Contacts of the strand formed by residues 735 - 739 (chain C) in PDB entry 1XSK
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 735 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685C GLY 5.3 1.6 - - - +
686C THR 3.0 3.8 + - - +
687C ALA* 3.6 26.2 - - + -
688C PHE* 2.8 32.4 + - - +
733C ASN 5.5 1.1 - - - +
734C TRP* 1.3 79.9 - - - +
736C LEU* 1.3 64.2 + - - +
737C CYS* 4.2 1.5 + - + -
760C VAL* 2.9 32.6 - - + +
761C VAL 3.3 8.7 + - - -
762C LYS* 4.9 5.8 - - - -
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Residues in contact with LEU 736 (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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668C LEU* 3.6 21.8 - - + -
688C PHE* 3.4 28.7 - - + +
689C HIS 4.5 0.2 - - - +
690C LEU* 4.3 7.4 - - + -
714C LEU* 4.7 9.9 - - + -
725C VAL* 5.2 16.8 - - + -
734C TRP* 4.4 12.3 - - + -
735C THR* 1.3 77.0 + - - +
737C CYS* 1.3 64.4 + - - +
738C LEU* 3.2 33.5 + - + -
761C VAL* 2.8 45.4 + - + +
763C PRO* 5.9 0.2 - - + -
768C LEU* 6.3 3.6 - - + -
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Residues in contact with CYS 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688C PHE 2.8 11.9 + - - +
689C HIS* 3.6 33.6 - - + +
690C LEU 3.1 22.3 + - - -
735C THR* 4.2 2.4 + - + +
736C LEU* 1.3 75.1 - - - +
738C LEU* 1.3 58.4 + - - +
739C ARG* 3.0 15.3 + - - -
755C SER* 4.6 0.9 - - - -
757C GLN* 4.3 11.0 - - - -
758C GLY 3.7 30.3 - - - -
759C LEU 3.4 4.5 - - - +
760C VAL* 4.1 15.7 - - + +
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Residues in contact with LEU 738 (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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690C LEU* 4.2 22.0 - - + -
723C ILE* 5.4 2.2 - - + -
736C LEU* 3.2 28.9 - - + -
737C CYS* 1.3 69.8 - - - +
739C ARG* 1.3 67.1 + - - +
740C ASN 3.3 0.3 + - - -
741C VAL* 3.0 40.4 + - + +
744C VAL* 5.1 3.1 - - + -
758C GLY* 3.5 9.4 - - - -
759C LEU* 2.7 28.4 + - + +
761C VAL* 4.5 17.7 - - + -
770C ILE* 4.1 34.5 - - + -
772C LEU* 4.9 1.8 - - + -
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Residues in contact with ARG 739 (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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636C THR* 4.3 0.9 - - + -
637C HIS 4.0 0.6 + - - -
638C LEU* 2.3 40.4 + - - +
639C TRP* 3.9 2.4 - - - +
641C ASN* 2.7 29.6 + - - +
671C LEU* 5.3 3.8 - - - +
689C HIS* 2.5 57.6 + - - +
690C LEU 3.0 23.6 + - - +
691C PHE* 3.5 35.0 - - + -
692C ASN* 4.8 9.9 + - - +
737C CYS* 3.0 8.9 + - - -
738C LEU* 1.3 69.8 - - - +
740C ASN* 1.3 73.4 + - - +
741C VAL* 3.0 10.7 + - - +
757C GLN* 3.4 33.6 - - - +
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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