Contacts of the strand formed by residues 471 - 474 (chain E) in PDB entry 6NYY
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 471 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527D GLU* 2.9 32.1 + - - +
530D LEU* 3.4 30.1 - - - +
531D ILE* 6.2 1.2 - - - +
534D ARG* 5.1 2.0 - - - +
551D ARG* 4.3 12.3 - - - +
319E GLU* 2.4 48.0 + - - +
322E GLU* 2.6 30.9 + - - +
323E PHE* 4.2 18.3 - - + -
341E PRO* 4.3 12.2 - - + +
343E GLY 3.5 2.2 + - - -
344E ALA* 3.3 16.2 - - + +
345E ILE* 2.8 30.6 + - - +
469E PHE 4.5 4.1 - - - -
470E ASP* 1.3 79.3 - - - +
472E GLN* 1.3 59.3 + - - +
473E ILE* 3.9 11.0 - - + -
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Residues in contact with GLN 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ARG* 3.5 25.2 + - - +
552D VAL 5.8 0.2 - - - +
555D GLY* 4.6 4.2 - - - -
556D LEU 4.3 6.1 + - - -
345E ILE* 3.7 17.9 - - + +
347E THR* 4.5 17.9 + - + +
456E PRO* 4.6 11.9 - - - +
464E LEU* 5.4 16.7 - - + +
469E PHE 6.0 0.4 - - - +
470E ASP 4.2 1.0 + - - -
471E ARG* 1.3 71.7 - - - +
473E ILE* 1.3 63.5 + - - +
474E PHE* 4.2 1.3 + - + -
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Residues in contact with ILE 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ARG* 3.9 14.1 - - - +
556D LEU* 3.7 20.6 - - + -
316E ALA* 4.0 15.5 - - + -
319E GLU* 3.8 15.9 - - + +
320E ILE* 3.7 29.8 - - + -
344E ALA* 4.2 19.7 - - + -
345E ILE 3.0 14.0 + - - +
346E LEU* 3.3 17.1 - - + -
347E THR* 2.8 28.5 + - - -
471E ARG* 4.2 8.5 - - + -
472E GLN* 1.3 78.0 - - - +
474E PHE* 1.3 61.5 + - - +
475E ILE* 3.9 6.7 + - + -
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Residues in contact with PHE 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D LEU* 4.7 5.5 - - + +
558D LYS* 2.5 43.9 + - - +
561D GLN* 6.0 1.3 - - - -
600D GLY* 3.8 36.6 - - - -
601D LYS* 3.6 39.5 - - + +
316E ALA* 4.9 0.5 - - - +
347E THR* 3.2 24.9 - - - +
348E GLY* 3.7 18.4 - - - -
349E PRO* 4.4 6.3 - - + -
472E GLN* 4.2 2.1 + - + +
473E ILE* 1.3 73.4 - - - +
475E ILE* 1.3 59.8 + - - +
476E GLY* 3.7 26.2 - - - -
477E PRO* 4.9 2.7 - - + -
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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