Contacts of the strand formed by residues 608 - 612 (chain F) in PDB entry 6Q2J
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 608 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523F LYS* 4.4 21.9 + - - +
543F TRP* 4.6 8.5 - - + -
556F SER* 3.3 27.8 - - - +
557F THR* 6.0 0.2 - - - -
607F GLY* 1.3 70.2 - - - -
609F CYS* 1.3 59.5 + - - +
610F ASN* 3.9 5.1 + - - +
619F PHE 3.4 2.4 - - - +
620F CYS* 3.3 1.6 - - - -
621F GLU 2.6 42.7 + - - +
622F PRO* 4.2 10.8 - - + +
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Residues in contact with CYS 609 (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 PHE* 3.8 20.0 - - + -
556F SER 3.4 8.3 + - - -
557F THR* 3.6 9.3 + - - -
583F GLN* 3.3 20.1 - - - +
602F ILE* 4.0 13.5 - - + -
605F GLY* 3.8 19.5 - - - -
607F GLY 3.5 7.6 + - - -
608F THR* 1.3 73.5 - - - +
610F ASN* 1.3 60.7 + - - +
611F CYS* 4.6 1.6 - - - -
619F PHE 3.1 4.5 - - - -
620F CYS* 2.0 48.2 - - - -
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Residues in contact with ASN 610 (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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520F ALA* 3.6 8.1 - - - +
521F VAL* 4.2 6.1 + - - +
522F SER 3.4 23.3 - - - +
523F LYS* 3.3 33.0 - - + +
557F THR* 5.5 0.2 - - - -
583F GLN* 5.3 0.7 - - - -
608F THR* 3.9 5.3 + - - +
609F CYS* 1.3 74.1 - - - +
611F CYS* 1.3 64.0 + - - +
612F PHE* 4.3 15.7 - - - -
618F CYS* 3.3 3.6 - - - -
619F PHE* 2.9 55.9 + - - +
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Residues in contact with CYS 611 (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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520F ALA* 3.0 25.6 + - + +
521F VAL* 3.9 6.3 - - - -
582F PRO* 3.9 22.9 - - + -
583F GLN* 4.0 25.1 - - - -
586F LEU* 5.4 0.9 - - + -
602F ILE* 4.1 5.6 - - - -
609F CYS 4.6 1.3 - - - -
610F ASN* 1.3 76.9 - - - +
612F PHE* 1.3 65.6 + - - +
613F PRO* 3.5 9.2 - - - +
617F LYS 3.5 4.0 - - - -
618F CYS* 2.0 48.0 - - - -
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Residues in contact with PHE 612 (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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202A HIS* 5.7 10.8 - + + -
247A GLN 5.7 2.0 - - - -
249A ARG* 5.6 7.2 - - + -
521F VAL* 3.6 35.4 - - + -
523F LYS* 6.2 1.8 - - + -
586F LEU* 5.7 0.6 - - - +
610F ASN* 4.3 17.3 - - + -
611F CYS* 1.3 74.4 - - - +
613F PRO* 1.3 63.7 - - + +
614F GLU* 3.4 13.5 - - + +
615F GLU* 4.8 17.5 - - + +
616F GLU* 2.8 21.8 + - - -
617F LYS* 2.9 23.1 + - + +
619F PHE* 3.7 38.4 - + - -
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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