Contacts of the helix formed by residues 594 - 611 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588D LEU 3.1 20.5 + - - -
590D GLU 4.4 1.0 + - - -
591D GLY 4.0 4.9 + - - -
592D GLY 3.2 17.8 + - - +
593D ASP* 1.3 73.8 - - - +
595D TRP* 1.3 62.5 + - + +
596D HIS* 2.8 44.7 + - + +
597D HIS* 2.8 23.7 + - - +
598D GLY 2.9 22.5 + - - -
687D HIS* 3.4 14.3 - - - -
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Residues in contact with TRP 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ALA* 3.5 30.1 - - + -
544D TRP* 4.1 40.1 - + + +
547D PHE* 3.2 51.8 - + + -
551D ARG* 5.0 0.7 - - - -
594D ASN* 1.3 79.8 - - + +
596D HIS* 1.3 63.8 + + + +
598D GLY* 3.1 3.0 + - - +
599D VAL* 3.0 28.1 + - - +
686D TYR 4.8 3.1 - - - +
687D HIS* 3.7 31.2 - + + +
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Residues in contact with HIS 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D LEU* 4.1 4.9 - - + -
547D PHE* 3.7 25.2 - + - -
572D PHE* 2.7 34.4 + - - +
573D ALA* 2.7 21.4 + - - +
575D GLY* 4.6 3.4 - - - -
588D LEU* 4.1 37.8 - - + +
589D LEU* 3.5 18.6 - - + -
594D ASN* 2.8 20.7 + - + +
595D TRP* 1.3 78.5 - + + +
597D HIS* 1.3 61.6 + - - +
599D VAL* 3.5 0.6 + - - -
600D GLN* 3.1 22.5 + - - +
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Residues in contact with HIS 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ARG* 4.8 6.7 - - - -
589D LEU* 2.8 51.5 + - + +
590D GLU 4.9 0.2 - - - -
591D GLY 4.4 1.0 + - - -
592D GLY 3.7 7.3 + - - -
593D ASP* 3.0 28.5 + - - +
594D ASN* 2.8 52.7 + - - +
596D HIS* 1.3 75.2 - - - +
598D GLY* 1.3 65.5 + - - +
600D GLN* 3.0 14.8 + - - +
601D ARG* 2.9 32.9 + - - +
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Residues in contact with GLY 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594D ASN 2.9 12.8 + - - -
595D TRP 3.1 4.6 + - - -
597D HIS* 1.3 78.4 - - - +
599D VAL* 1.3 60.3 + - - +
601D ARG* 3.3 11.2 + - - +
602D LEU 3.1 17.0 + - - -
686D TYR* 3.3 44.9 - - - +
687D HIS* 4.0 0.4 - - - -
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Residues in contact with VAL 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D PHE* 3.7 22.0 - - + -
550D LEU* 4.6 7.0 - - + -
551D ARG* 4.4 21.5 - - + +
554D TYR* 4.1 24.2 - - + -
571D GLU 3.3 16.4 - - - +
572D PHE 4.4 0.2 - - - -
573D ALA* 3.9 22.7 - - + +
595D TRP 3.0 15.3 + - - +
596D HIS 3.8 5.4 - - - +
598D GLY* 1.3 72.2 - - - +
600D GLN* 1.3 64.0 + - - +
602D LEU* 3.3 7.6 + - + +
603D VAL* 3.1 20.1 + - - +
686D TYR 4.7 0.2 + - - -
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Residues in contact with GLN 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D TYR* 3.0 38.3 + - - +
279D MET* 3.0 44.9 - - + +
571D GLU* 3.0 16.8 + - + +
572D PHE* 4.2 4.7 - - + -
586D TRP* 4.6 1.0 - - - -
589D LEU* 3.9 29.6 - - - +
596D HIS 3.1 13.1 + - - +
597D HIS* 3.0 16.6 + - - +
599D VAL* 1.3 74.8 - - - +
601D ARG* 1.3 64.9 + - - +
603D VAL 4.5 0.2 - - - +
604D ARG* 3.4 5.4 + - - +
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Residues in contact with ARG 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C HIS* 4.3 15.6 + - - -
593D ASP* 2.7 42.6 + - - -
597D HIS* 2.9 23.9 + - - +
598D GLY* 3.4 13.5 - - - +
600D GLN* 1.3 79.1 - - - +
602D LEU* 1.3 56.1 + - - +
604D ARG* 3.3 9.6 + - - +
605D ASP* 3.0 32.9 + - - +
685D HIS* 3.5 36.3 + - + +
686D TYR* 3.8 16.2 - - + +
687D HIS* 3.6 17.0 + - - -
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Residues in contact with LEU 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D ARG* 3.5 45.3 - - + +
554D TYR* 4.5 12.3 - - + -
598D GLY 3.1 8.3 + - - +
599D VAL* 3.6 10.1 - - - +
600D GLN 3.2 0.4 - - - -
601D ARG* 1.3 75.6 - - - +
603D VAL* 1.3 60.6 + - + +
605D ASP* 4.4 0.2 - - - -
606D LEU* 2.7 54.9 + - + +
679D LEU* 4.4 4.7 - - + -
681D THR* 3.7 18.4 - - + -
686D TYR* 3.3 44.6 - - + +
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Residues in contact with VAL 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D MET* 3.8 14.6 - - + -
281D PHE* 3.8 19.1 - - + -
554D TYR* 4.0 25.1 - - + -
558D TRP* 4.4 9.0 - - + -
566D LEU* 4.1 9.4 - - + -
571D GLU* 3.8 24.9 - - + +
599D VAL 3.1 20.3 + - - +
601D ARG 3.4 0.4 - - - -
602D LEU* 1.3 75.9 - - - +
604D ARG* 1.3 58.4 + - - +
606D LEU* 3.4 8.4 + - + +
607D ASN* 2.9 43.5 + - - +
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Residues in contact with ARG 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C ARG* 5.4 3.6 - - - +
605C ASP* 4.6 10.5 + - - -
608C LEU* 3.9 23.6 - - - +
278D TRP* 3.0 82.7 + - - +
279D MET* 3.2 27.3 - - + +
600D GLN 3.4 4.4 + - - +
601D ARG* 3.3 12.9 + - - +
602D LEU 3.2 0.2 - - - -
603D VAL* 1.3 78.0 - - - +
605D ASP* 1.3 67.8 + - - +
607D ASN* 3.0 3.5 + - - +
608D LEU* 2.9 57.2 + - + +
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Residues in contact with ASP 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP* 6.0 1.3 - - - -
604C ARG* 4.3 17.0 + - - -
601D ARG* 3.0 17.8 + - - +
602D LEU 3.9 2.2 - - - +
604D ARG* 1.3 87.2 + - - +
606D LEU* 1.3 55.3 + - - +
608D LEU* 3.9 7.9 - - - +
609D THR* 2.4 39.4 + - - +
679D LEU* 4.4 5.8 - - + -
685D HIS* 3.3 26.1 + - - -
686D TYR* 2.9 29.8 + - - +
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Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D TYR* 3.5 35.7 - - + +
555D GLY* 4.0 8.5 - - - +
558D TRP* 3.4 39.8 - - + +
602D LEU* 2.7 30.5 + - + +
603D VAL* 3.4 10.5 - - - +
605D ASP* 1.3 76.4 - - - +
607D ASN* 1.3 59.7 + - - +
609D THR* 4.2 0.8 - - - -
610D TYR* 3.0 31.4 + - - +
679D LEU* 3.3 40.4 - - + -
722D TRP* 4.2 6.0 - - + -
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Residues in contact with ASN 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D SER* 2.4 29.4 + - - -
279D MET 3.0 26.6 + - - +
280D GLY 3.6 16.6 - - - +
281D PHE* 3.8 18.2 - - - +
558D TRP* 2.9 15.5 + - - +
603D VAL* 2.9 33.5 + - - +
604D ARG 3.0 0.2 + - - -
606D LEU* 1.3 76.8 - - - +
608D LEU* 1.3 57.8 + - - +
610D TYR* 3.7 2.6 + - - +
611D ARG* 2.8 37.3 + - - +
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Residues in contact with LEU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP* 3.4 24.5 - - + -
604C ARG* 4.3 17.7 - - - +
608C LEU* 4.9 4.7 - - + -
278D TRP 5.6 0.2 - - - +
280D GLY* 4.1 19.3 - - - +
604D ARG* 2.9 55.8 + - + +
605D ASP* 4.1 8.7 - - - +
607D ASN* 1.3 76.7 - - - +
609D THR* 1.3 55.1 + - - +
611D ARG* 2.5 37.8 - - + +
612D HIS* 3.5 2.4 - - - +
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Residues in contact with THR 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP* 3.9 18.8 - - + -
605D ASP* 2.4 27.6 + - - +
606D LEU 4.2 0.2 - - - -
608D LEU* 1.3 70.6 - - - +
610D TYR* 1.3 59.9 + - - +
611D ARG 2.3 20.0 - - - +
613D HIS* 3.4 35.0 + - + +
616D MET* 4.5 0.3 - - - +
678D ILE* 3.8 25.5 + - + +
679D LEU* 4.1 6.4 - - + +
722D TRP* 3.8 28.5 - - + -
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Residues in contact with TYR 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D PRO* 3.4 24.6 - - + +
243D ILE 3.0 34.5 + - - -
244D SER* 4.4 8.5 - - - -
558D TRP* 3.6 32.5 - + + +
562D GLY 4.5 1.4 + - - -
563D LYS* 3.7 12.0 - - - +
564D LYS* 3.5 28.0 - - + +
606D LEU 3.0 21.4 + - - +
607D ASN 3.8 6.1 - - - +
609D THR* 1.3 78.3 - - - +
611D ARG* 1.3 62.9 + - + +
613D HIS 3.5 6.1 - - - +
616D MET* 3.1 36.7 - - + +
617D HIS* 2.8 34.3 - - + +
620D ASP* 4.7 0.6 + - - -
722D TRP* 4.0 5.3 - - + -
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Residues in contact with ARG 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D PRO* 3.9 31.3 - - + +
244D SER* 5.9 1.1 - - - -
277D LYS 5.3 2.0 + - - -
280D GLY* 2.7 43.9 + - - -
281D PHE 3.7 7.5 + - - -
282D THR* 3.5 21.6 - - + +
329D GLY 5.4 5.5 + - - -
607D ASN* 2.8 24.9 + - - +
608D LEU* 2.5 20.3 - - - +
609D THR 2.3 25.5 - - - +
610D TYR* 1.3 81.7 - - + +
612D HIS* 1.3 65.7 + - + +
617D HIS* 4.1 0.7 - - - -
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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