Contacts of the strand formed by residues 461 - 466 (chain A) in PDB entry 4REW
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 TYR 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ILE* 3.2 13.2 - - - +
403A ARG 3.1 22.5 + - - +
404A SER 5.0 0.7 - - - -
405A GLN 3.0 28.7 - - - +
406A SER* 4.2 4.2 - - - +
407A ARG* 3.4 45.0 + - + +
410A ASP* 4.9 5.6 - - - +
453A LEU* 3.8 16.2 - - + -
454A TYR 3.5 15.0 - - - +
455A GLN* 3.6 35.0 + - + -
456A VAL* 4.3 2.9 - - - +
458A SER 5.1 7.9 + - - -
459A ARG 5.2 1.6 - - - -
460A THR* 1.3 84.7 - - - +
462A LEU* 1.3 61.3 + - - +
205B PRO* 3.9 11.4 - - + +
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Residues in contact with LEU 462 (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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399A HIS* 3.7 16.8 - - + -
400A LEU* 3.7 34.8 - - + +
401A GLY 3.2 17.7 - - - +
402A ILE* 3.5 19.5 - - + +
452A GLN 3.7 0.3 - - - +
453A LEU* 3.2 7.2 - - - +
454A TYR* 2.7 43.9 + - + +
456A VAL* 3.5 24.0 - - + +
461A TYR* 1.3 74.1 - - - +
463A LEU* 1.3 75.6 + - - +
464A ASP 4.4 1.1 - - - +
208B LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 463 (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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400A LEU* 3.0 27.4 - - - +
401A GLY* 3.2 13.1 + - - +
410A ASP* 6.2 1.3 - - - +
411A ILE* 5.1 10.3 - - + -
414A GLU* 4.7 12.3 - - + -
451A LEU* 3.9 38.1 - - + +
452A GLN 3.6 19.1 - - - +
453A LEU* 3.9 16.1 - - + +
462A LEU* 1.3 79.7 - - - +
464A ASP* 1.3 68.2 + - - +
465A PHE* 3.8 16.1 - - + -
548A LEU* 4.7 16.4 - - + -
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Residues in contact with ASP 464 (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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399A HIS* 4.0 8.1 + - - -
400A LEU* 3.3 23.4 - - + +
450A SER 4.5 0.9 - - - +
451A LEU* 3.0 30.7 - - - +
452A GLN 2.9 11.4 + - - +
454A TYR* 3.3 30.0 + - + -
462A LEU* 4.1 0.4 + - + -
463A LEU* 1.3 71.9 - - - +
465A PHE* 1.3 71.3 + - - +
466A ARG* 3.3 12.1 + - - +
212B LEU* 4.2 1.8 - - - +
240B HIS* 2.8 41.7 + - - +
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Residues in contact with PHE 465 (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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400A LEU* 3.0 19.2 - - + +
401A GLY* 4.6 11.0 - - - -
449A MET* 3.5 12.8 - - + -
450A SER 3.5 1.8 - - - -
451A LEU* 3.8 18.8 - - + -
463A LEU* 3.8 31.4 - - + -
464A ASP* 1.3 81.2 - - - +
466A ARG* 1.3 58.2 + - - +
537A PHE* 4.0 1.8 - - - -
541A CYS* 3.4 29.6 - - + -
544A LEU* 4.1 14.8 - - + -
545A ILE* 3.8 31.4 - - + -
548A LEU* 5.2 4.0 - - + -
240B HIS* 3.3 3.1 - - - -
241B LEU* 2.6 56.0 + - + +
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Residues in contact with ARG 466 (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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168A ASP 4.7 1.1 - - - -
169A GLY* 3.3 23.4 + - - -
170A GLU* 2.6 28.4 + - - -
433A TYR* 3.0 40.0 + - - -
449A MET* 3.1 7.9 - - - +
450A SER* 2.7 54.6 + - - +
452A GLN* 5.0 4.2 - - - +
454A TYR* 4.2 9.3 + - - -
464A ASP* 3.3 14.1 + - - +
465A PHE* 1.3 74.8 - - - +
467A SER* 1.3 74.9 + - - +
537A PHE* 3.4 6.0 - - - -
239B ASN* 3.5 20.9 - - + +
240B HIS* 3.1 30.0 - - - +
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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