Contacts of the strand formed by residues 466 - 470 (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 ARG 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A GLU* 4.8 4.6 + - - -
460A ARG* 5.2 3.4 + - - +
463A GLY* 3.1 25.0 + - - +
464A LEU 3.2 0.2 - - - -
465A ASP* 1.3 106.2 + - - +
467A LEU* 1.3 62.1 + - - +
468A PHE* 3.7 19.1 + - + -
477A ARG* 4.2 29.0 - - - +
479A GLY 3.4 8.0 + - - +
480A ASP* 3.2 26.2 + - - -
481A ARG* 3.3 22.1 + - - -
571A TRP* 3.8 27.7 - - + -
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 4.2 12.6 - - + +
284A TYR* 5.5 1.6 - - - -
287A HIS* 3.7 36.1 - - + -
292A LEU* 4.1 14.4 - - + -
293A MET* 4.3 10.5 - - + -
466A ARG* 1.3 72.6 - - - +
468A PHE* 1.3 62.5 - - - +
477A ARG* 3.6 5.0 - - - +
478A LEU* 2.8 42.0 + - + -
479A GLY 2.8 21.3 + - - +
480A ASP 4.6 5.8 - - - +
481A ARG* 4.0 18.9 - - + +
523A TYR* 3.6 31.2 - - + -
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Residues in contact with PHE 468 (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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463A GLY 3.9 8.3 - - - -
466A ARG* 3.7 31.2 - - + -
467A LEU* 1.3 76.7 - - - +
469A LEU* 1.3 60.0 + - - +
475A MET* 3.8 33.2 - - + -
476A TRP 3.2 17.9 - - - -
477A ARG* 3.7 30.7 - - + -
478A LEU* 5.0 1.1 - - - -
523A TYR* 3.1 45.1 + - - +
525A LEU* 3.7 41.7 - - + +
570A ASP 3.8 18.8 - - - -
571A TRP* 4.0 10.3 - + - -
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Residues in contact with LEU 469 (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 GLU* 3.8 35.2 - - + +
280A ILE* 3.9 25.4 - - + -
283A THR* 3.8 12.8 - - - +
468A PHE* 1.3 76.2 - - - +
470A GLU* 1.3 74.5 + - - +
471A CYS* 4.6 6.3 - - + -
474A HIS 3.4 1.9 - - - +
475A MET* 3.5 4.0 - - - -
476A TRP* 2.8 41.9 + - + +
478A LEU* 4.0 16.6 - - + -
523A TYR* 3.8 27.8 - - + +
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Residues in contact with GLU 470 (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 GLU* 5.8 0.2 - - - +
389A ALA 3.8 10.7 - - - +
391A ILE* 3.9 19.1 - - + +
394A GLY* 3.3 1.0 - - - -
395A ALA* 2.8 36.7 + - + +
396A SER* 2.8 34.6 + - - -
469A LEU* 1.3 81.5 - - - +
471A CYS* 1.3 67.9 + - - +
473A ALA* 5.3 4.3 - - - +
474A HIS 3.3 11.4 - - - +
475A MET* 3.5 12.6 - - - -
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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
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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