Contacts of the helix formed by residues 587 - 609 (chain A) in PDB entry 1LMU
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 ARG 587 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A ILE* 4.6 4.2 - - - +
586A CYS* 1.3 92.3 - - - +
588A TYR* 1.3 64.7 + - - +
589A GLN* 3.4 33.9 - - + +
590A ASP* 3.2 35.7 + - + +
591A PHE* 3.3 4.9 + - - +
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Residues in contact with TYR 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP* 4.4 2.4 + - - -
160A VAL* 4.0 27.7 - - + +
163A LEU* 4.9 1.3 - - + -
164A ALA* 3.6 40.4 - - + -
167A ARG* 2.7 45.4 + - - +
581A ILE* 4.9 7.1 - - + +
587A ARG* 1.3 69.6 - - - +
589A GLN* 1.3 71.9 + - + +
591A PHE* 2.9 16.7 + + - +
592A MET* 2.9 52.3 + - + +
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Residues in contact with GLN 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ARG* 3.4 35.8 - - + +
588A TYR* 1.3 85.3 - - + +
590A ASP* 1.3 69.0 + - - +
592A MET* 4.2 5.4 - - - +
593A GLN* 3.1 53.0 + - + +
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Residues in contact with ASP 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A VAL* 5.7 0.6 - - - +
586A CYS* 3.3 17.2 - - - -
587A ARG* 3.2 34.3 + - + +
588A TYR 3.1 0.2 - - - -
589A GLN* 1.3 83.4 - - - +
591A PHE* 1.3 57.6 + - - +
593A GLN* 5.8 1.1 - - - -
594A PRO* 3.2 24.4 - - - +
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Residues in contact with PHE 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.8 27.1 - - + -
168A ALA* 3.4 34.5 - - + -
197A ARG* 4.1 10.8 - - - -
574A TRP* 4.0 24.1 + + - -
577A VAL* 2.9 42.6 - - + -
578A LEU* 4.7 5.4 - - + -
581A ILE* 4.2 14.1 - - + -
586A CYS* 4.4 0.4 - - - -
587A ARG 3.3 7.0 + - - +
588A TYR* 2.9 9.3 + + - +
590A ASP* 1.3 80.0 - - - +
592A MET* 1.3 76.3 + - + +
593A GLN 3.5 0.5 + - - -
594A PRO* 3.5 6.7 - - - +
595A LEU* 3.5 23.7 + - + +
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Residues in contact with MET 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP* 5.0 5.4 - - - +
167A ARG* 4.5 9.4 - - - -
168A ALA* 4.4 10.5 - - - -
171A LEU* 3.6 31.4 - - + -
588A TYR* 2.9 55.3 + - + +
589A GLN* 4.1 4.9 - - - +
591A PHE* 1.3 81.7 - - + +
593A GLN* 1.3 68.3 + - + +
595A LEU* 3.0 34.9 + - + +
596A VAL* 3.2 12.8 + - + +
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Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A GLN* 3.1 39.2 + - + +
590A ASP* 5.8 1.0 - - - -
592A MET* 1.3 76.3 - - + +
594A PRO* 1.3 71.5 - - + +
596A VAL* 2.8 32.3 - - + +
597A GLY* 3.2 2.6 + - - -
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Residues in contact with PRO 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TRP* 5.6 0.7 - - - -
590A ASP* 3.2 27.1 - - - +
591A PHE* 3.5 7.9 - - - +
593A GLN* 1.3 100.3 - - + +
595A LEU* 1.3 60.5 + - - -
597A GLY* 3.1 11.6 + - - +
598A THR* 3.1 18.8 + - - +
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Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 4.4 16.2 - - + +
171A LEU* 4.3 9.2 - - + -
172A TYR* 5.0 1.3 - - + +
574A TRP* 2.9 59.8 - - + +
591A PHE* 3.5 20.7 + - + +
592A MET* 3.0 33.2 + - + +
594A PRO* 1.3 78.5 - - - +
596A VAL* 1.3 63.8 + - - +
598A THR* 2.6 25.4 + - - -
599A LEU* 3.3 28.4 + - + -
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Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.6 35.7 - - + -
171A LEU* 5.1 4.7 - - + -
592A MET* 3.2 7.6 + - + +
593A GLN* 2.8 25.4 - - - +
595A LEU* 1.3 86.9 - - - +
597A GLY* 1.3 64.5 + - - +
599A LEU* 2.9 15.4 + - + +
600A TYR* 2.8 53.5 + - + +
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Residues in contact with GLY 597 (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 GLN 3.2 3.2 + - - -
594A PRO* 3.1 9.8 + - - -
596A VAL* 1.3 88.4 - - - +
598A THR* 1.3 61.9 + - - +
600A TYR* 3.3 16.9 + - - +
601A GLN* 3.5 9.4 + - - +
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Residues in contact with THR 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A MET* 4.9 5.2 - - - -
570A MET* 3.9 34.0 - - + +
574A TRP* 3.8 17.1 - - + +
594A PRO* 3.1 14.2 + - + +
595A LEU 2.6 20.4 + - - -
597A GLY* 1.3 74.2 - - - +
599A LEU* 1.3 67.1 + - - +
601A GLN* 3.1 8.1 + - - +
602A LEU* 3.0 25.9 + - - +
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Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 4.7 11.0 - - + -
69A VAL* 5.0 2.5 - - + -
171A LEU* 3.5 42.4 - - + +
172A TYR* 3.5 42.0 - - + +
175A ASN* 4.0 14.1 - - + +
176A MET* 5.3 5.4 - - - -
595A LEU* 3.8 18.2 - - + +
596A VAL* 2.9 18.1 + - + +
598A THR* 1.3 84.2 + - - +
600A TYR* 1.3 64.0 + - + +
602A LEU* 3.0 7.0 + - + +
603A ILE* 2.9 28.6 + - + +
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Residues in contact with TYR 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.9 29.1 - - + +
69A VAL* 4.0 11.7 - - + +
596A VAL* 2.8 60.2 + - + +
597A GLY* 3.8 9.2 - - - +
598A THR 3.3 0.4 - - - -
599A LEU* 1.3 78.1 - - + +
601A GLN* 1.3 64.2 + - - +
603A ILE* 3.3 1.6 + - - +
604A GLU* 3.1 22.7 + - - +
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Residues in contact with GLN 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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597A GLY 3.5 6.9 + - - +
598A THR* 3.1 11.7 + - - +
600A TYR* 1.3 82.0 - - - +
602A LEU* 1.3 71.8 + - + +
604A GLU* 3.2 15.6 + - - +
605A GLN* 3.2 23.2 + - - +
608A ARG* 5.5 6.4 + - - -
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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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172A TYR* 3.7 33.0 - - + +
176A MET* 3.9 25.1 - - + +
562A PRO* 4.4 20.9 - - + -
564A MET* 3.1 37.7 - - + -
565A ALA* 5.8 0.9 - - + -
570A MET* 4.7 1.6 - - + -
598A THR* 3.0 21.0 + - - +
599A LEU* 3.0 9.5 + - + +
601A GLN* 1.3 84.3 - - + +
603A ILE* 1.3 64.4 + - - +
605A GLN* 3.2 11.6 + - - +
606A ALA* 3.0 22.1 + - - +
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Residues in contact with ILE 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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63A LEU* 5.0 1.3 - - + +
66A LEU* 3.5 35.2 - - + +
67A PRO* 3.0 49.1 - - + -
175A ASN* 3.7 24.0 - - + +
176A MET* 5.0 8.5 - - - -
179A ALA* 5.1 6.7 - - + -
599A LEU* 2.9 19.2 + - + +
600A TYR 4.1 1.3 - - - +
602A LEU* 1.3 78.6 - - + +
604A GLU* 1.3 65.1 + - - +
606A ALA* 3.1 6.5 + - - +
607A LYS* 3.1 35.2 + - + +
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Residues in contact with GLU 604 (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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600A TYR 3.1 12.9 + - - +
601A GLN* 3.7 12.3 - - - +
602A LEU 3.2 0.4 - - - -
603A ILE* 1.3 79.0 - - - +
605A GLN* 1.3 63.7 + - - +
607A LYS* 3.2 43.6 + - - +
608A ARG* 3.5 34.4 + - - +
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Residues in contact with GLN 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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562A PRO* 3.5 38.4 - - + +
601A GLN* 3.2 20.3 + - - +
602A LEU* 3.2 13.5 + - + +
603A ILE 3.2 0.4 - - - -
604A GLU* 1.3 80.3 - - - +
606A ALA* 1.3 56.3 + - - +
608A ARG* 2.8 46.4 + - + +
609A THR* 3.3 10.2 + - - +
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Residues in contact with ALA 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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176A MET* 5.1 1.1 - - + -
179A ALA* 4.1 26.0 - - + -
180A TYR* 4.6 18.8 - - + +
183A LEU* 3.2 28.2 - - + +
602A LEU 3.0 12.9 + - - +
603A ILE* 3.1 9.6 + - - +
605A GLN* 1.3 75.4 - - - +
607A LYS* 1.3 64.3 + - + +
609A THR* 3.0 18.8 + - - -
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Residues in contact with LYS 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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63A LEU* 3.4 57.7 + - + +
64A ALA* 4.7 11.3 + - - +
66A LEU 5.0 4.4 + - - -
183A LEU* 5.0 2.8 - - - +
603A ILE* 3.1 24.1 + - + +
604A GLU* 3.3 37.5 + - - +
606A ALA* 1.3 76.8 - - - +
608A ARG* 1.3 61.3 + - + +
609A THR 3.6 4.0 + - - +
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Residues in contact with ARG 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLN* 5.5 5.8 + - - -
604A GLU* 3.5 37.0 + - - +
605A GLN* 2.8 27.8 + - + +
607A LYS* 1.3 78.1 - - + +
609A THR* 1.3 60.6 + - - +
610A PRO* 3.4 9.1 - - - +
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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
----------------------------------------------------------
180A TYR* 5.5 2.7 + - + -
183A LEU* 4.0 22.8 - - + +
560A SER* 4.3 25.0 + - - +
605A GLN* 3.5 14.0 + - - +
606A ALA* 3.0 20.0 + - - +
607A LYS 4.2 3.5 - - - +
608A ARG* 1.3 76.6 - - - +
610A PRO* 1.3 88.6 - - + +
611A VAL* 3.7 4.0 + - - +
613A ARG* 6.2 2.7 - - - -
614A PHE* 4.7 7.6 - - + -
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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