Contacts of the strand formed by residues 595 - 601 (chain C) in PDB entry 1S9K
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 GLN 595 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584C ASP* 3.4 11.9 + - - +
585C THR* 4.4 0.3 + - - -
594C GLN* 1.3 86.7 + - - +
596C MET* 1.3 66.9 + - - +
597C ILE* 3.3 29.6 - - - +
639C PHE* 3.3 30.2 - - + +
640C VAL 3.2 14.8 - - - +
641C GLU* 4.5 2.2 - - - +
642C ILE* 5.0 0.2 - - - -
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Residues in contact with MET 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C GLN* 4.1 1.3 - - - -
584C ASP* 3.7 7.6 - - + +
585C THR* 3.7 37.5 - - - +
594C GLN 3.4 0.6 + - - -
595C GLN* 1.3 73.0 - - - +
597C ILE* 1.3 67.7 + - - +
598C LEU* 3.4 29.4 - - + -
611C PHE* 4.6 8.1 - - + -
639C PHE 3.8 0.5 - - - -
640C VAL* 2.6 68.3 + - + +
642C ILE* 4.0 17.7 - - + -
658C PHE* 3.8 28.5 - - + -
673C PHE* 4.7 9.4 - - - -
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Residues in contact with ILE 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C ARG 4.0 0.3 - - - +
583C GLN* 3.6 1.2 - - - -
584C ASP* 2.7 55.7 + - + +
595C GLN* 3.3 28.9 - - - +
596C MET* 1.3 71.2 - - - +
598C LEU* 1.3 63.4 + - - +
599C THR* 3.9 16.7 + - - +
637C MET* 4.7 15.5 - - + -
638C LEU 3.8 6.1 - - - +
639C PHE* 4.7 20.6 - - + +
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Residues in contact with LEU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL* 3.8 18.4 - - + -
582C ARG 3.6 0.4 - - - -
583C GLN* 3.6 17.5 - - + -
596C MET* 3.4 26.2 + - + -
597C ILE* 1.3 73.9 - - - +
599C THR* 1.3 60.3 + - - +
603C PHE* 3.7 3.7 - - + -
609C VAL* 4.4 7.0 - - + -
637C MET* 3.1 6.1 - - - +
638C LEU* 2.9 47.6 + - + +
640C VAL* 4.0 19.5 - - + -
658C PHE* 3.6 28.9 - - + -
660C VAL* 3.8 28.7 - - + -
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Residues in contact with THR 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL* 3.8 0.9 - - - -
581C GLU* 2.8 38.6 + - - +
582C ARG* 2.7 43.7 + - - +
597C ILE* 3.9 9.8 + - - +
598C LEU* 1.3 73.0 - - - +
600C GLY* 1.3 61.8 + - - +
603C PHE* 3.9 2.5 - - - -
636C ASN* 4.1 12.1 - - - +
637C MET* 3.4 28.2 - - + +
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Residues in contact with GLY 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C MET 3.0 15.5 - - - -
581C GLU* 3.7 11.0 - - - -
599C THR* 1.3 77.0 - - - +
601C GLN* 1.3 64.3 + - - -
603C PHE* 3.2 18.5 - - - -
636C ASN* 2.9 33.4 + - - +
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Residues in contact with GLN 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C PRO* 4.1 17.2 - - + +
419C HIS* 3.0 32.7 + - - +
578C PRO* 3.1 1.6 - - - +
579C MET* 2.8 48.9 + - + +
581C GLU* 4.4 14.2 + - - +
600C GLY* 1.3 78.0 - - - +
602C ASN* 1.3 79.8 + - - +
603C PHE* 3.4 5.1 - - - -
636C ASN* 4.4 12.1 - - + +
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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