Contacts of the strand formed by residues 475 - 480 (chain A) in PDB entry 6EJ9
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 MET 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ILE* 4.0 4.9 - - + -
393A GLY 3.5 16.4 - - - +
394A GLY* 3.9 14.6 - - - -
395A ALA* 3.6 12.3 - - + +
468A PHE* 3.8 20.1 - - + -
469A LEU 3.5 1.8 - - - +
470A GLU* 3.5 33.0 - - - -
474A HIS* 1.3 78.4 + - - +
476A TRP* 1.3 61.7 + - - +
524A THR 3.3 28.7 - - - +
525A LEU* 3.6 11.4 - - + -
568A ILE 3.2 8.1 + - - -
569A VAL* 3.8 25.8 - - + -
570A ASP* 3.1 24.6 + - - +
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Residues in contact with TRP 476 (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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267A ALA* 3.8 21.5 - - + -
270A ARG* 3.8 43.3 - - + -
271A ALA* 3.9 27.8 - - + -
272A LYS 5.3 0.7 - - - -
276A CYS* 3.7 12.7 - - - -
280A ILE* 4.2 14.1 - - + -
468A PHE* 3.2 6.2 - - - -
469A LEU* 2.8 47.5 + - + +
471A CYS* 3.0 30.4 + - + -
472A ASP* 5.1 4.9 - - + -
474A HIS* 3.3 42.0 - + + +
475A MET* 1.3 72.0 - - - +
477A ARG* 1.3 61.6 + - - +
478A LEU* 3.7 18.7 + - + +
570A ASP* 3.5 3.4 - - - -
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Residues in contact with ARG 477 (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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263A GLU* 3.6 45.7 + - - +
267A ALA* 4.5 1.6 - - - +
270A ARG* 5.4 0.9 + - - -
466A ARG* 4.2 31.3 - - + +
467A LEU 3.6 8.1 - - - +
468A PHE* 3.7 31.8 - - + -
476A TRP* 1.3 71.0 - - - +
478A LEU* 1.3 64.2 + - - +
479A GLY 3.7 6.5 - - - +
570A ASP* 3.0 50.2 + - + +
571A TRP* 4.0 20.4 - - - +
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Residues in contact with LEU 478 (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 GLY* 5.8 1.2 - - - -
263A GLU* 3.9 7.0 - - - +
264A ALA* 4.1 24.4 + - + +
267A ALA* 4.0 21.8 - - + -
280A ILE* 4.0 24.9 - - + +
283A THR* 3.9 33.2 - - + -
284A TYR* 4.2 18.1 - - + +
467A LEU* 2.8 26.6 + - + +
469A LEU* 4.0 18.4 - - + +
476A TRP* 3.9 17.0 - - + +
477A ARG* 1.3 81.1 - - - +
479A GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 479 (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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263A GLU* 3.3 23.5 + - - -
287A HIS* 6.2 1.3 - - - -
466A ARG* 3.4 9.2 - - - +
467A LEU* 2.8 29.9 + - - +
477A ARG* 3.7 2.9 - - - +
478A LEU* 1.3 80.6 - - - +
480A ASP* 1.3 63.6 + - - -
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Residues in contact with ASP 480 (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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263A GLU* 4.1 6.7 - - - +
287A HIS* 3.0 23.4 + - - -
465A ASP 3.7 6.5 - - - +
466A ARG* 3.2 30.5 + - - -
467A LEU* 4.6 0.7 - - - +
479A GLY* 1.3 76.0 - - - -
481A ARG* 1.3 63.4 + - - +
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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