Contacts of the strand formed by residues 492 - 497 (chain A) in PDB entry 1E3H
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 LEU 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A GLY* 1.3 73.9 - - - +
493A ILE* 1.3 69.8 + - - +
503A TYR* 4.3 15.7 - - + -
504A VAL 3.3 20.6 - - - +
505A ALA* 3.8 19.5 - - + +
506A LEU* 5.3 0.6 - - - +
517A GLY* 3.6 4.1 - - - -
518A ASP* 2.8 27.9 + - - +
519A MSE 2.9 42.7 + - + -
521A PHE* 4.9 2.7 - - + -
539A LEU* 4.2 18.6 - - + -
542A ILE* 4.4 11.7 - - + -
546A VAL* 4.4 16.4 - - + -
550A ALA* 4.7 9.9 - - + -
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Residues in contact with ILE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 6.3 0.4 - - + -
330A ARG* 3.8 43.7 - - + +
333A VAL* 4.0 31.9 - - + -
334A ILE* 4.2 26.2 - - + -
492A LEU* 1.3 79.0 - - - +
494A SER* 1.3 63.2 + - - +
502A HIS 3.5 1.2 - - - +
503A TYR* 3.3 6.6 - - - +
504A VAL* 2.8 43.0 + - + +
506A LEU* 4.1 19.3 - - + -
516A PHE* 5.0 6.5 - - + +
517A GLY* 4.3 7.6 - - - -
518A ASP* 3.6 2.7 - - - -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 3.0 17.6 + - - -
492A LEU 4.2 0.2 - - - -
493A ILE* 1.3 72.7 - - - +
495A GLN* 1.3 60.8 + - - +
501A THR* 3.6 10.2 - - - +
502A HIS 3.3 4.0 - - - -
503A TYR* 3.1 31.6 + - - -
518A ASP* 2.6 17.9 + - - +
539A LEU* 4.0 27.5 - - - +
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Residues in contact with GLN 495 (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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327A SER* 5.8 1.4 + - - -
330A ARG* 3.3 40.3 + - + +
331A GLU* 5.7 0.9 - - - +
334A ILE* 3.2 36.8 - - + +
493A ILE* 4.1 1.0 - - - +
494A SER* 1.3 72.1 + - - +
496A GLU* 1.3 73.0 + - - +
497A ILE* 3.4 10.8 + - + +
501A THR* 4.3 3.6 - - - -
502A HIS* 2.6 41.8 + - + +
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Residues in contact with GLU 496 (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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495A GLN* 1.3 82.5 + - - +
497A ILE* 1.3 57.0 + - - +
498A ASN 3.5 4.0 + - - -
499A GLY* 3.6 33.1 + - - +
500A GLU 3.2 16.2 - - - +
501A THR* 3.7 16.0 + - + +
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Residues in contact with ILE 497 (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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334A ILE* 3.4 31.6 - - + -
335A ALA* 5.6 1.8 - - - +
495A GLN* 3.4 13.8 + - + +
496A GLU* 1.3 70.7 - - - +
498A ASN* 1.3 77.8 + - + +
500A GLU* 2.8 17.0 + - - +
502A HIS* 3.4 32.4 + - + +
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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