Contacts of the helix formed by residues 594 - 611 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B LEU 3.0 25.3 + - - -
589B LEU 4.9 0.4 - - - -
590B GLU 5.7 0.4 - - - -
591B GLY 5.6 1.8 - - - -
592B GLY 3.5 9.8 + - - +
593B ASP* 1.3 75.0 - - - +
595B TRP* 1.3 66.9 + - + +
596B HIS* 2.7 46.8 + - + +
597B HIS* 2.8 33.2 + - - +
598B GLY 3.3 1.6 + - - -
687B HIS* 3.1 23.1 - - - -
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Residues in contact with TRP 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ALA* 3.8 26.0 - - + -
544B TRP* 3.9 39.7 - + + +
547B PHE* 3.4 54.9 - + + +
551B ARG* 4.9 1.3 - - - +
594B ASN* 1.3 78.0 - - + +
596B HIS* 1.3 64.8 + - + +
598B GLY* 3.2 2.8 + - - -
599B VAL* 3.0 25.6 + - - +
686B TYR 4.6 5.1 - - - +
687B HIS* 3.7 32.0 + + + +
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Residues in contact with HIS 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.3 4.9 - - + -
547B PHE* 3.8 23.9 - + - -
572B PHE* 2.9 30.3 + - + +
573B ALA* 3.0 21.2 + - - +
575B GLY* 4.9 1.6 - - - -
588B LEU* 3.6 38.6 - - + +
589B LEU* 3.4 18.8 - - + -
594B ASN* 2.7 34.6 + - + +
595B TRP* 1.3 74.5 - + + +
597B HIS* 1.3 53.8 + - - +
599B VAL* 3.2 4.7 + - - +
600B GLN* 3.0 29.3 + - - +
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Residues in contact with HIS 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A ARG* 4.6 11.4 - - - -
695A GLY* 5.9 1.3 - - - -
589B LEU* 3.6 17.8 - - + +
590B GLU* 3.3 31.5 + - - -
591B GLY 5.2 0.2 - - - -
592B GLY 3.5 13.4 + - - -
593B ASP* 3.1 28.2 + - - +
594B ASN* 2.8 48.9 + - - +
596B HIS* 1.3 76.4 - - - +
598B GLY* 1.3 58.1 + - - +
600B GLN* 3.4 12.1 + - - +
601B ARG* 2.8 38.1 + - - +
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Residues in contact with GLY 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ASN 3.3 5.1 + - - -
595B TRP 3.2 7.1 + - - -
597B HIS* 1.3 80.5 - - - +
599B VAL* 1.3 56.4 + - - +
601B ARG* 4.0 4.9 - - - +
602B LEU* 2.9 23.7 + - - +
686B TYR* 3.2 46.6 - - - +
687B HIS* 4.0 4.6 + - - -
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Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B PHE* 4.1 20.4 - - + +
550B LEU* 4.2 6.7 - - + -
551B ARG* 4.4 21.1 - - + +
554B TYR* 4.1 24.2 - - + -
571B GLU 3.2 20.6 - - - +
573B ALA* 4.0 20.0 - - + +
595B TRP 3.0 17.7 + - - +
596B HIS 3.6 7.0 - - - +
598B GLY* 1.3 74.2 - - - +
600B GLN* 1.3 60.7 + - - +
602B LEU* 3.0 9.0 + - + +
603B VAL* 2.9 28.1 + - - +
686B TYR 5.7 0.2 - - - +
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Residues in contact with GLN 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TYR* 2.9 33.6 + - - +
279B MET* 3.4 31.0 - - + +
571B GLU* 2.9 17.7 + - + +
572B PHE* 4.0 6.8 - - + +
586B TRP* 4.1 2.6 - - - -
589B LEU* 3.2 34.5 - - - +
596B HIS 3.0 16.9 + - - +
597B HIS* 3.7 11.0 + - - +
599B VAL* 1.3 74.1 - - - +
601B ARG* 1.3 63.6 + - - +
603B VAL 3.3 1.4 + - - -
604B ARG* 3.2 19.6 + - - +
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Residues in contact with ARG 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET* 6.2 0.6 - - - +
593B ASP* 2.5 45.8 + - - -
597B HIS* 2.8 28.7 + - - +
598B GLY* 3.5 7.2 - - - +
600B GLN* 1.3 77.8 - - - +
602B LEU* 1.3 60.5 + - - +
604B ARG* 3.5 7.5 + - - +
605B ASP* 3.3 26.6 + - - +
684B MET 5.4 0.6 + - - -
685B HIS* 3.6 45.8 + - + +
686B TYR* 3.8 14.7 - - + +
687B HIS* 3.5 16.0 + - - -
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Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ARG* 3.2 48.0 - - + +
554B TYR* 5.0 3.8 - - + -
598B GLY 2.9 14.7 + - - +
599B VAL 3.0 8.0 + - - +
601B ARG* 1.3 74.0 - - - +
603B VAL* 1.3 61.2 + - + +
605B ASP* 3.1 1.6 + - - +
606B LEU* 2.7 56.5 + - + +
679B LEU* 4.3 6.5 - - + -
681B THR* 3.8 22.4 - - + -
686B TYR* 3.4 36.7 - - + +
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Residues in contact with VAL 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B MET* 3.9 14.6 - - + -
281B PHE* 4.1 12.6 - - + -
554B TYR* 3.9 27.8 - - + -
558B TRP* 4.4 10.3 - - + -
566B LEU* 4.2 11.0 - - + -
571B GLU* 3.7 20.6 - - + +
599B VAL 2.9 17.5 + - - +
600B GLN 3.7 6.5 - - - +
602B LEU* 1.3 75.8 - - - +
604B ARG* 1.3 58.8 + - - +
606B LEU* 3.2 10.2 + - + +
607B ASN* 2.9 41.3 + - - +
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Residues in contact with ARG 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ARG* 5.3 3.6 - - - +
605A ASP* 5.1 7.9 + - - -
608A LEU* 3.8 25.9 - - - +
278B TRP* 2.9 84.1 + - - +
279B MET* 3.3 22.6 - - - +
600B GLN 3.2 9.3 + - - +
601B ARG* 3.6 11.9 - - - +
602B LEU 3.2 0.2 - - - -
603B VAL* 1.3 78.7 - - - +
605B ASP* 1.3 61.7 + - - +
607B ASN* 3.1 2.8 + - - +
608B LEU* 2.8 58.5 + - + +
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Residues in contact with ASP 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TRP* 6.1 0.9 - - - -
604A ARG* 5.2 6.6 + - - -
601B ARG* 3.3 9.8 + - - +
602B LEU 3.1 6.8 + - - +
604B ARG* 1.3 85.7 + - - +
606B LEU* 1.3 65.8 + - - +
608B LEU* 4.5 7.5 - - - +
609B THR* 2.7 34.6 + - - +
679B LEU* 4.4 8.1 - - + -
685B HIS* 4.6 7.3 - - - -
686B TYR* 2.4 39.8 + - - +
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B TYR* 4.0 24.2 - - + +
555B GLY* 4.2 6.1 - - - +
558B TRP* 3.7 31.5 - - + -
602B LEU* 2.7 49.3 + - + +
603B VAL* 3.4 10.5 - - - +
605B ASP* 1.3 72.4 - - - +
607B ASN* 1.3 55.7 + - - +
610B TYR* 2.7 38.6 + - - +
679B LEU* 3.2 39.5 - - + -
722B TRP* 4.0 17.2 - - + -
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Residues in contact with ASN 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 2.5 30.6 + - - -
279B MET 2.7 23.3 + - - +
280B GLY 3.4 23.3 - - - +
281B PHE* 3.6 25.2 - - - -
558B TRP* 3.2 12.8 + - - +
603B VAL* 2.9 17.2 + - - +
604B ARG 3.1 8.0 + - - +
606B LEU* 1.3 77.5 - - - +
608B LEU* 1.3 57.4 + - - +
610B TYR* 3.4 3.0 - - - +
611B ARG* 3.0 36.0 + - - +
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TRP* 3.4 14.4 - - + -
604A ARG* 4.1 26.0 - - - +
608A LEU* 4.7 4.5 - - + -
277B LYS 5.8 0.4 - - - +
278B TRP 5.2 1.3 - - - +
280B GLY* 4.0 20.9 - - - +
604B ARG* 2.8 64.4 + - + +
605B ASP* 4.3 6.7 - - - +
607B ASN* 1.3 75.3 - - - +
609B THR* 1.3 51.8 + - - +
611B ARG* 2.2 39.8 - - + +
612B HIS* 3.6 1.2 - - - +
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Residues in contact with THR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TRP* 3.6 23.5 - - + -
605B ASP* 2.7 26.0 + - - +
608B LEU* 1.3 71.3 - - - +
610B TYR* 1.3 64.4 + - - +
611B ARG 2.8 11.7 - - - +
613B HIS* 3.5 36.1 + - + +
616B MET* 4.5 0.7 - - - +
678B ILE* 3.9 33.3 + - + +
679B LEU* 4.5 4.4 - - + +
722B TRP* 3.9 18.6 - - + -
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Residues in contact with TYR 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.5 23.2 - - + +
243B ILE 3.0 36.7 + - - -
244B SER* 4.3 9.4 - - - -
558B TRP* 3.7 30.7 - + + -
563B LYS* 4.0 11.1 - - - +
564B LYS* 3.7 25.0 + - + +
606B LEU 2.7 20.1 + - - +
607B ASN 3.4 2.5 - - - +
609B THR* 1.3 79.8 - - - +
611B ARG* 1.3 68.9 + - + +
613B HIS 3.3 7.8 - - - +
616B MET* 3.3 36.6 - - + +
617B HIS* 2.8 31.3 - - + +
620B ASP* 4.6 1.4 + - - -
722B TRP* 4.1 6.6 - - + -
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.8 24.7 - - + +
244B SER* 5.6 1.1 - - - -
277B LYS 5.2 1.8 + - - -
280B GLY* 2.7 45.8 + - - -
281B PHE 3.5 8.7 + - - -
282B THR* 3.4 24.4 - - + +
329B GLY 5.5 4.4 + - - -
607B ASN* 3.0 20.7 + - - +
608B LEU* 2.2 39.1 - - + +
609B THR 2.8 5.4 - - - +
610B TYR* 1.3 82.0 - - + +
612B HIS* 1.3 60.9 + - - +
613B HIS 3.3 0.4 - - - -
617B HIS* 4.1 8.3 - - - -
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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