Contacts of the helix formed by residues 678 - 695 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A GLN* 5.4 1.8 - - - +
764A GLN* 4.3 18.5 - - + +
620B ILE* 4.0 17.5 - - - +
670B GLU* 4.7 4.2 + - + +
676B ILE* 4.0 21.5 - - + +
677B TYR* 1.3 80.6 - - - +
679B HIS* 1.3 64.2 + - - +
680B GLN* 3.0 21.4 + - - +
681B SER* 2.6 34.0 + - - -
682B ASP* 3.3 4.7 + - - -
741B PRO* 5.3 2.1 - - - +
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Residues in contact with HIS 679 (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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763A ASN* 3.5 23.8 - - - -
764A GLN* 2.8 25.2 - - + +
765A GLU* 3.9 10.5 - - - -
611B MET* 6.2 0.6 - - - +
615B ALA* 3.3 36.9 + - + +
618B LYS* 3.9 12.8 + - - +
619B CYS 3.1 34.8 + - - -
620B ILE* 3.9 15.0 - - + +
678B THR* 1.3 75.9 - - - +
680B GLN* 1.3 58.6 + - - +
682B ASP* 3.3 13.0 + - - +
683B VAL* 3.2 25.1 + - - +
747B PHE* 3.7 5.6 - - + -
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Residues in contact with GLN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A GLN* 2.9 41.2 + - + +
765A GLU 4.5 1.0 - - - -
678B THR* 3.0 10.5 + - - +
679B HIS* 1.3 81.4 + - - +
681B SER* 1.3 63.0 + - - +
682B ASP 3.2 0.7 - - - -
683B VAL* 3.3 22.9 + - - +
684B TRP 3.4 5.4 + - - -
741B PRO* 3.5 31.9 - - + +
742B SER* 5.3 2.6 - - - -
744B ARG* 3.0 33.4 + - - +
745B PRO 3.1 19.5 - - - +
746B THR* 3.8 18.3 - - - +
747B PHE* 5.6 0.2 - - - -
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Residues in contact with SER 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ALA* 3.7 13.4 + - - +
670B GLU* 3.5 20.6 + - - -
671B ALA* 4.4 6.1 - - - -
676B ILE 4.2 9.0 - - - -
677B TYR* 3.5 10.7 - - - +
678B THR* 2.6 39.9 + - - -
680B GLN* 1.3 76.7 - - - +
682B ASP* 1.3 66.4 + - - +
684B TRP* 3.4 12.8 + - - +
685B SER* 3.4 14.4 + - - -
744B ARG* 3.8 2.9 - - - +
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Residues in contact with ASP 682 (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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611B MET* 3.5 18.0 - - + +
619B CYS 4.5 1.2 - - - +
620B ILE* 3.7 10.5 - - - +
621B HIS* 2.9 27.4 + - - -
622B ARG* 3.1 25.7 + - - -
624B LEU* 4.0 5.6 - - + +
678B THR 3.3 7.9 + - - +
679B HIS* 3.4 14.4 + - - +
681B SER* 1.3 83.9 + - - +
683B VAL* 1.3 59.7 + - - +
685B SER* 3.1 9.6 + - - -
686B PHE* 2.9 27.7 + - - +
747B PHE* 3.7 14.8 - - + -
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Residues in contact with VAL 683 (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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679B HIS 3.2 14.9 + - - +
680B GLN* 3.4 19.5 - - - +
681B SER 3.2 0.4 - - - -
682B ASP* 1.3 76.9 - - - +
684B TRP* 1.3 62.6 + - - +
686B PHE* 3.2 5.1 + - - +
687B GLY 3.1 16.6 + - - -
736B CYS* 3.5 33.2 - - + +
744B ARG* 4.0 9.4 - - + -
745B PRO* 3.2 30.1 - - + +
747B PHE* 3.8 31.0 - - + +
750B LEU* 4.3 4.5 - - + -
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Residues in contact with TRP 684 (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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665B LYS 5.0 1.8 + - - -
666B TRP 3.5 17.6 + - - -
667B MET 3.6 9.8 + - - -
668B ALA* 3.5 16.6 - - + -
669B PRO* 3.4 36.8 - - + -
680B GLN 3.4 2.4 + - - -
681B SER 3.4 11.1 + - - +
682B ASP 3.2 0.4 - - - -
683B VAL* 1.3 79.1 - - - +
685B SER* 1.3 63.4 - - - +
687B GLY 3.0 10.4 + - - -
688B VAL* 3.3 17.9 + - + +
701B TYR* 6.1 0.9 - - - -
713B LEU* 4.2 20.6 - - + -
717B HIS 6.0 0.2 - - - -
718B ARG* 3.7 30.5 - - - -
736B CYS 3.4 13.9 + - - +
737B TRP* 3.3 52.3 + + + -
738B HIS 3.9 3.6 - - - -
744B ARG* 3.6 16.6 - - - +
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Residues in contact with SER 685 (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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622B ARG 5.3 4.7 + - - -
623B ASP* 5.6 0.2 - - - -
624B LEU* 3.5 36.2 + - - +
666B TRP* 2.8 28.2 + - - +
667B MET* 4.7 2.4 - - - -
668B ALA 4.7 0.2 + - - -
681B SER 3.4 10.7 + - - -
682B ASP* 3.1 12.3 + - - -
684B TRP* 1.3 79.7 - - - +
686B PHE* 1.3 57.6 + - - +
688B VAL* 3.1 6.6 + - - +
689B LEU* 2.9 27.9 + - - +
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Residues in contact with PHE 686 (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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604B ALA* 3.7 24.5 - - + -
607B VAL* 3.9 13.5 - - + -
608B ALA* 3.9 23.3 - - + -
624B LEU* 3.8 18.1 - - + +
682B ASP 2.9 12.2 + - - +
683B VAL 3.2 9.2 - - - +
684B TRP 3.1 0.2 - - - -
685B SER* 1.3 78.0 - - - +
687B GLY* 1.3 58.6 + - - +
689B LEU* 3.2 12.3 + - + +
690B LEU* 2.8 57.9 + - + +
732B MET* 4.9 0.2 - - - -
736B CYS* 4.2 5.4 - - - -
747B PHE* 3.8 21.8 - + + -
750B LEU* 3.6 30.3 - - + -
754B LEU* 4.0 7.2 - - + -
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Residues in contact with GLY 687 (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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683B VAL 3.1 6.5 + - - -
684B TRP 3.0 9.5 + - - -
686B PHE* 1.3 74.5 - - - +
688B VAL* 1.3 63.3 + - - +
690B LEU* 3.2 12.3 + - - +
691B TRP 3.1 16.6 + - - -
733B MET* 3.8 4.3 - - - +
736B CYS* 3.8 20.0 - - - -
737B TRP* 3.3 22.2 - - - -
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Residues in contact with VAL 688 (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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665B LYS 4.0 19.7 - - - +
666B TRP* 3.5 35.2 - - + +
684B TRP* 3.3 19.2 + - + +
685B SER 3.1 7.7 + - - +
687B GLY* 1.3 72.8 - - - +
689B LEU* 1.3 66.2 + - - +
691B TRP* 3.2 5.0 + - + +
692B GLU* 3.0 21.5 + - + +
700B PRO* 4.3 11.4 - - + -
719B MET* 4.2 16.8 - - + -
737B TRP* 3.6 24.7 - - + +
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Residues in contact with LEU 689 (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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569B LEU* 4.8 2.7 - - + -
607B VAL* 4.2 19.3 - - + -
624B LEU* 4.0 15.9 - - + -
625B ALA* 3.6 33.2 - - - +
626B ALA* 3.7 8.3 - - + +
629B VAL* 3.9 18.4 - - + -
666B TRP* 4.5 0.4 - - - +
685B SER 2.9 13.4 + - - +
686B PHE* 3.5 21.1 - - + +
688B VAL* 1.3 78.9 - - - +
690B LEU* 1.3 63.6 + - - +
692B GLU* 3.1 16.7 + - - +
693B ILE* 2.9 48.8 + - + +
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Residues in contact with LEU 690 (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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604B ALA* 3.7 30.3 - - + -
686B PHE* 2.8 40.5 + - + +
687B GLY* 3.2 11.2 - - - +
689B LEU* 1.3 76.8 - - - +
691B TRP* 1.3 62.1 + - - +
693B ILE* 3.1 9.0 + - + +
694B PHE* 3.0 44.2 + - + -
729B LEU* 4.7 2.7 - - + +
732B MET* 3.8 36.1 - - + +
733B MET* 3.7 26.0 - - + +
736B CYS* 4.8 0.2 - - - -
754B LEU* 5.2 1.8 - - + -
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Residues in contact with TRP 691 (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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687B GLY 3.1 9.3 + - - +
688B VAL* 3.2 13.7 + - - +
690B LEU* 1.3 79.4 - - - +
692B GLU* 1.3 67.4 + - + +
694B PHE 3.4 2.1 + - - -
695B THR* 2.9 50.0 + - + +
698B GLY* 3.6 17.3 - - - -
699B SER 3.5 21.5 - - - -
700B PRO* 3.6 28.0 - - + -
701B TYR 5.5 0.4 - - - -
702B PRO* 5.7 0.9 - - + -
719B MET* 3.7 36.4 - - + +
720B ASP 3.4 20.5 + - - -
722B PRO* 3.7 21.6 - - + +
733B MET* 3.9 19.7 - - - -
737B TRP* 4.3 5.6 - + + -
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Residues in contact with GLU 692 (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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2B PO4 4.4 2.3 + - - -
570B ARG* 4.4 3.8 - - - +
573B LEU* 4.0 1.9 - - - +
626B ALA* 3.1 40.5 + - + +
661B ARG* 3.4 13.9 + - - -
666B TRP* 2.7 45.4 + - + +
688B VAL* 3.0 15.6 + - + +
689B LEU* 3.1 15.3 + - - +
691B TRP* 1.3 83.9 - - + +
693B ILE* 1.3 58.0 + - + +
695B THR* 3.1 10.1 + - - -
697B GLY* 2.7 33.2 + - - -
698B GLY 4.1 13.7 - - - +
700B PRO* 4.8 0.9 - - + -
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Residues in contact with ILE 693 (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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569B LEU* 4.1 23.3 - - + -
573B LEU* 4.0 13.8 - - + +
600B LEU* 3.7 29.0 - - + +
603B CYS* 4.6 5.2 - - + -
604B ALA* 4.1 28.9 - - + +
607B VAL* 5.2 0.7 - - + -
689B LEU* 2.9 41.3 + - + +
690B LEU* 3.1 8.9 + - - +
692B GLU* 1.3 76.8 - - + +
694B PHE* 1.3 80.2 + - + +
695B THR 3.2 0.2 - - - -
696B LEU* 3.1 26.9 + - - +
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Residues in contact with PHE 694 (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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600B LEU* 3.9 33.7 - - + -
601B VAL* 4.5 8.1 - - + -
604B ALA* 4.9 1.3 - - + -
690B LEU* 3.0 32.4 + - + +
691B TRP 3.7 3.8 - - - +
693B ILE* 1.3 92.5 - - + +
695B THR* 1.3 57.0 + - - +
696B LEU* 3.3 5.8 - - - +
722B PRO* 3.9 20.8 - - + +
723B SER 4.0 9.9 - - - +
724B ASN* 4.5 7.9 - - - +
725B CYS* 3.9 16.4 - - + -
729B LEU* 3.6 45.8 - - + -
733B MET* 3.4 25.1 - - + -
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Residues in contact with THR 695 (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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577B ARG* 4.1 6.1 + - - -
691B TRP* 2.9 50.3 + - + +
692B GLU* 3.1 6.8 + - - -
693B ILE 3.2 0.2 - - - -
694B PHE* 1.3 77.9 - - - +
696B LEU* 1.3 70.0 + - - +
697B GLY 4.1 0.2 - - - -
698B GLY* 2.9 36.4 + - - -
722B PRO* 4.0 15.7 - - + -
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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
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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