Contacts of the strand formed by residues 758 - 763 (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 GLY 758 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737C CYS* 3.7 3.4 - - - -
738C LEU 3.5 11.2 - - - -
740C ASN* 4.0 4.0 - - - -
741C VAL 4.0 7.0 - - - -
742C VAL* 5.4 3.6 - - - -
755C SER* 2.8 29.6 + - - -
756C GLU 3.4 3.2 - - - -
757C GLN* 1.3 82.5 - - - +
759C LEU* 1.3 69.4 + - - +
760C VAL* 3.6 1.6 - - - +
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Residues in contact with LEU 759 (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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736C LEU 4.1 0.2 - - - +
737C CYS* 3.4 1.0 - - - -
738C LEU* 2.7 48.1 + - + +
741C VAL* 2.8 22.2 + - + +
742C VAL* 3.7 19.8 - - - +
743C LYS 4.5 0.2 - - - -
744C VAL* 3.5 31.0 - - + +
752C GLN* 3.3 37.7 - - + +
753C ALA* 3.4 22.7 - - - +
754C GLU* 4.4 11.4 - - + +
755C SER 4.8 1.8 - - - +
758C GLY* 1.3 72.2 - - - +
760C VAL* 1.3 57.6 + - - +
761C VAL* 4.9 4.5 - - + -
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Residues in contact with VAL 760 (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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735C THR* 2.9 31.0 - - + +
736C LEU 3.8 3.8 - - - +
737C CYS* 4.1 13.5 - - + -
751C SER 4.0 0.2 - - - +
752C GLN* 3.2 4.3 - - - +
753C ALA* 2.7 52.6 + - + +
754C GLU 4.2 3.4 - - - +
755C SER* 3.4 31.6 - - - +
758C GLY 3.6 3.1 - - - +
759C LEU* 1.3 73.8 - - - +
761C VAL* 1.3 62.2 + - - +
762C LYS* 6.2 0.7 - - + -
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Residues in contact with VAL 761 (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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735C THR* 3.3 6.6 + - - -
736C LEU* 2.8 52.9 + - + +
738C LEU* 4.5 21.3 - - + -
747C LEU* 3.9 24.9 - - + -
751C SER 3.5 8.3 - - - +
752C GLN* 4.5 4.5 - - + -
759C LEU* 4.9 4.3 - - + -
760C VAL* 1.3 82.1 - - - +
762C LYS* 1.3 66.4 + - - +
763C PRO* 3.9 3.5 - - + +
768C LEU* 3.9 31.2 - - + -
770C ILE* 4.9 6.3 - - + -
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Residues in contact with LYS 762 (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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733C ASN* 4.4 29.0 - - - +
734C TRP 3.3 24.7 - - - +
735C THR* 4.9 4.9 - - - +
750C GLY* 3.1 4.8 - - - -
751C SER* 2.8 47.2 + - - +
760C VAL* 6.2 0.9 - - + -
761C VAL* 1.3 74.3 - - - +
763C PRO* 1.3 87.1 + - + +
764C GLN* 3.6 9.0 + - - +
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Residues in contact with PRO 763 (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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734C TRP* 3.4 63.9 - - + +
736C LEU* 5.9 0.2 - - + -
749C ASP 3.6 8.3 - - - +
750C GLY* 4.3 0.7 - - - -
761C VAL* 3.9 6.2 - - + +
762C LYS* 1.3 111.3 + - + +
764C GLN* 1.3 72.6 + - - +
766C ASN* 5.8 5.8 - - - +
768C LEU* 4.5 13.9 - - + -
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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