 14.2 + - - +
683A VAL* 3.1 8.5 + - - +
685A SER* 1.3 76.8 - - - +
687A GLY* 1.3 57.8 + - - +
689A LEU* 3.2 11.2 + - + +
690A LEU* 2.8 61.1 + - + +
736A CYS* 4.2 3.4 - - - -
747A PHE* 3.7 19.3 - + + -
750A LEU* 3.8 28.5 - - + -
754A LEU* 4.0 9.4 - - + -
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A VAL 3.1 6.9 + - - -
684A TRP 3.0 9.6 + - - -
686A PHE* 1.3 77.0 - - - +
688A VAL* 1.3 60.9 + - - +
690A LEU* 3.1 11.2 + - - +
691A TRP 3.1 17.2 + - - -
733A MET* 3.8 4.9 - - - +
736A CYS* 3.7 23.6 - - - -
737A TRP* 3.6 18.5 - - - -
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Residues in contact with VAL 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LYS 3.9 19.5 - - - +
666A TRP* 3.3 40.2 - - + +
684A TRP* 3.3 20.1 + - + +
685A SER 3.0 8.2 + - - +
687A GLY* 1.3 73.9 - - - +
689A LEU* 1.3 62.7 + - - +
691A TRP* 3.0 7.5 + - + +
692A GLU* 2.9 20.5 + - + +
700A PRO* 4.1 18.2 - - + -
701A TYR* 6.4 0.4 - - + -
719A MET* 4.5 7.0 - - + -
737A TRP* 3.6 24.5 - - + +
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Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A LEU* 4.3 10.5 - - + -
607A VAL* 4.3 17.3 - - + -
624A LEU* 3.6 26.9 - - + -
625A ALA* 3.4 32.3 - - - +
626A ALA* 3.7 11.0 - - + +
629A VAL* 4.0 7.4 - - + -
666A TRP* 4.6 0.6 - - - +
685A SER 2.8 12.6 + - - +
686A PHE* 3.3 17.3 - - + +
687A GLY 3.2 0.2 - - - -
688A VAL* 1.3 78.1 - - - +
690A LEU* 1.3 61.4 + - - +
692A GLU* 3.0 15.1 + - - +
693A ILE* 3.0 49.0 + - + +
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Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ALA* 3.6 32.3 - - + -
686A PHE* 2.8 47.0 + - + +
687A GLY* 3.3 10.8 - - - +
689A LEU* 1.3 74.3 - - + +
691A TRP* 1.3 64.3 + - - +
693A ILE* 3.2 6.9 + - + +
694A PHE* 3.0 42.3 + - + -
729A LEU* 4.9 2.5 - - + +
732A MET* 3.8 36.1 - - + -
733A MET* 3.8 23.3 - - + +
736A CYS* 4.6 1.6 - - - -
754A LEU* 4.8 1.3 - - + -
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Residues in contact with TRP 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A GLY 3.1 11.1 + - - +
688A VAL 3.0 14.0 + - - +
690A LEU* 1.3 77.5 - - - +
692A GLU* 1.3 61.6 + - - +
694A PHE* 3.5 1.6 + - - +
695A THR* 2.9 58.2 + - + +
698A GLY* 3.9 5.6 - - - -
699A SER 3.8 15.9 - - - -
700A PRO* 3.7 30.5 - - + -
701A TYR 5.3 0.9 - - - -
702A PRO* 5.6 2.2 - - + -
719A MET* 3.5 42.1 - - + +
720A ASP 3.0 25.8 + - - -
722A PRO* 3.6 16.8 - - + +
730A TYR* 5.3 0.4 - + - -
733A MET* 3.9 20.6 - - - -
737A TRP* 4.0 6.3 - + + -
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Residues in contact with GLU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PO4 4.5 1.6 + - - -
570A ARG* 4.3 4.3 - - - +
573A LEU* 3.8 1.9 - - + +
626A ALA* 3.1 41.5 + - + +
627A ARG 4.9 0.5 + - - -
661A ARG* 3.5 14.0 + - - -
666A TRP* 2.7 42.7 + - - +
688A VAL* 2.9 14.0 + - + +
689A LEU* 3.0 14.3 + - - +
691A TRP* 1.3 77.5 - - + +
693A ILE* 1.3 62.5 + - + +
695A THR* 3.3 8.6 + - - -
697A GLY* 2.7 32.1 + - - -
698A GLY 3.8 14.6 - - - +
700A PRO* 4.5 9.2 - - + -
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Residues in contact with ILE 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LEU* 4.1 20.2 - - + -
573A LEU* 3.5 13.7 - - + +
600A LEU* 3.6 39.3 - - + +
603A CYS* 4.4 7.2 - - + +
604A ALA* 3.8 33.0 - - + +
689A LEU* 3.0 40.1 + - + +
690A LEU* 3.2 10.9 + - + +
692A GLU* 1.3 77.1 - - + +
694A PHE* 1.3 64.3 + - + +
696A LEU* 3.3 25.5 + - - +
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Residues in contact with PHE 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A SER* 5.2 0.7 - - - -
600A LEU* 4.0 37.9 - - + +
601A VAL* 4.2 17.5 - - + -
604A ALA* 5.1 2.2 - - + -
690A LEU* 3.0 45.8 + - + +
691A TRP 3.5 1.3 + - - +
693A ILE* 1.3 77.2 - - + +
695A THR* 1.3 58.9 + - - +
696A LEU* 3.2 10.4 + - - +
722A PRO* 4.2 18.8 - - + +
723A SER 4.0 14.4 - - - +
724A ASN* 4.3 15.6 - - - +
725A CYS* 4.5 9.9 - - + -
729A LEU* 3.3 43.3 - - + -
733A MET* 3.9 13.0 - - + -
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Residues in contact with THR 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ARG* 3.6 9.9 + - - -
691A TRP* 2.9 41.3 + - + +
692A GLU* 3.3 4.2 + - - -
694A PHE* 1.3 76.3 - - - +
696A LEU* 1.3 69.1 + - - +
697A GLY 3.5 0.3 + - - -
698A GLY* 2.9 34.4 + - - -
722A PRO* 3.8 26.7 - - + -
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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