Contacts of the strand formed by residues 817 - 823 (chain B) in PDB entry 1ED8
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 PHE 817 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B LYS* 3.6 3.7 + - - +
544B ASN* 3.0 51.5 + - + +
545B ILE 2.9 23.7 + - - -
546B ILE* 4.0 17.3 - - + -
641B LEU* 4.2 7.2 - - - +
642B ALA* 3.0 29.2 - - + +
807B ILE* 4.6 13.2 - - + -
810B LEU* 3.6 30.1 - - + -
811B SER* 4.0 19.1 - - - -
813B ASN 5.7 0.4 - - - -
816B GLY* 1.4 73.8 - - - +
818B PHE* 1.3 71.1 + - - +
819B LEU* 3.9 21.3 - - + -
855B PHE* 4.2 22.2 - + - -
946B LEU* 4.5 2.6 - - - +
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Residues in contact with PHE 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ILE* 3.5 32.8 - - + +
547B LEU* 4.6 10.5 - - + -
632B ILE* 3.8 34.8 - - + -
633B LEU* 4.5 19.7 - - + -
636B ALA* 4.2 20.2 - - + -
641B LEU* 4.9 0.4 - - + +
642B ALA 3.0 5.3 + - - +
643B THR* 3.4 5.0 - - + -
644B GLY 3.0 25.8 + - - -
659B LEU* 4.3 16.4 - - + -
817B PHE* 1.3 77.7 - - - +
819B LEU* 1.3 68.0 + - - +
820B GLN* 4.1 28.5 - - + -
942B MET* 3.9 14.8 - - - -
946B LEU* 4.7 9.0 - - + -
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Residues in contact with LEU 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B ILE 2.8 11.3 + - - +
546B ILE* 3.3 16.2 - - + -
547B LEU* 2.7 33.8 + - - +
644B GLY* 3.5 29.6 - - - +
646B VAL* 4.2 7.9 - - + -
803B THR* 4.8 3.6 - - + +
806B ALA* 4.1 18.8 - - + -
807B ILE* 4.0 25.4 - - + -
810B LEU* 4.0 8.5 - - + -
817B PHE* 3.9 17.3 - - + -
818B PHE* 1.3 81.3 - - - +
820B GLN* 1.3 63.0 + - - +
821B VAL* 3.8 20.2 - - + -
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Residues in contact with GLN 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B LEU* 3.3 19.0 - - + +
549B ILE* 4.6 4.0 - - + -
609B TRP* 3.0 32.9 + - - -
644B GLY 3.1 7.0 + - - +
645B ASN* 3.6 3.4 + - - +
646B VAL* 2.8 33.4 + - - +
655B THR* 3.2 39.8 + - - +
656B PRO* 4.1 4.0 - - - +
659B LEU* 3.6 36.8 - - + +
818B PHE* 4.1 9.5 - - + -
819B LEU* 1.3 74.2 - - - +
821B VAL* 1.3 65.0 + - - +
822B GLU* 5.0 3.6 - - - +
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Residues in contact with VAL 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ILE* 4.4 7.2 - - + -
547B LEU 2.8 8.1 + - - +
548B LEU* 3.3 28.2 - - + +
549B ILE* 2.7 33.8 + - - +
646B VAL* 3.3 9.9 - - + -
799B LEU* 3.5 28.3 - - + -
803B THR* 3.5 28.3 - - + +
819B LEU* 3.8 28.0 - - + -
820B GLN* 1.3 78.3 - - - +
822B GLU* 1.3 55.0 + - - +
845B LEU* 5.0 0.8 - - + +
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Residues in contact with GLU 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B ILE* 3.4 13.5 - - + +
551B ASP* 2.9 13.5 - - + +
646B VAL 2.8 12.4 + - - +
647B SER* 2.7 27.6 + - - +
648B THR* 3.3 20.6 + - - -
649B ALA* 4.3 1.2 - - - +
655B THR* 3.0 31.7 + - + -
656B PRO* 3.6 7.0 - - + +
799B LEU* 3.8 10.9 - - - +
820B GLN* 5.1 4.5 - - - +
821B VAL* 1.3 73.3 - - - +
823B GLY* 1.3 59.2 + - - +
824B ALA* 3.3 22.5 + - - +
952B ZN 1.9 5.6 - - - -
962B MG 1.9 31.9 - - - -
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Residues in contact with GLY 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B ILE 2.8 12.6 + - - -
550B GLY* 3.8 2.4 - - - -
551B ASP 3.1 22.0 + - - -
648B THR* 4.1 3.1 - - - -
799B LEU* 3.8 18.1 - - - +
822B GLU* 1.3 67.4 - - - +
824B ALA* 1.3 61.2 + - - -
825B SER 3.5 2.6 + - - -
826B ILE* 3.9 13.1 + - - +
841B GLU* 5.2 4.7 - - - -
844B ASP* 5.5 1.3 - - - -
845B LEU* 4.0 15.4 - - - +
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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