Contacts of the helix formed by residues 594 - 611 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A LEU 2.7 26.8 + - - -
590A GLU 4.0 5.5 + - - -
592A GLY 3.7 6.7 + - - +
593A ASP* 1.3 74.4 - - - +
595A TRP* 1.3 66.6 + - + +
596A HIS* 2.8 44.3 + - + +
597A HIS* 2.9 37.4 + - - +
598A GLY 3.3 1.4 + - - -
687A HIS* 3.2 19.2 - - - -
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Residues in contact with TRP 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A ALA* 3.6 26.5 - - + -
544A TRP* 3.9 34.8 - + + +
547A PHE* 3.6 50.4 - + + +
551A ARG* 4.3 2.7 - - - -
594A ASN* 1.3 74.0 - - + +
596A HIS* 1.3 57.9 + - + +
598A GLY* 3.2 2.8 + - - -
599A VAL* 3.0 32.1 + - - +
686A TYR 4.5 0.7 - - - +
687A HIS* 3.1 54.5 + + + +
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Residues in contact with HIS 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 4.4 5.4 - - + -
547A PHE* 3.7 26.1 - + - -
572A PHE* 3.1 17.1 + - - +
573A ALA 3.1 27.9 + - - -
575A GLY* 4.9 1.6 - - - -
588A LEU* 3.7 44.2 - - + +
589A LEU* 3.5 20.6 - - + +
594A ASN* 2.8 31.8 + - + +
595A TRP* 1.3 71.9 - - + +
597A HIS* 1.3 59.4 + - - +
599A VAL* 3.3 3.8 + - - +
600A GLN* 3.1 22.3 + - - +
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Residues in contact with HIS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 3.0 46.3 + - + +
590A GLU 4.1 2.1 + - - -
592A GLY 3.3 16.8 + - - -
593A ASP* 3.1 23.9 + - - +
594A ASN* 2.9 53.4 + - - +
596A HIS* 1.3 77.2 - - - +
598A GLY* 1.3 57.6 + - - +
600A GLN* 3.3 11.5 + - - +
601A ARG* 2.8 38.5 + - - +
676B ARG* 4.2 13.4 + - - -
695B GLY* 6.2 0.9 - - - -
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Residues in contact with GLY 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ASN 3.3 4.0 + - - -
595A TRP 3.2 8.1 + - - -
597A HIS* 1.3 78.5 - - - +
599A VAL* 1.3 59.9 + - - +
601A ARG* 3.4 13.5 + - - +
602A LEU* 3.0 21.1 + - - +
686A TYR* 3.4 38.9 - - - +
687A HIS* 3.9 4.9 - - - -
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 3.5 28.0 - - + -
550A LEU* 3.9 21.5 - - + -
551A ARG* 4.2 20.9 - - + +
554A TYR* 3.9 19.1 - - + -
571A GLU 3.4 12.6 - - - +
573A ALA* 4.1 11.2 - - + +
595A TRP 3.0 15.3 + - - +
596A HIS 3.8 6.1 - - - +
597A HIS 3.3 0.2 - - - -
598A GLY* 1.3 73.2 - - - +
600A GLN* 1.3 66.5 + - - +
602A LEU* 3.1 7.0 + - + +
603A VAL* 3.0 22.7 + - - +
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Residues in contact with GLN 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 2.8 34.2 + - - +
279A MET* 3.3 43.9 - - + +
571A GLU* 3.0 16.5 + - + +
572A PHE* 4.1 7.5 - - + +
586A TRP* 4.2 2.8 - - - -
589A LEU* 3.6 30.7 - - - +
596A HIS 3.1 13.4 + - - +
597A HIS* 3.3 14.3 + - - +
599A VAL* 1.3 76.0 - - - +
601A ARG* 1.3 62.0 + - - +
603A VAL* 3.4 0.4 + - - -
604A ARG* 3.3 10.0 + - - +
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Residues in contact with ARG 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ASP* 2.8 44.0 + - - -
597A HIS* 2.8 26.8 + - - +
598A GLY* 3.5 13.9 - - - +
599A VAL 3.1 0.2 - - - -
600A GLN* 1.3 78.9 - - - +
602A LEU* 1.3 59.6 + - - +
604A ARG* 3.8 6.3 + - - +
605A ASP* 3.2 31.0 + - - +
684A MET 5.5 0.2 + - - -
685A HIS* 3.6 43.2 + - + +
686A TYR* 3.8 13.2 - - + +
687A HIS* 3.8 13.1 + - - -
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A ARG* 3.4 50.9 - - + +
554A TYR* 4.7 4.0 - - + -
598A GLY 3.0 13.7 + - - +
599A VAL* 3.1 9.6 + - - +
601A ARG* 1.3 75.7 - - - +
603A VAL* 1.3 61.5 + - + +
605A ASP* 3.1 1.4 + - - +
606A LEU* 2.7 56.1 + - + +
679A LEU* 4.1 6.1 - - + -
681A THR* 3.9 13.5 - - + -
686A TYR* 3.5 36.5 - - + +
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Residues in contact with VAL 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A MET* 4.1 5.6 - - + -
281A PHE* 3.9 27.4 - - + -
554A TYR* 4.0 25.6 - - + -
558A TRP* 4.5 8.7 - - + -
566A LEU* 4.4 7.9 - - + -
571A GLU* 3.6 29.6 - - + +
599A VAL 3.0 14.8 + - - +
600A GLN 3.4 7.2 + - - +
602A LEU* 1.3 74.8 - - - +
604A ARG* 1.3 63.8 + - - +
606A LEU* 3.1 12.2 + - + +
607A ASN* 2.9 27.3 + - - +
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Residues in contact with ARG 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TRP* 2.8 87.4 + - - +
279A MET* 3.2 27.1 - - - +
600A GLN 3.3 13.1 + - - +
601A ARG* 3.9 7.0 - - - +
602A LEU 3.3 0.6 - - - -
603A VAL* 1.3 78.0 - - - +
605A ASP* 1.3 69.2 + - - +
607A ASN* 3.1 3.8 + - - +
608A LEU* 2.9 52.5 + - + +
604B ARG* 5.3 3.8 - - - +
605B ASP* 5.2 6.5 + - - -
608B LEU* 4.1 16.4 - - - +
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Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A ARG* 3.2 12.1 + - - +
602A LEU 3.1 8.6 + - - +
604A ARG* 1.3 91.1 + - - +
606A LEU* 1.3 61.8 + - - +
608A LEU* 3.9 6.1 - - - +
609A THR* 2.5 39.1 + - - +
679A LEU* 4.5 5.6 - - + -
685A HIS* 4.3 8.0 - - - -
686A TYR* 2.5 39.7 + - - +
278B TRP* 5.3 0.6 - - - -
604B ARG* 5.1 7.3 + - - -
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Residues in contact with LEU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A TYR* 3.7 37.7 - - + +
555A GLY* 4.2 5.8 - - - +
558A TRP* 3.7 36.9 - - + -
602A LEU* 2.7 32.8 + - + +
603A VAL* 3.2 14.1 - - - +
605A ASP* 1.3 76.3 - - - +
607A ASN* 1.3 53.0 + - - +
609A THR* 3.2 1.9 + - - -
610A TYR* 2.7 37.2 + - - +
679A LEU* 3.1 38.6 - - + -
722A TRP* 4.5 6.1 - - + -
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Residues in contact with ASN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER* 2.6 27.2 + - - -
279A MET 2.7 21.1 + - - +
280A GLY* 3.3 28.8 - - - +
281A PHE* 3.5 25.3 - - - +
558A TRP* 2.9 16.0 + - - +
603A VAL* 2.9 16.0 + - - +
604A ARG 3.4 7.4 - - - +
606A LEU* 1.3 75.7 - - - +
608A LEU* 1.3 57.9 + - - +
610A TYR* 3.5 2.8 - - - +
611A ARG* 2.9 36.3 + - - +
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LYS 5.8 0.2 - - - +
278A TRP 5.0 1.8 - - - +
280A GLY* 4.1 19.3 - - - -
604A ARG* 2.9 57.8 + - + +
605A ASP* 4.2 6.5 - - - +
607A ASN* 1.3 77.7 - - - +
609A THR* 1.3 57.5 + - - +
611A ARG* 3.0 28.0 - - + +
612A HIS* 3.5 4.9 - - - +
278B TRP* 3.3 16.9 - - + -
604B ARG* 3.8 27.6 - - - +
608B LEU* 4.7 5.6 - - + -
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Residues in contact with THR 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ASP* 2.5 26.3 + - - +
606A LEU* 3.8 2.0 - - - -
608A LEU* 1.3 72.7 - - - +
610A TYR* 1.3 58.8 + - - +
611A ARG 2.3 21.5 - - - +
613A HIS* 3.6 24.1 + - + +
616A MET* 4.6 0.9 - - + +
678A ILE* 4.1 36.0 + - + +
679A LEU* 4.3 5.4 - - + +
722A TRP* 3.8 27.4 - - + -
278B TRP* 4.0 18.6 - - + -
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Residues in contact with TYR 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO* 3.6 12.8 - - + +
243A ILE 3.0 44.8 + - - -
244A SER* 4.1 9.0 - - - -
558A TRP* 3.5 26.5 - + + +
562A GLY 5.2 0.4 - - - -
563A LYS* 3.7 12.6 - - - +
564A LYS* 3.4 34.1 - - + +
606A LEU 2.7 21.8 + - - +
607A ASN 3.5 6.7 - - - +
609A THR* 1.3 69.7 - - - +
611A ARG* 1.3 69.0 + - + +
613A HIS 3.4 6.6 - - - +
616A MET* 3.0 41.0 - - + +
617A HIS* 2.8 30.7 - - + +
620A ASP* 4.4 0.9 + - - -
722A TRP* 4.1 5.3 - - + -
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Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 3.6 26.0 - - + +
244A SER* 5.7 0.4 - - - -
277A LYS 5.2 1.6 + - - -
280A GLY* 2.8 39.4 + - - -
281A PHE 3.8 9.7 + - - -
282A THR* 3.5 23.2 - - + +
607A ASN* 2.9 19.6 + - - +
608A LEU* 3.6 14.6 - - + +
609A THR 2.3 32.6 - - - +
610A TYR* 1.3 81.1 - - + +
612A HIS* 1.3 64.7 + - + +
613A HIS 2.8 1.9 + - - -
617A HIS* 3.9 9.6 - - - -
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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
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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