Contacts of the strand formed by residues 783 - 790 (chain C) in PDB entry 4X52
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 LYS 783 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C GLU 3.9 1.1 + - - +
782C GLY* 1.3 73.2 + - - -
784C LEU* 1.3 64.5 + - - +
785C LEU* 3.3 17.1 + - + +
843C ALA 3.2 4.0 - - - +
844C GLN* 3.5 2.6 - - - -
845C VAL* 2.8 39.4 + - - +
847C VAL* 4.3 33.7 - - + +
850C PHE* 6.1 2.5 - - - -
877C PHE* 4.4 16.2 - - + -
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Residues in contact with LEU 784 (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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742C ARG* 3.6 39.4 - - + +
743C VAL* 4.8 8.7 - - + -
746C HIS* 3.6 50.8 + - + +
782C GLY 4.3 0.6 + - - -
783C LYS* 1.3 73.5 - - - +
785C LEU* 1.3 64.4 + - - +
786C PHE* 4.0 14.1 - - + -
822C LYS 4.9 4.7 - - - +
842C VAL* 3.4 31.2 - - + -
843C ALA 3.5 5.4 - - - -
844C GLN* 3.5 13.0 + - - +
888C GLN* 4.9 1.3 - - - +
889C TYR* 5.3 0.2 - - + -
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Residues in contact with LEU 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783C LYS* 3.3 18.8 + - + +
784C LEU* 1.3 82.7 - - - +
786C PHE* 1.3 64.7 + - - +
820C PHE* 3.7 26.2 - - + -
821C ALA 3.6 14.6 - - - +
822C LYS* 3.9 17.5 - - + -
842C VAL* 3.5 6.2 - - - +
843C ALA* 2.8 34.0 + - - -
845C VAL* 3.7 27.6 - - + -
847C VAL* 4.1 5.8 - - + -
877C PHE* 3.6 36.6 - - + -
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Residues in contact with PHE 786 (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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743C VAL 5.3 0.7 - - - -
746C HIS* 3.8 40.8 - - + -
747C PHE* 3.9 9.0 - - - -
784C LEU* 4.0 14.4 - - + -
785C LEU* 1.3 74.7 - - - +
787C TYR* 1.3 59.7 - - - +
819C TYR 4.3 0.2 - - - +
820C PHE* 3.4 10.4 - - - -
821C ALA 2.8 38.6 + - - +
822C LYS 3.6 21.5 - - - -
823C ASP* 3.8 1.6 - - - +
824C ALA* 3.4 36.1 - - + -
827C SER* 3.9 9.4 + - - -
840C MET* 3.6 31.9 - - + -
841C PHE 3.5 6.3 - - - -
842C VAL* 3.8 20.4 - - + -
891C ILE* 4.4 4.0 - - + -
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Residues in contact with TYR 787 (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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786C PHE* 1.3 75.2 - - - +
788C ALA* 1.3 62.1 + - - +
789C THR* 3.6 26.8 + - + -
797C ILE* 3.9 7.5 - - + +
802C PHE* 3.3 41.1 - + + -
803C ASP 4.3 8.8 + - - -
806C LEU* 4.0 33.7 + - - +
808C GLU* 5.6 5.6 - - + -
818C ILE* 3.8 20.2 - - + -
819C TYR* 3.3 22.7 - - + -
820C PHE* 4.0 12.1 - + + -
827C SER* 3.4 5.2 - - - -
840C MET* 4.0 1.6 - - - -
841C PHE* 2.7 42.8 + + + +
843C ALA* 5.7 0.7 - - + -
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Residues in contact with ALA 788 (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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787C TYR* 1.3 80.6 - - - +
789C THR* 1.3 65.3 + - - +
827C SER* 2.8 40.0 + - - +
828C HIS* 3.9 4.0 - - - +
831C CYS* 3.9 16.9 - - + +
838C VAL* 3.9 10.1 - - + -
839C VAL 3.4 9.9 - - - +
840C MET* 3.8 13.4 - - + -
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Residues in contact with THR 789 (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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787C TYR* 3.6 13.3 - - + -
788C ALA* 1.3 77.6 - - - +
790C SER* 1.3 74.5 + - - +
793C TYR* 3.6 20.0 - - + +
797C ILE* 3.7 13.9 - - + -
806C LEU* 4.2 5.4 - - - +
831C CYS* 4.0 9.8 - - - -
833C TYR* 4.0 11.1 - - - -
838C VAL* 3.3 4.0 - - - -
839C VAL* 2.9 33.4 + - + +
841C PHE* 3.7 34.1 - - + -
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Residues in contact with SER 790 (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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800A ASN* 5.3 0.3 + - - -
901A GOL 4.1 11.1 + - - -
789C THR* 1.3 90.8 + - - +
791C ARG* 1.3 64.7 + - - +
792C ALA* 3.0 21.5 + - - +
793C TYR* 3.0 29.6 + - - +
794C VAL 3.8 1.9 + - - -
833C TYR* 3.4 28.4 - - - -
837C ASN* 3.4 15.6 + - - +
838C VAL* 4.7 0.2 - - - +
839C VAL* 4.1 1.8 - - - +
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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