Contacts of the strand formed by residues 595 - 599 (chain F) 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 VAL 595 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556F PHE* 3.6 5.7 - - - +
557F VAL* 3.0 37.7 + - + +
579F LEU* 6.3 0.2 - - + -
586F LEU* 3.6 39.0 - - + -
587F THR 3.6 8.5 - - - +
588F LYS* 4.9 1.3 - - - +
593F SER 4.3 2.5 - - - +
594F LYS* 1.3 72.7 - - - +
596F MET* 1.3 61.1 + - - +
608F TRP* 4.3 12.6 - - + -
626F LEU* 4.1 25.4 - - + -
635F VAL* 4.0 13.7 + - + +
636F PHE 4.4 3.4 - - - -
637F ILE* 4.2 17.5 - - + -
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Residues in contact with MET 596 (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 GLY* 3.4 39.3 - - - +
555F GLY 3.3 5.4 - - - +
556F PHE* 3.7 18.2 - - + -
557F VAL 5.2 0.4 - - - -
585F CYS 3.9 0.2 - - - +
586F LEU* 3.0 26.1 - - - +
587F THR* 3.0 41.5 + - + +
588F LYS 4.3 0.4 - - - +
589F GLY* 3.6 26.5 - - - +
595F VAL* 1.3 75.2 - - - +
597F ILE* 1.3 65.8 + - - +
598F THR* 4.0 9.2 - - + +
605F PHE* 6.1 0.2 - - + -
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Residues in contact with ILE 597 (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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548F SER* 3.4 26.0 - - - +
551F LYS* 3.4 17.7 - - + +
552F THR* 3.6 2.7 - - - -
553F ASN 3.1 0.5 + - - -
554F GLY* 2.2 34.7 + - - -
555F GLY 2.9 12.3 + - - +
557F VAL* 4.4 14.3 - - + +
571F PHE* 4.8 2.9 - - + -
581F GLN* 4.2 23.1 - - + +
584F GLN* 3.2 33.0 - - + +
585F CYS 3.6 3.8 - - - +
586F LEU* 4.3 20.0 - - + -
596F MET* 1.3 73.7 - - - +
598F THR* 1.3 56.8 - - - +
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Residues in contact with THR 598 (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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553F ASN* 3.5 13.2 - - + +
554F GLY* 3.2 27.6 - - - +
584F GLN* 3.2 7.5 - - - +
585F CYS* 2.6 35.6 + - - +
587F THR* 3.8 22.7 - - - +
596F MET* 4.0 9.4 - - + +
597F ILE* 1.3 72.3 - - - +
599F HIS* 1.3 78.5 + - + +
605F PHE* 4.1 9.2 - - + -
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Residues in contact with HIS 599 (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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553F ASN* 3.3 25.6 + - - +
583F ASP* 4.5 11.7 - - - +
584F GLN* 3.5 13.3 - - + +
598F THR* 1.3 85.8 - - + +
600F CYS* 1.3 60.6 + - - +
601F ASN* 4.2 2.8 + - - +
604F GLU* 4.4 9.2 + - - +
605F PHE* 3.3 17.6 - + - -
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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