Contacts of the strand formed by residues 616 - 619 (chain B) in PDB entry 6IWQ
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 ARG 616 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610B TYR* 3.5 2.8 - - - -
611B PHE* 2.8 40.9 + - + -
614B LEU* 2.5 49.6 - - + +
615B HIS* 1.3 78.6 - - - +
617B PHE* 1.3 63.9 + - - +
618B THR* 4.1 11.7 - - + +
625B CYS* 4.0 8.9 - - + +
640B CYS* 3.1 41.1 + - - +
642B SER* 6.2 1.6 - - - -
647B GLN 5.1 1.1 - - - +
648B LYS* 2.5 50.4 - - + +
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Residues in contact with PHE 617 (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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537B ILE* 4.0 28.0 - - + -
573B ILE* 4.2 10.3 - - + -
579B LEU* 4.6 18.2 - - + -
608B TRP* 5.2 6.1 - - + -
609B GLN 3.8 4.3 - - - -
610B TYR* 3.5 49.6 - + + -
616B ARG* 1.3 73.7 - - - +
618B THR* 1.3 61.4 + - - +
625B CYS* 3.3 5.4 - - - +
626B LEU* 2.9 57.2 + - + -
649B TRP* 3.7 31.7 - + + -
651B MET* 4.0 23.3 - - + -
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Residues in contact with THR 618 (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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607B GLU 3.6 5.7 - - - +
608B TRP* 3.9 5.1 - - - -
609B GLN* 3.2 34.0 + - - +
611B PHE* 3.1 35.0 - - + -
616B ARG* 4.5 20.0 - - + +
617B PHE* 1.3 78.2 - - - +
619B HIS* 1.3 71.3 + - - +
620B ILE* 3.2 5.7 + - - +
623B GLY* 5.4 0.5 - - - -
624B LYS 3.4 10.1 - - - -
625B CYS* 4.4 4.9 - - + -
640B CYS* 4.8 3.1 - - - -
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Residues in contact with HIS 619 (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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588B LYS* 3.5 26.9 - - + +
607B GLU* 3.6 28.0 + - + +
608B TRP* 4.3 20.8 - + + -
617B PHE 4.3 0.4 + - - -
618B THR* 1.3 76.2 + - - +
620B ILE* 1.3 74.2 + - - +
621B PRO* 2.8 40.0 + - + +
622B SER* 3.3 19.5 + - - +
623B GLY* 3.2 17.8 - - - -
624B LYS 2.7 18.5 + - - +
626B LEU* 4.9 0.2 - - - +
637B ILE* 3.2 28.4 - - + +
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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