Contacts of the strand formed by residues 551 - 554 (chain B) in PDB entry 1GXD
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 THR 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B TYR* 3.3 44.7 - - + +
498B PRO* 3.8 18.5 - - - +
542B ALA* 4.2 2.2 - - + -
543B PHE 3.2 16.9 + - - +
544B ASN* 4.5 3.5 - - - +
550B LYS* 1.3 78.0 + - - +
552B TYR* 1.3 64.6 + - - +
553B ILE* 3.8 11.9 + - + -
561B ARG* 3.2 6.9 - - - +
562B TYR* 2.9 47.3 + - - +
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Residues in contact with TYR 552 (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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542B ALA* 3.3 13.1 - - - -
543B PHE* 3.1 40.7 + + + -
545B TRP* 3.9 6.3 + - - -
548B ASN* 2.8 50.7 + - + +
550B LYS* 4.1 8.7 - - + -
551B THR* 1.3 75.5 - - - +
553B ILE* 1.3 62.1 + - - +
554B PHE* 3.0 29.0 - - + -
559B PHE* 3.6 17.0 - + + -
560B TRP 3.3 5.2 - - - +
561B ARG* 3.3 35.0 + - - -
581B TRP* 3.4 27.9 - + - -
187D GLU* 5.3 1.9 - - - +
188D PHE* 3.5 13.8 + + - +
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Residues in contact with ILE 553 (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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495B TYR* 4.8 3.8 - - + +
506B PHE* 4.0 17.5 - - + -
532B LEU* 4.9 5.4 - - + -
539B VAL* 3.3 39.0 - - + -
541B ALA 3.8 4.0 - - - +
542B ALA* 5.0 0.4 - - + -
551B THR* 3.9 26.2 - - + +
552B TYR* 1.3 69.0 - - - +
554B PHE* 1.3 61.7 + - - +
555B ALA* 5.5 0.4 - - + -
559B PHE* 3.2 3.7 - - - -
560B TRP* 2.6 64.0 + - + -
562B TYR* 4.1 22.7 - - + +
569B MET* 4.8 9.4 - - + -
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Residues in contact with PHE 554 (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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539B VAL* 3.7 4.0 - - - -
540B ASP* 3.1 27.4 + - + -
541B ALA* 3.5 33.0 + - + +
542B ALA 4.6 0.2 - - - -
543B PHE* 3.7 22.4 - + - -
552B TYR* 3.0 47.3 - + + -
553B ILE* 1.3 73.8 - - - +
555B ALA* 1.3 62.4 + - - +
556B GLY 3.9 1.6 - - - +
559B PHE* 3.7 13.2 - + + -
577B ILE* 3.7 32.5 - - + -
581B TRP* 4.1 20.0 - - - -
588B LEU* 4.0 18.2 - - + +
591B VAL* 4.0 9.2 - - + -
602B PHE* 4.1 13.9 - + - -
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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