Contacts of the strand formed by residues 655 - 660 (chain F) in PDB entry 2AJQ
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 655 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452F ARG* 4.8 0.2 + - - -
474F ILE 3.2 11.2 - - - +
475F ASP* 3.8 14.5 - - + +
625F TRP* 4.7 2.0 - - - -
650F ALA 4.0 0.2 - - - +
651F TRP* 3.3 5.6 - - - -
652F VAL* 2.8 43.9 + - + +
653F HIS 3.3 3.4 + - - -
654F ASP* 1.3 85.1 - - - +
656F ILE* 1.3 65.6 + - - +
657F GLN* 3.0 14.6 + - - +
700F TRP* 2.9 23.7 + - - -
704F HIS* 2.6 45.1 + - + -
922X 2DT 4.6 11.7 + - - +
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Residues in contact with ILE 656 (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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227F GLN* 5.9 0.2 - - - +
472F ALA 3.9 0.2 - - - +
474F ILE* 2.7 70.5 + - + +
625F TRP* 4.0 20.0 - - + -
626F ILE* 3.4 33.0 - - + -
629F THR* 5.0 5.2 - - + +
648F TYR* 4.5 22.4 - - + +
650F ALA 3.3 7.9 - - - +
651F TRP* 4.1 10.1 - - + -
655F GLU* 1.3 78.9 - - - +
657F GLN* 1.3 68.9 + - - +
658F VAL* 4.1 14.4 - - + -
673F ALA* 4.9 3.8 - - + -
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Residues in contact with GLN 657 (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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232F PHE* 4.4 6.1 - - + -
471F GLN* 2.8 31.3 + - - +
472F ALA 3.5 1.3 - - - -
473F GLY* 3.5 21.5 - - - -
474F ILE 4.2 0.2 - - - +
648F TYR* 4.2 0.5 - - - -
649F MET* 3.0 34.7 + - + +
650F ALA* 2.9 18.2 + - + +
652F VAL* 6.0 0.2 - - + -
655F GLU* 3.0 25.6 + - + +
656F ILE* 1.3 86.8 + - - +
658F VAL* 1.3 62.2 + - - +
700F TRP* 3.4 35.1 - - + +
703F CYS* 3.6 5.9 + - - +
704F HIS* 3.5 10.3 + - - -
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Residues in contact with VAL 658 (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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471F GLN* 3.5 2.8 - - - -
472F ALA* 2.9 42.8 + - + +
474F ILE* 4.6 1.1 - - + -
646F PHE* 4.1 24.9 - - + -
647F ALA 3.7 9.6 - - - +
648F TYR* 4.2 16.8 - - + -
649F MET* 3.8 4.0 - - - +
656F ILE* 4.2 23.8 - - + -
657F GLN* 1.3 78.1 - - - +
659F GLY* 1.3 75.3 + - - +
660F CYS* 3.7 7.0 - - - -
669F VAL* 4.2 24.9 - - + -
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Residues in contact with GLY 659 (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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457F ALA* 4.0 4.0 - - - -
469F TRP* 3.3 14.4 - - - -
470F VAL 3.6 6.3 - - - -
642F TRP* 4.8 2.2 - - - -
646F PHE* 3.0 7.3 - - - +
647F ALA 2.7 39.3 + - - -
649F MET* 3.7 19.1 - - - +
658F VAL* 1.3 73.8 - - - +
660F CYS* 1.3 57.8 + - - -
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Residues in contact with CYS 660 (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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469F TRP* 3.1 8.0 - - - +
470F VAL* 2.7 43.3 + - - +
472F ALA* 4.1 6.3 - - - -
645F ASP 3.6 3.8 - - - -
646F PHE* 4.5 0.4 - - - -
658F VAL* 3.7 14.1 - - - -
659F GLY* 1.3 80.3 - - - -
661F ARG* 1.3 62.1 + - - +
662F THR 3.2 17.1 + - - +
665F ILE* 3.8 8.3 - - + -
666F ALA* 3.6 29.6 - - + +
669F VAL* 3.8 20.4 - - - -
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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