Contacts of the strand formed by residues 447 - 451 (chain A) in PDB entry 3I5Y
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 GLU 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A HIS* 2.9 30.0 + - - -
366A GLN* 3.9 12.2 + - - +
370A ARG* 4.4 9.7 + - - +
374A TYR* 2.5 45.3 + - + +
375A LYS 3.4 2.0 + - - -
376A ALA* 3.2 5.4 - - - +
377A ILE 3.0 24.1 + - - -
445A VAL* 3.5 5.1 - - - +
446A HIS* 1.3 85.2 - - - +
448A VAL* 1.3 62.9 + - - +
449A LEU* 3.5 10.6 - - + +
467A THR* 4.7 0.9 - - - -
475A SER* 3.2 27.2 + - - +
477A VAL* 4.6 5.5 - - - +
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Residues in contact with VAL 448 (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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377A ILE* 3.3 10.1 - - + +
379A PHE* 3.6 24.0 - - + -
445A VAL* 4.6 1.1 - - + -
447A GLU* 1.3 76.6 - - - +
449A LEU* 1.3 66.9 + - - +
450A GLN* 4.5 3.0 - - + +
463A ARG* 3.4 33.4 - - + +
464A ILE* 3.9 13.9 - - + +
466A ARG* 4.0 9.0 - - + -
467A THR* 3.8 30.7 - - + +
475A SER 3.0 6.3 + - - -
476A SER* 3.2 6.7 - - - -
477A VAL 3.1 23.7 + - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 5.1 1.1 - - + +
362A HIS* 3.9 17.0 - - + +
363A ILE* 3.7 35.9 - - + -
374A TYR* 4.1 8.3 - - - +
376A ALA* 4.9 7.6 - - + -
377A ILE 2.7 14.5 + - - +
378A ILE* 3.3 22.4 - - + -
379A PHE* 2.8 28.4 + - - -
429A ILE* 6.2 0.7 - - + -
447A GLU* 3.5 26.9 - - + +
448A VAL* 1.3 81.3 - - - +
450A GLN* 1.3 64.4 + - - +
477A VAL* 3.5 9.9 - - + -
479A PHE* 4.1 20.4 - - + -
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Residues in contact with GLN 450 (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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379A PHE* 3.9 8.1 - - + -
448A VAL* 4.5 3.6 - - + -
449A LEU* 1.3 80.0 - - - +
451A ILE* 1.3 61.9 + - - +
452A GLY 3.7 1.1 + - - +
454A PRO* 4.1 9.9 - - - +
460A TYR* 3.3 35.2 - - - -
463A ARG* 2.9 49.5 + - - +
464A ILE* 3.7 16.0 - - - +
476A SER* 5.6 0.6 - - - -
477A VAL 3.0 10.5 + - - +
478A LEU* 3.7 25.3 - - + +
479A PHE* 2.7 36.6 + - - +
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Residues in contact with ILE 451 (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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352A PHE* 4.4 9.6 - - + -
355A SER* 3.9 26.2 - - - +
356A ILE* 4.1 8.5 - - + +
359A ALA* 3.7 28.9 - - + -
378A ILE* 3.8 16.2 - - + -
379A PHE 3.1 14.6 + - - +
380A ALA* 3.9 0.9 - - - -
381A PRO* 3.6 22.0 - - - +
385A PHE* 3.9 23.8 - - + -
389A LEU* 3.7 31.4 - - + -
449A LEU 4.3 0.4 - - - -
450A GLN* 1.3 73.4 - - - +
452A GLY* 1.3 60.5 + - - +
463A ARG* 5.1 1.5 + - - -
479A PHE* 3.7 6.3 - - + -
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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