Contacts of the helix formed by residues 594 - 611 (chain C) in PDB entry 1M7X
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 ASN 594 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C LEU 3.1 21.4 + - - +
590C GLU 3.9 5.3 + - - -
592C GLY 3.2 18.9 + - - +
593C ASP* 1.3 75.3 - - - +
595C TRP* 1.3 68.0 + - + +
596C HIS* 2.9 47.6 + - + +
597C HIS* 2.9 27.0 + - - +
598C GLY 3.1 8.1 + - - -
687C HIS* 3.2 15.9 - - - -
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Residues in contact with TRP 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C ALA* 3.4 31.9 - - + -
544C TRP* 4.3 21.6 - + + +
547C PHE* 3.5 50.4 - + + -
551C ARG* 4.8 1.1 - - - -
594C ASN* 1.3 75.8 - - + +
596C HIS* 1.3 60.5 + + + +
598C GLY* 3.4 2.1 + - - -
599C VAL* 3.1 28.8 + - - +
686C TYR 4.1 4.0 - - - +
687C HIS* 3.4 41.8 + + + +
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Residues in contact with HIS 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 4.5 1.6 - - + -
547C PHE* 3.7 21.2 - + - -
572C PHE* 2.8 29.9 + - - +
573C ALA* 3.0 23.0 + - - +
575C GLY 5.2 2.2 - - - -
588C LEU* 3.9 36.7 - - + +
589C LEU* 3.9 15.9 - - + -
594C ASN* 2.9 28.0 + - + +
595C TRP* 1.3 73.9 - + + +
597C HIS* 1.3 64.1 + - - +
598C GLY 3.0 0.9 - - - -
599C VAL* 2.9 15.9 + - - +
600C GLN* 2.9 13.9 + - - +
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Residues in contact with HIS 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589C LEU* 2.8 52.1 + - + +
591C GLY 3.8 5.7 + - - -
592C GLY 3.4 6.9 + - - -
593C ASP* 3.1 29.6 - - - +
594C ASN* 2.9 49.9 + - - +
596C HIS* 1.3 75.7 - - - +
598C GLY* 1.3 52.8 + - - +
600C GLN* 3.2 12.6 + - - +
601C ARG* 2.8 41.6 + - - +
676D ARG* 4.9 6.5 - - - -
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Residues in contact with GLY 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C ASN 3.1 7.9 + - - -
595C TRP 3.7 1.1 - - - -
596C HIS 3.0 1.0 - - - -
597C HIS* 1.3 80.4 - - - +
599C VAL* 1.3 56.4 + - - +
601C ARG* 3.3 5.2 + - - +
602C LEU* 2.9 23.9 + - - +
686C TYR* 3.2 50.5 - - - -
687C HIS* 4.1 2.8 + - - -
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Residues in contact with VAL 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C PHE* 3.7 25.6 - - + +
550C LEU* 4.7 7.4 - - + -
551C ARG* 5.0 12.1 - - + +
554C TYR* 4.0 20.0 - - + -
570C ASN 4.0 9.9 - - - +
571C GLU 3.1 18.2 - - - +
573C ALA* 3.8 14.8 - - + +
595C TRP 3.1 16.3 + - - +
596C HIS 2.9 7.4 + - - +
598C GLY* 1.3 72.8 - - - +
600C GLN* 1.3 60.8 + - - +
602C LEU* 3.1 10.6 + - + +
603C VAL* 2.9 34.2 + - + +
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Residues in contact with GLN 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C TYR* 3.3 30.2 + - - +
279C MET* 3.1 41.1 - - + +
571C GLU* 2.7 19.7 + - - +
572C PHE* 4.2 8.8 - - + +
589C LEU* 3.4 32.7 - - - +
596C HIS 2.9 9.0 + - - +
597C HIS* 3.5 16.3 + - - +
599C VAL* 1.3 75.6 - - - +
601C ARG* 1.3 63.5 + - - +
603C VAL 3.6 0.5 + - - -
604C ARG* 3.3 7.4 + - - +
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Residues in contact with ARG 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C ASP* 2.8 41.6 + - - -
597C HIS* 2.8 20.0 + - - +
598C GLY* 3.4 7.3 - - - +
600C GLN* 1.3 77.0 - - - +
602C LEU* 1.3 66.7 + - - +
604C ARG* 3.3 14.9 + - - +
605C ASP* 3.2 27.5 + - - +
684C MET* 6.2 0.6 - - - +
685C HIS* 4.2 16.0 - - + +
686C TYR* 3.7 32.0 - - + +
687C HIS* 3.8 8.3 - - - -
684D MET* 6.1 2.2 - - - +
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Residues in contact with LEU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ARG* 3.3 46.4 - - + +
554C TYR* 4.3 10.8 - - + -
598C GLY 2.9 14.2 + - - +
599C VAL* 3.3 10.3 - - + +
601C ARG* 1.3 75.2 - - - +
603C VAL* 1.3 57.1 + - - +
605C ASP* 2.7 25.3 + - + +
606C LEU* 2.8 45.0 + - + +
679C LEU* 4.9 2.5 - - + -
681C THR* 4.2 13.7 - - - +
686C TYR* 3.2 42.8 - - + +
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Residues in contact with VAL 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C MET* 4.3 2.5 - - + -
281C PHE* 4.0 20.0 - - + -
554C TYR* 3.9 26.9 - - + -
558C TRP* 4.4 7.9 - - + -
566C LEU* 4.0 11.9 - - + -
571C GLU* 3.8 28.9 - - + -
599C VAL 2.9 15.8 + - - +
600C GLN 3.9 4.7 - - - +
602C LEU* 1.3 75.0 - - - +
604C ARG* 1.3 60.1 + - - +
606C LEU* 3.9 11.3 - - + +
607C ASN* 2.8 42.7 + - - +
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Residues in contact with ARG 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP* 2.8 82.6 + - - +
279C MET* 3.3 24.4 - - + +
600C GLN 3.3 10.1 + - - +
601C ARG* 3.3 16.9 + - - +
602C LEU 2.9 1.0 + - - -
603C VAL* 1.3 75.4 - - - +
605C ASP* 1.3 75.5 + - - +
607C ASN* 3.2 4.2 + - - +
608C LEU* 3.0 48.6 + - + +
604D ARG* 5.5 3.4 - - - +
605D ASP* 4.3 17.8 + - - -
608D LEU* 4.3 12.3 - - - +
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Residues in contact with ASP 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C ARG* 3.2 12.8 + - - +
602C LEU 2.7 12.2 + - - +
604C ARG* 1.3 82.5 + - - +
606C LEU* 1.3 66.7 + - + +
608C LEU* 3.1 7.3 + - - +
609C THR* 2.9 31.9 + - - +
679C LEU* 4.6 5.2 - - + -
685C HIS* 5.7 3.6 - - - +
686C TYR* 2.5 37.1 + - - +
278D TRP* 6.3 0.4 - - - -
604D ARG* 4.6 12.2 + - - +
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Residues in contact with LEU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C TYR* 3.6 38.6 - - + +
555C GLY* 4.2 11.2 - - - -
558C TRP* 3.7 23.0 - - + +
602C LEU* 2.8 40.2 + - + +
603C VAL* 3.9 13.5 - - - +
605C ASP* 1.3 71.8 - - - +
607C ASN* 1.3 53.7 + - - +
609C THR* 3.8 0.5 - - - -
610C TYR* 2.7 37.4 + - - +
679C LEU* 3.3 41.5 - - + -
722C TRP* 4.3 7.1 - - + -
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Residues in contact with ASN 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C SER* 2.6 28.6 + - - -
279C MET 2.8 18.8 + - - +
280C GLY 3.2 23.3 - - - +
281C PHE* 3.9 13.7 - - - -
558C TRP* 2.9 17.9 + - - -
603C VAL* 2.8 29.7 + - - +
604C ARG 3.2 7.7 + - - +
605C ASP 3.1 0.2 - - - -
606C LEU* 1.3 77.5 - - - +
608C LEU* 1.3 59.7 + - - +
610C TYR* 3.3 5.1 + - - +
611C ARG* 2.9 37.9 + - - +
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Residues in contact with LEU 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP 5.2 1.8 - - - +
280C GLY* 4.3 16.8 - - - +
604C ARG* 3.0 54.9 + - + +
605C ASP* 3.1 6.0 + - - +
607C ASN* 1.3 77.0 - - - +
609C THR* 1.3 51.2 + - - +
611C ARG* 2.4 39.0 - - + +
612C HIS* 3.6 2.1 - - - +
278D TRP* 3.4 23.8 - - + -
604D ARG* 3.9 24.5 - - - +
608D LEU* 4.9 4.5 - - + -
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Residues in contact with THR 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C ASP* 2.9 20.3 + - - +
606C LEU 4.1 0.7 - - - -
608C LEU* 1.3 71.5 - - - +
610C TYR* 1.3 60.0 + - - +
611C ARG 2.4 19.2 - - - +
613C HIS* 3.4 41.9 + - + +
678C ILE* 3.9 28.7 + - + +
679C LEU* 4.0 8.8 - - - +
722C TRP* 3.9 19.0 - - + -
278D TRP* 3.8 19.8 - - + -
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Residues in contact with TYR 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C PRO* 3.2 29.3 - - + +
243C ILE* 2.9 28.4 + - - -
244C SER* 4.2 12.6 - - - -
558C TRP* 3.7 27.4 - + + -
562C GLY 5.1 1.1 - - - -
563C LYS* 3.8 14.9 - - - +
564C LYS* 3.4 30.4 - - + +
606C LEU 2.7 25.5 + - - +
607C ASN* 3.5 4.0 - - - +
609C THR* 1.3 72.7 - - - +
611C ARG* 1.3 59.0 + - + +
613C HIS 3.6 3.8 - - - +
616C MET* 3.5 28.5 - - + +
617C HIS* 2.8 39.2 - - + +
620C ASP* 4.3 2.6 + - - -
722C TRP* 4.0 11.8 - - + -
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Residues in contact with ARG 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PRO* 3.6 28.1 - - + +
244C SER* 5.6 0.4 - - - -
277C LYS 5.2 0.8 + - - -
280C GLY* 2.4 53.2 + - - -
281C PHE 3.4 11.1 + - - -
282C THR* 3.6 21.1 - - - +
607C ASN* 2.9 21.2 + - - +
608C LEU* 2.4 33.8 - - + +
609C THR 2.4 12.3 - - - +
610C TYR* 1.3 82.7 - - + +
612C HIS* 1.3 59.4 + - - +
613C HIS 3.2 2.2 - - - -
617C HIS* 3.9 6.5 - - - -
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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