Contacts of the strand formed by residues 474 - 477 (chain A) in PDB entry 2EIE
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 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A LEU* 3.5 17.2 - - - +
436A TYR* 2.8 46.2 + - + +
437A PHE* 3.1 20.9 + - + +
439A ARG* 2.7 31.5 + - - +
452A THR 3.7 0.3 - - - +
453A PHE* 4.3 0.5 - - - -
454A ILE* 2.8 45.0 + - + +
472A THR 4.3 1.1 - - - +
473A PRO* 1.3 76.5 - - - +
475A ILE* 1.3 63.8 + - - +
483A PHE* 3.9 12.8 - - + -
484A TYR 3.4 8.7 - - - +
485A LYS* 4.8 2.9 - - + -
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 4.3 15.3 - - + -
451A SER* 3.6 28.7 - - - +
452A THR 3.3 5.4 - - - +
453A PHE* 3.8 23.1 - - + -
474A GLU* 1.3 80.7 - - - +
476A TYR* 1.3 63.8 + - - +
477A VAL* 3.8 8.9 + - + -
482A THR 3.7 1.2 - - - +
483A PHE* 3.3 4.6 - - - -
484A TYR* 2.8 41.1 + - + -
486A GLN* 3.6 38.8 - - + +
528A PHE* 4.7 6.1 - - + -
530A PRO* 5.2 4.7 - - + -
531A ASN 6.0 0.9 - - - +
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Residues in contact with TYR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 4.6 6.8 + + - -
397A LEU* 3.6 26.5 - - + -
416A ILE* 3.7 31.7 - - + +
431A ALA* 4.2 4.3 - - + -
432A SER* 4.5 0.7 - - - -
451A SER* 3.2 8.1 - - - -
452A THR* 3.0 33.3 + - - +
454A ILE* 4.9 0.8 - - + +
474A GLU 4.3 0.2 - - - -
475A ILE* 1.3 73.0 - - - +
477A VAL* 1.3 59.2 + - - +
478A PRO* 3.4 31.3 + - + +
481A ASP* 2.6 40.1 + - - +
482A THR 3.6 22.7 - - - -
483A PHE* 3.6 42.3 - + + -
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Residues in contact with VAL 477 (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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451A SER* 4.4 7.6 - - - -
475A ILE* 4.2 12.8 - - + -
476A TYR* 1.3 78.3 - - - +
478A PRO* 1.4 58.9 - - + +
479A GLU* 3.7 19.1 - - + +
480A GLN* 3.3 29.6 + - + +
481A ASP* 2.9 23.0 + - - -
482A THR 2.9 17.4 + - - +
484A TYR* 3.7 25.6 - - + -
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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