Contacts of the strand formed by residues 551 - 559 (chain F) in PDB entry 2JJD
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 ILE 551 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508F GLU 5.7 0.2 - - - +
511F TRP* 3.9 30.3 - - + +
512F ARG* 4.7 8.7 - - + +
515F TRP* 4.1 26.0 - - + -
547F THR* 3.4 4.5 - - - -
548F HIS* 3.1 34.3 + - + +
549F GLY 3.2 2.6 - - - +
550F GLU* 1.3 82.6 - - + +
552F THR* 1.3 64.9 + - - +
553F ILE* 3.4 13.9 - - + -
571F VAL* 3.2 30.7 - - + -
572F THR 3.2 2.2 - - - +
573F LEU* 3.2 33.0 - - + -
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Residues in contact with THR 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545F SER* 4.3 14.1 - - - -
546F VAL 3.4 12.8 - - - +
547F THR* 3.7 13.0 - - - -
550F GLU 4.9 0.2 + - - -
551F ILE* 1.3 74.9 + - - +
553F ILE* 1.3 78.6 + - - +
554F GLU* 4.7 2.2 - - + +
570F LEU 3.3 4.5 - - - +
572F THR* 2.8 46.5 + - - +
574F ASN* 4.6 12.3 - - - +
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Residues in contact with ILE 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F TRP* 3.7 47.3 - - + +
541F PRO* 3.3 18.1 - - + +
545F SER* 3.1 3.7 - - - -
546F VAL* 2.8 46.8 + - + +
548F HIS* 5.2 3.1 - - + +
551F ILE* 3.4 23.8 - - + +
552F THR* 1.3 86.2 - - - +
554F GLU* 1.3 59.4 + - - +
569F PHE* 3.5 39.7 - - + -
570F LEU 3.7 1.1 - - - -
571F VAL* 3.7 8.3 - - + -
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Residues in contact with GLU 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F GLY 3.6 8.1 - - - +
545F SER* 4.1 13.0 - - - -
552F THR* 4.2 3.5 - - + +
553F ILE* 1.3 74.3 - - - +
555F ILE* 1.3 62.2 + - - +
556F LYS* 3.8 0.3 + - - +
569F PHE* 3.1 7.9 - - - -
570F LEU* 2.8 47.9 + - + +
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Residues in contact with ILE 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541F PRO* 3.5 25.5 - - - +
542F THR* 3.5 21.1 - - + +
543F GLU 3.4 26.6 - - - +
544F GLY 3.4 9.1 + - - +
554F GLU* 1.3 72.8 - - - +
556F LYS* 1.3 61.2 + - - +
557F ASN 3.5 17.9 - - - +
558F ASP* 3.8 23.3 - - + -
567F ARG* 4.0 13.9 - - - -
568F ASP 3.4 6.5 - - - +
569F PHE* 3.8 15.9 - - + -
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Residues in contact with LYS 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F GLU 3.8 2.7 + - - +
555F ILE* 1.3 74.9 - - - +
557F ASN* 1.3 59.2 + - - +
568F ASP* 2.8 20.7 + - + +
569F PHE* 5.2 2.7 - - - +
570F LEU* 5.3 13.5 - - + +
586F VAL* 6.5 0.9 - - + -
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Residues in contact with ASN 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555F ILE* 3.5 9.5 - - - +
556F LYS* 1.3 78.8 - - + +
558F ASP* 1.3 64.7 + - - +
559F THR* 5.5 2.2 - - - +
566F ILE 4.4 0.9 - - - +
567F ARG* 3.5 0.7 - - - -
568F ASP* 3.0 47.3 + - + +
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Residues in contact with ASP 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542F THR* 5.6 3.4 - - + +
555F ILE* 3.8 20.9 - - + -
557F ASN* 1.3 78.6 - - - +
559F THR* 1.3 59.5 + - - +
560F LEU 4.2 1.0 + - - -
566F ILE 3.3 8.1 - - - +
567F ARG* 4.5 12.6 - - + +
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Residues in contact with THR 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F ASN* 5.5 2.2 - - - +
558F ASP* 1.3 73.4 - - - +
560F LEU* 1.3 58.2 + - - +
561F SER* 3.3 8.9 + - - -
565F SER* 4.4 1.6 - - - -
566F ILE* 2.9 43.8 + - - +
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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