Contacts of the helix formed by residues 600 - 617 (chain B) in PDB entry 2ETM
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 600 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B VAL* 3.7 13.1 - - - +
592B GLU* 4.7 5.3 + - + +
598B ARG* 4.8 9.5 + - + +
599B PHE* 1.3 84.6 - - - +
601B SER* 1.3 67.7 + - - +
602B ALA* 3.4 16.0 + - - +
603B SER* 2.7 29.1 + - - -
604B ASP 3.1 4.5 + - - -
663B PRO* 5.4 1.7 - - - +
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Residues in contact with SER 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLU* 4.4 17.6 + - - +
542B PHE 5.8 1.8 - - - -
543B VAL* 3.9 14.3 - - - +
600B THR* 1.3 74.5 - - - +
602B ALA* 1.3 61.9 + - - +
604B ASP* 3.2 25.2 - - - +
605B VAL* 3.3 12.8 + - - +
668B ARG* 3.1 33.3 + - - +
669B PHE* 4.6 3.3 - - - -
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Residues in contact with ALA 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B THR* 2.8 11.3 + - - +
601B SER* 1.3 81.6 + - - +
603B SER* 1.3 64.4 + - - +
604B ASP 3.1 1.1 - - - -
605B VAL* 3.2 8.5 + - - +
606B TRP 3.2 15.4 + - - -
663B PRO* 3.8 35.2 - - + +
666B ARG* 3.3 20.1 + - + +
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Residues in contact with SER 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B VAL* 4.8 0.2 - - - +
590B ALA* 3.6 19.0 - - - +
592B GLU* 3.8 7.2 + - - -
593B SER* 3.2 24.1 + - - -
598B ARG 4.1 1.6 - - - -
599B PHE* 3.4 12.1 - - - +
600B THR* 2.7 41.5 + - - -
602B ALA* 1.3 72.1 - - - +
604B ASP* 1.3 69.6 + - - +
606B TRP* 2.9 13.3 + - - +
607B MET* 3.0 20.5 + - - +
666B ARG* 3.9 2.0 - - - +
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Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 5.1 2.8 - - - +
542B PHE 4.2 3.6 - - - +
543B VAL* 3.5 18.7 - - - +
544B HIS* 2.8 27.4 + - - +
545B ARG* 3.1 22.5 + - - -
547B ILE* 3.8 19.0 - - + +
600B THR 3.1 4.8 + - - -
601B SER* 3.2 14.6 - - - +
603B SER* 1.3 80.1 + - - +
605B VAL* 1.3 56.6 + - - +
607B MET* 3.0 16.1 + - - +
608B PHE* 2.8 27.5 + - - +
669B PHE* 4.4 8.5 - - + -
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Residues in contact with VAL 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLU* 5.4 1.3 - - - +
601B SER 3.3 9.8 + - - +
602B ALA* 3.2 12.5 + - - +
603B SER 3.2 0.6 - - - -
604B ASP* 1.3 77.2 - - - +
606B TRP* 1.3 64.5 + - - +
608B PHE* 3.2 2.6 + - - +
609B GLY 3.0 17.8 + - - -
658B CYS* 3.6 35.0 - - + +
666B ARG* 4.1 8.3 - - + -
667B PRO* 3.3 28.9 - - + +
668B ARG* 4.6 3.1 - - - -
669B PHE* 3.5 33.4 - - + -
672B LEU* 4.1 8.1 - - + -
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Residues in contact with TRP 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LYS 5.6 0.2 + - - -
588B TRP 3.2 20.4 + - - -
589B MET 3.1 13.5 + - - -
590B ALA* 3.5 24.0 - - + -
591B PRO* 3.6 13.0 - - + -
602B ALA 3.2 3.0 + - - -
603B SER 2.9 9.4 + - - +
605B VAL* 1.3 78.1 - - - +
607B MET* 1.3 62.8 + - - +
609B GLY 3.1 9.0 + - - -
610B VAL* 3.4 17.7 + - + +
623B PHE* 6.4 1.8 - + - -
635B ILE* 3.6 43.9 - - + +
640B ARG* 3.8 17.9 - - - -
658B CYS 3.5 13.2 - - - +
659B TRP* 3.3 52.8 + + + -
660B ALA 3.8 4.7 - - - -
666B ARG* 3.5 22.7 - - - +
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Residues in contact with MET 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ARG* 3.1 42.0 - - - +
546B ASP* 3.2 6.7 - - - +
547B ILE* 3.2 36.3 - - + +
585B PRO* 5.8 0.7 - - - -
588B TRP* 3.1 33.2 - - - +
589B MET* 4.4 13.2 - - - -
590B ALA 4.7 1.1 - - - +
599B PHE* 5.4 4.7 - - + -
603B SER* 3.0 16.1 + - - +
604B ASP* 3.4 26.9 - - - +
606B TRP* 1.3 74.1 - - + +
608B PHE* 1.3 66.7 + - - +
610B VAL* 2.8 15.6 + - - +
611B CYS 3.0 9.2 + - - -
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Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ALA* 3.6 17.5 - - - -
530B LEU* 3.8 28.7 - - + -
531B SER* 3.7 16.2 - - - -
534B LEU* 3.5 17.9 - - + -
547B ILE* 3.9 13.8 - - + +
604B ASP 2.8 16.2 + - - +
605B VAL 3.2 7.6 + - - +
607B MET* 1.3 72.8 - - - +
609B GLY* 1.3 56.9 + - - +
611B CYS* 3.1 5.2 + - + +
612B MET* 2.9 63.9 + - + +
615B ILE* 6.3 0.2 - - + -
658B CYS* 4.7 0.7 - - - -
669B PHE* 3.5 28.9 - + + -
672B LEU* 3.9 15.7 - - + -
676B LEU* 3.7 14.1 - - + -
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Residues in contact with GLY 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B VAL 3.0 13.2 + - - -
606B TRP 3.1 5.3 + - - -
607B MET 3.1 0.4 - - - -
608B PHE* 1.3 78.0 - - - +
610B VAL* 1.3 58.5 + - - +
612B MET* 3.8 20.5 + - - +
613B TRP 3.4 12.3 + - - -
655B MET* 3.9 3.5 - - - +
658B CYS* 4.0 8.1 - - - -
659B TRP* 3.0 28.8 - - - -
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Residues in contact with VAL 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LYS 4.0 5.4 - - - +
588B TRP* 3.6 41.5 - - + +
606B TRP* 3.6 22.9 - - + +
607B MET 2.8 7.2 + - - +
609B GLY* 1.3 75.0 - - - +
611B CYS* 1.3 62.6 + - - +
613B TRP* 3.2 4.0 + - - +
614B GLU* 2.9 25.8 + - - +
622B PRO* 3.7 30.1 - - + -
623B PHE* 6.0 1.1 - - + -
641B LEU* 4.0 11.4 - - + -
659B TRP* 3.6 15.7 - - + +
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Residues in contact with CYS 611 (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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530B LEU* 3.9 28.7 - - - -
547B ILE* 4.2 11.0 - - + +
548B ALA* 3.6 17.7 - - - +
549B ALA* 3.5 26.7 - - - -
552B VAL* 4.5 0.9 - - - -
588B TRP* 4.7 0.6 - - - -
607B MET 3.0 11.0 + - - +
608B PHE* 3.4 12.3 - - + +
610B VAL* 1.3 77.6 - - - +
612B MET* 1.3 56.2 + - - +
614B GLU* 2.9 15.6 + - - +
615B ILE* 2.8 36.1 + - - +
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Residues in contact with MET 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ALA* 4.0 12.3 - - + -
608B PHE* 2.9 46.5 + - + +
609B GLY* 3.8 11.0 - - - +
611B CYS* 1.3 76.1 - - - +
613B TRP* 1.3 62.0 + - - +
615B ILE* 3.3 10.3 + - + +
616B LEU* 3.0 30.7 + - + +
651B LEU* 3.9 22.9 - - + -
654B LEU* 4.7 8.3 - - + -
655B MET* 3.8 31.0 - - + +
658B CYS* 3.9 26.9 - - - -
672B LEU* 4.9 0.4 - - + -
676B LEU* 4.0 15.7 - - - -
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Residues in contact with TRP 613 (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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609B GLY 3.4 11.2 + - - +
610B VAL* 3.2 12.7 + - - +
611B CYS 3.1 0.2 - - - -
612B MET* 1.3 76.8 - - - +
614B GLU* 1.3 73.6 + - + +
616B LEU* 3.3 4.3 + - - +
617B MET* 3.0 65.0 + - + +
620B VAL* 3.8 15.3 - - + -
621B LYS 3.8 8.5 - - - -
622B PRO* 3.6 31.4 - - + -
623B PHE 5.2 1.1 - - - -
641B LEU* 3.7 34.9 - - + +
642B PRO* 2.7 43.3 + - + -
644B PRO* 3.6 16.2 - - + +
652B TYR* 5.2 0.4 - + - -
655B MET* 4.1 9.1 - - - -
659B TRP* 4.2 11.2 - + + -
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Residues in contact with GLU 614 (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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508B ARG* 3.7 19.1 + - - -
511B LEU* 4.8 0.4 - - - -
548B ALA* 4.9 0.2 - - - +
549B ALA* 2.8 39.6 + - + -
550B ARG 4.9 0.3 + - - -
588B TRP* 3.0 41.1 + - - +
610B VAL 2.9 13.0 + - - +
611B CYS* 2.9 13.5 + - - +
613B TRP* 1.3 79.8 - - + +
615B ILE* 1.3 58.9 + - - +
617B MET* 3.1 9.0 + - - +
619B GLY* 2.9 28.2 + - - -
620B VAL 3.4 21.5 - - - +
621B LYS* 4.4 0.9 - - - -
622B PRO* 3.8 12.7 - - + +
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Residues in contact with ILE 615 (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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507B LEU* 3.9 22.2 - - + -
511B LEU* 3.7 14.5 - - + +
523B LEU* 3.6 50.3 - - + +
526B TYR* 4.3 7.4 - - + -
527B ALA* 4.3 18.2 - - + +
530B LEU* 3.7 31.0 - - + -
549B ALA* 5.0 1.6 - - + -
608B PHE* 6.3 0.4 - - + -
611B CYS* 2.8 21.8 + - - +
612B MET* 3.5 10.5 - - - +
614B GLU* 1.3 77.3 - - + +
616B LEU* 1.3 62.3 + - + +
617B MET 3.2 0.9 + - - -
618B HIS 3.2 8.8 + - - -
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Residues in contact with LEU 616 (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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520B LEU* 4.0 18.2 - - + -
523B LEU* 4.0 27.6 - - + +
524B ILE* 4.6 4.0 - - + +
612B MET* 3.0 15.7 + - + +
613B TRP 3.3 1.1 + - - +
615B ILE* 1.3 76.2 - - + +
617B MET* 1.3 59.4 + - - +
618B HIS* 3.3 13.7 + - - -
644B PRO* 3.7 23.4 - - + +
645B PRO* 4.6 8.2 - - - +
647B CYS* 3.2 34.1 - - + -
651B LEU* 3.3 22.7 - - + -
655B MET* 3.2 20.6 - - + -
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Residues in contact with MET 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B TRP* 3.0 63.8 + - + +
614B GLU* 3.1 6.4 + - - +
616B LEU* 1.3 77.2 - - - +
618B HIS* 1.3 71.6 + - - +
619B GLY 3.4 0.2 - - - -
620B VAL* 2.9 45.5 - - + +
642B PRO* 5.8 2.9 - - + -
644B PRO* 3.3 29.6 - - + -
645B PRO* 4.0 12.6 - - + -
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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