Contacts of the helix formed by residues 575 - 586 (chain A) in PDB entry 4RM9
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 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A GLY* 1.3 77.3 - - - -
576A THR* 1.3 54.7 + - - +
577A LYS* 2.9 40.1 + - + +
578A GLN* 3.3 24.5 + - + +
579A ARG* 2.7 34.9 + - - +
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Residues in contact with THR 576 (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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240A PHE* 4.5 10.8 - - + -
244A GLU* 4.0 19.4 + - - +
259A PRO* 5.0 7.8 - - + +
261A ASP* 5.9 0.9 - - - +
264A ALA* 4.1 10.8 - - + +
265A PRO* 3.8 12.3 - - + +
267A PHE* 5.6 1.3 - - + +
575A ASN* 1.3 69.0 + - - +
577A LYS* 1.3 76.8 + - - +
579A ARG* 3.0 14.4 + - - +
580A ILE* 2.7 60.9 + - + +
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Residues in contact with LYS 577 (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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261A ASP* 3.9 12.0 + - - +
263A LYS 4.9 2.7 - - - +
264A ALA* 3.5 30.5 - - - +
265A PRO* 3.3 27.1 - - + -
575A ASN* 2.9 43.0 + - + +
576A THR* 1.3 86.2 + - - +
578A GLN* 1.3 57.1 + - - +
580A ILE* 3.2 2.8 + - - +
581A ASP* 2.8 42.5 + - - +
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Residues in contact with GLN 578 (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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573A GLN 5.7 0.7 - - - +
574A GLY* 3.8 11.4 - - - -
575A ASN* 3.2 35.7 + - + +
576A THR 3.1 0.2 - - - -
577A LYS* 1.3 80.1 - - - +
579A ARG* 1.3 60.5 + - + +
581A ASP* 3.4 8.2 + - - +
582A GLU* 3.2 31.3 + - - +
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Residues in contact with ARG 579 (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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238A ILE* 3.9 16.3 - - + +
239A GLY 3.0 22.7 + - - -
240A PHE* 3.3 25.0 - - + +
241A PRO* 4.4 0.8 - - - +
244A GLU* 2.9 41.0 + - - -
571A ILE 3.3 23.1 - - - +
572A ARG* 3.4 12.0 + - - -
573A GLN 3.3 24.7 + - - +
574A GLY 3.2 19.6 + - - -
575A ASN* 2.7 15.3 + - - +
576A THR* 3.7 15.0 + - - +
578A GLN* 1.3 72.2 - - + +
580A ILE* 1.3 64.6 + - - +
582A GLU* 3.2 22.5 - - - +
583A PHE* 3.0 22.0 + - - +
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Residues in contact with ILE 580 (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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240A PHE* 4.2 13.7 - - + -
265A PRO* 3.4 30.3 - - + +
266A ASP 3.3 30.3 - - - +
267A PHE* 3.7 15.3 - - + -
268A VAL 5.4 1.6 - - - +
576A THR* 2.7 35.3 + - + +
577A LYS* 3.6 5.6 - - - +
579A ARG* 1.3 72.1 - - - +
581A ASP* 1.3 68.2 + - - +
583A PHE* 3.2 9.7 - - + +
584A GLU* 3.1 32.7 + - + +
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Residues in contact with ASP 581 (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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577A LYS* 2.8 30.2 + - - +
578A GLN* 3.6 8.4 + - - +
579A ARG 3.2 0.2 - - - -
580A ILE* 1.3 80.5 - - - +
582A GLU* 1.3 59.7 - - - +
584A GLU* 3.2 11.5 + - - +
585A ALA* 3.0 25.7 + - - +
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Residues in contact with GLU 582 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A LYS 4.4 5.2 - - - +
238A ILE* 3.8 19.5 - - + +
571A ILE* 5.1 1.9 - - - +
573A GLN 5.3 1.3 - - - +
578A GLN* 3.2 20.9 + - - +
579A ARG* 3.2 32.7 - - - +
581A ASP* 1.3 75.6 - - - +
583A PHE* 1.3 64.5 + - - +
585A ALA* 3.2 10.0 + - + +
586A LEU* 3.1 29.1 + - + +
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Residues in contact with PHE 583 (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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208A ILE* 4.3 7.0 - - + -
209A LYS 4.2 1.6 - - - -
210A ASN* 3.2 38.6 + - + +
216A LEU* 3.8 17.5 - - + -
227A ILE* 3.8 36.6 - - + -
238A ILE* 3.4 13.6 - - + +
240A PHE* 5.5 0.7 - - + -
267A PHE* 3.7 19.1 - + + -
268A VAL 3.6 20.4 - - - -
269A PHE* 3.7 21.1 - - + -
579A ARG 3.0 14.5 + - - +
580A ILE* 3.2 14.4 - - + +
582A GLU* 1.3 77.1 - - - +
584A GLU* 1.3 76.8 + - - +
586A LEU* 3.1 17.2 + - + +
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Residues in contact with GLU 584 (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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210A ASN* 2.7 19.6 + - - +
211A LYS* 2.9 45.2 + - + +
212A LYS* 2.9 20.8 + - + +
268A VAL* 3.9 10.9 - - - +
270A TYR* 5.8 0.7 - - - -
580A ILE* 3.1 24.1 + - + +
581A ASP* 3.2 10.3 + - - +
583A PHE* 1.3 94.9 - - - +
585A ALA* 1.3 58.4 + - - +
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Residues in contact with ALA 585 (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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212A LYS* 3.6 12.8 + - - +
581A ASP 3.0 13.3 + - - +
582A GLU* 3.5 14.6 - - + +
583A PHE 3.2 0.4 - - - -
584A GLU* 1.3 73.5 - - - +
586A LEU* 1.3 68.7 + - + +
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Residues in contact with LEU 586 (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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210A ASN* 3.5 6.4 + - - -
212A LYS* 3.5 10.2 - - - -
214A THR* 2.9 35.8 + - - +
216A LEU* 3.9 34.3 - - + +
227A ILE* 4.0 13.9 - - + -
229A GLU* 4.9 21.2 - - + +
237A LYS* 4.8 13.5 - - + -
238A ILE* 3.8 22.9 - - + -
582A GLU* 3.1 25.0 + - + +
583A PHE* 3.1 13.5 + - - +
584A GLU 3.1 0.2 - - - -
585A ALA* 1.3 85.2 - - + +
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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
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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