Contacts of the strand formed by residues 476 - 480 (chain E) in PDB entry 3EI4
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 VAL 476 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E ILE* 3.9 28.5 - - + -
470E GLN 3.6 2.7 - - - -
471E ILE* 3.8 17.7 - - + +
475E SER* 1.3 78.1 - - - +
477E ARG* 1.3 62.8 + - - +
489E GLU* 3.4 3.1 - - - -
490E TRP* 2.8 45.1 + - + +
498E ILE* 3.7 16.2 - - + -
508E VAL* 4.8 3.1 - - + -
510E VAL* 3.9 10.8 - - + -
519E LEU* 4.4 9.2 - - + -
526E LEU* 3.1 28.7 - - + +
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Residues in contact with ARG 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450E GLY* 2.6 38.2 + - - +
451E PHE 5.1 0.2 - - - -
452E VAL* 3.3 37.9 - - - +
468E LEU 4.0 0.2 - - - +
469E ILE* 3.2 6.7 - - - +
470E GLN* 2.6 70.7 + - + +
472E THR* 4.8 0.7 - - - -
475E SER* 3.6 16.5 + - - +
476E VAL* 1.3 72.3 - - - +
478E LEU* 1.3 60.7 + - - +
479E VAL* 4.0 1.5 + - + -
486E LEU* 3.4 42.3 - - + +
488E SER 3.9 2.7 - - - -
489E GLU* 3.6 18.8 + - + +
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Residues in contact with LEU 478 (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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463E VAL* 3.9 4.9 - - + -
467E GLN* 3.5 40.8 - - + +
468E LEU 3.5 15.5 - - - +
469E ILE* 4.8 3.8 - - + -
476E VAL 4.0 0.2 + - - -
477E ARG* 1.3 73.5 - - - +
479E VAL* 1.3 55.2 + - - +
486E LEU* 3.6 1.1 - - - +
487E VAL* 2.6 40.1 + - + +
488E SER* 2.9 22.4 + - - +
521E ILE* 3.9 14.4 - - + -
522E HIS 3.9 5.4 - - - +
525E GLU 3.8 30.3 - - - +
526E LEU* 3.7 27.6 - - + -
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Residues in contact with VAL 479 (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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449E MET 3.3 20.9 - - - +
450E GLY* 3.5 32.3 - - - +
451E PHE* 3.7 17.7 - - + -
467E GLN* 3.2 11.1 - - - +
468E LEU* 2.6 47.4 + - + +
477E ARG* 4.8 2.9 - - + +
478E LEU* 1.3 79.9 - - - +
480E SER* 1.3 67.0 + - - +
484E LYS* 4.1 9.0 - - + -
485E ALA 3.2 21.1 - - - +
486E LEU* 4.5 1.8 - - - -
487E VAL* 4.7 1.1 - - - -
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Residues in contact with SER 480 (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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466E GLN 4.5 0.4 - - - -
467E GLN* 4.3 9.4 - - - -
468E LEU* 5.1 0.7 - - - -
478E LEU 4.3 0.2 + - - -
479E VAL* 1.3 73.0 - - - +
481E GLN* 1.3 67.5 + - - +
482E GLU 3.5 8.7 - - - -
483E PRO 2.6 23.2 + - - +
484E LYS* 3.1 20.2 - - - +
485E ALA* 3.0 18.7 + - - +
487E VAL* 3.8 21.8 - - - +
524E GLN* 5.9 1.3 - - - -
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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