Contacts of the helix formed by residues 639 - 653 (chain B) in PDB entry 3JWR
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 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B LEU* 1.3 77.1 - - - +
640B ASP* 1.3 60.7 + - - +
641B LEU* 3.2 10.9 + - - +
642B GLU* 3.0 37.5 + - - +
643B ILE* 3.1 31.4 + - - +
752B LYS* 4.7 4.5 - - - +
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Residues in contact with ASP 640 (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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582B LEU 5.0 6.1 - - - +
583B ASN* 5.7 1.2 + - - +
584B LEU* 4.1 3.4 - - + +
587B ASN* 3.5 26.5 + - + +
588B PHE* 3.8 22.6 - - + -
635B GLN* 5.8 0.9 + - - -
638B LEU 5.1 0.9 - - - +
639B THR* 1.3 73.2 - - - +
641B LEU* 1.3 64.2 + - - +
643B ILE* 4.0 16.2 - - - +
644B LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B PHE* 3.8 25.6 - - + -
639B THR* 3.2 9.1 + - - +
640B ASP* 1.3 80.6 - - - +
642B GLU* 1.3 60.8 + - - +
644B LEU* 3.9 5.2 - - + +
645B ALA* 3.2 23.7 + - - +
704B LEU* 4.4 7.4 - - + -
708B GLU* 4.0 24.5 - - + +
711B THR* 3.4 25.1 - - - +
712B THR* 3.4 29.2 - - - +
715B ILE* 4.4 10.0 - - + +
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Residues in contact with GLU 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LEU* 3.1 11.3 - - + +
639B THR* 3.0 36.2 + - - +
641B LEU* 1.3 76.4 - - + +
643B ILE* 1.3 66.6 + - - +
645B ALA* 3.2 6.5 + - - +
646B LEU* 2.9 30.6 + - + +
715B ILE* 4.1 19.1 - - + +
752B LYS* 2.9 51.0 + - - +
756B LEU* 4.2 18.6 - - + +
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Residues in contact with ILE 643 (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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582B LEU* 4.0 23.6 - - + +
584B LEU* 4.1 11.0 - - + -
629B LEU* 3.8 22.7 - - + +
635B GLN* 3.4 35.9 - - + +
638B LEU* 3.3 27.6 - - + +
639B THR 3.1 17.5 + - - +
640B ASP* 4.0 17.5 - - - +
641B LEU 3.5 0.2 - - - -
642B GLU* 1.3 75.5 - - - +
644B LEU* 1.3 63.2 + - - +
646B LEU* 3.2 10.4 + - - +
647B LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B PHE* 4.5 1.6 - - + -
584B LEU* 3.7 31.3 - - + +
588B PHE* 4.4 18.4 - - + -
590B MET* 3.5 29.2 - - + -
640B ASP 3.1 15.4 + - - +
641B LEU* 3.9 3.8 - - + +
643B ILE* 1.3 79.0 - - - +
645B ALA* 1.3 60.6 + - - +
647B LEU* 3.4 1.7 + - - +
648B ILE* 2.9 48.1 + - + +
701B LEU* 3.7 22.2 - - + -
704B LEU* 4.3 10.8 - - + -
712B THR* 4.0 18.4 - - + +
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Residues in contact with ALA 645 (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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641B LEU 3.2 15.1 + - - +
642B GLU 3.2 5.5 + - - +
644B LEU* 1.3 77.5 - - - +
646B LEU* 1.3 59.7 + - - +
649B ALA* 2.9 32.4 + - - +
712B THR* 4.1 7.6 - - + +
715B ILE* 3.8 28.3 - - + -
716B ILE* 3.7 29.0 - - + +
719B ALA* 5.6 0.4 - - - -
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Residues in contact with LEU 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B MET* 4.0 36.6 - - + +
629B LEU* 4.7 7.0 - - + -
638B LEU* 4.3 13.5 - - + -
642B GLU* 2.9 27.3 + - + +
643B ILE* 3.2 9.8 + - - +
645B ALA* 1.3 77.1 - - + +
647B LEU* 1.3 57.7 + - - +
649B ALA* 3.7 3.8 - - - +
650B ALA* 2.8 32.1 + - - +
715B ILE* 5.9 2.9 - - + -
719B ALA* 5.2 6.3 - - + -
756B LEU* 4.1 42.4 - - + +
759B LEU* 4.5 8.5 - - + -
760B MET* 4.3 14.8 - - + +
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B THR* 6.5 0.2 - - + -
578B MET* 4.3 11.4 - - + -
579B PHE* 3.8 38.6 - - + +
582B LEU* 3.9 20.9 - - + -
584B LEU* 3.6 24.9 - - + -
622B ALA* 4.2 31.4 - - + +
625B MET* 4.8 7.9 - - + -
626B PHE* 5.2 2.2 - - + -
629B LEU* 6.2 0.9 - - + +
643B ILE 3.1 12.9 + - - +
644B LEU 3.7 3.4 - - - +
646B LEU* 1.3 77.1 - - - +
648B ILE* 1.3 67.1 + - - +
650B ALA* 3.3 2.9 + - - +
651B LEU* 3.1 32.6 + - + +
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Residues in contact with ILE 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B PHE* 4.3 12.1 - - + -
598B TRP* 3.7 27.8 - - + -
644B LEU* 2.9 44.0 - - + +
645B ALA 4.0 3.1 - - - +
647B LEU* 1.3 76.1 - - - +
649B ALA* 1.3 56.0 + - - +
651B LEU* 3.5 3.4 + - - +
652B SER* 2.5 35.9 + - - +
689B CYS* 4.4 9.9 - - - -
693B LEU* 4.4 6.5 - - + -
700B ILE* 3.9 18.8 - - + -
701B LEU* 4.0 13.0 - - + -
716B ILE* 4.1 24.0 - - + -
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Residues in contact with ALA 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B ALA 2.9 20.6 + - - +
646B LEU 3.7 3.4 - - - +
648B ILE* 1.3 74.2 - - - +
650B ALA* 1.3 60.1 + - - +
652B SER* 2.9 5.6 + - - -
653B HIS* 2.8 32.2 + - - +
716B ILE* 4.2 10.1 - - + +
719B ALA* 3.5 30.3 - - + -
720B ILE* 4.1 14.5 - - + +
760B MET* 4.3 5.6 - - + -
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Residues in contact with ALA 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA 3.6 11.3 - - - +
621B THR* 3.9 10.9 - - + +
622B ALA* 3.9 22.2 - - - -
625B MET* 4.2 16.8 - - + -
646B LEU 2.8 22.8 + - - +
647B LEU* 3.3 5.1 + - - +
649B ALA* 1.3 71.6 - - - +
651B LEU* 1.3 59.3 + - - +
653B HIS* 2.9 25.4 + - - -
760B MET* 4.1 12.0 - - + +
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Residues in contact with LEU 651 (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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575B THR* 4.1 15.0 - - + +
578B MET* 5.9 0.2 - - - -
579B PHE* 3.8 29.6 - - + -
598B TRP* 3.8 22.2 - - + -
602B VAL* 3.8 8.5 - - + +
606B TYR* 2.8 19.6 + - - -
615B TRP* 4.2 26.7 - - + -
618B ALA* 3.0 19.1 - - - +
619B PHE* 4.7 2.7 - - + -
622B ALA* 3.4 24.2 - - + -
647B LEU* 3.1 25.9 + - + +
648B ILE 3.6 5.4 - - - +
649B ALA 3.1 0.6 + - - -
650B ALA* 1.3 76.7 - - - +
652B SER* 1.3 59.6 + - - +
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Residues in contact with SER 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TRP* 4.9 2.8 - - - -
602B VAL* 4.8 7.6 - - - -
606B TYR* 3.3 4.5 - - - -
648B ILE* 2.5 28.1 + - - +
649B ALA* 2.9 3.2 + - - -
651B LEU* 1.3 77.7 - - - +
653B HIS* 1.3 57.9 + - - +
654B ASP 2.9 12.1 + - - -
655B LEU* 3.3 35.1 + - - +
685B HIS* 3.8 10.6 - - - +
689B CYS* 3.5 24.1 - - - -
720B ILE* 4.0 3.8 - - - +
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Residues in contact with HIS 653 (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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617B HIS* 3.2 17.3 - + - -
618B ALA* 4.4 5.8 - - - -
621B THR* 3.5 23.7 - - + +
649B ALA 2.8 13.4 + - - +
650B ALA* 2.9 21.7 + - - -
651B LEU 3.6 0.4 - - - -
652B SER* 1.3 76.0 - - - +
654B ASP* 1.3 74.1 + - + +
685B HIS* 2.8 23.4 - - - +
720B ILE* 4.0 16.0 - - + +
723B THR* 4.0 28.0 + - + +
760B MET* 4.3 6.7 - - + -
764B ASP* 2.6 13.6 + - - -
899B ZN 2.2 35.2 - - - -
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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