Contacts of the strand formed by residues 783 - 790 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781D GLU 3.9 1.1 + - - +
782D GLY* 1.3 73.9 - - - -
784D LEU* 1.3 65.0 + - - +
785D LEU* 3.4 16.7 + - + -
843D ALA 3.2 4.3 - - - +
844D GLN* 3.5 2.4 - - - -
845D VAL* 2.8 38.8 + - - +
847D VAL* 4.1 36.8 - - + +
850D PHE* 4.6 10.3 - - - -
877D PHE* 4.4 18.8 - - + -
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Residues in contact with LEU 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D ARG* 3.5 40.1 - - - +
743D VAL* 4.9 7.6 - - + -
746D HIS* 3.8 46.4 - - + +
782D GLY 4.3 0.2 + - - -
783D LYS* 1.3 73.0 - - - +
785D LEU* 1.4 68.4 + - - +
786D PHE* 4.0 14.8 - - + -
822D LYS 4.9 4.5 - - - +
842D VAL* 3.4 31.0 - - + -
843D ALA 3.5 4.5 - - - -
844D GLN* 3.5 14.6 + - - +
888D GLN* 4.9 1.6 - - - +
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Residues in contact with LEU 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783D LYS* 4.0 18.2 - - + +
784D LEU* 1.4 82.4 - - - +
786D PHE* 1.3 65.1 + - - +
820D PHE* 3.7 24.9 - - + -
821D ALA 3.6 14.8 - - - +
822D LYS* 3.9 17.9 - - + -
842D VAL* 3.5 5.7 - - - +
843D ALA* 2.8 35.4 + - - -
845D VAL* 3.8 27.8 - - + -
847D VAL* 4.0 6.7 - - + -
877D PHE* 3.7 35.4 - - + -
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Residues in contact with PHE 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743D VAL 5.3 0.4 - - - -
746D HIS* 3.8 41.7 - + + -
747D PHE* 3.8 9.0 - - - -
784D LEU* 4.0 14.6 - - + -
785D LEU* 1.3 73.9 - - - +
787D TYR* 1.3 60.1 + - - +
819D TYR 4.2 0.3 - - - +
820D PHE* 3.3 9.6 - - - -
821D ALA 2.8 36.8 + - - +
822D LYS 3.6 21.3 - - - -
823D ASP* 4.6 0.4 - - - +
824D ALA* 3.4 35.4 - - + -
827D SER* 3.8 8.9 + - - -
840D MET* 3.6 31.9 - - + -
841D PHE 3.5 6.3 - - - -
842D VAL* 3.8 21.1 - - + -
891D ILE* 4.4 4.3 - - + -
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Residues in contact with TYR 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D PHE* 1.3 75.8 - - - +
788D ALA* 1.3 61.7 + - - +
789D THR* 3.6 28.9 + - + -
797D ILE* 3.9 7.9 - - + +
802D PHE* 3.3 41.1 - + + -
803D ASP 4.3 8.8 + - - -
806D LEU* 3.9 33.8 + - - +
808D GLU* 6.3 3.1 - - + -
818D ILE* 3.7 20.9 - - + -
819D TYR* 3.3 23.1 - - + -
820D PHE* 4.0 13.2 - + + -
827D SER* 3.4 4.3 - - - -
840D MET* 3.9 1.6 - - - -
841D PHE* 2.8 39.9 + + + +
843D ALA* 5.7 0.4 - - + -
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Residues in contact with ALA 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D TYR* 1.3 78.6 - - - +
789D THR* 1.3 65.5 + - - +
827D SER* 2.8 40.1 + - - +
828D HIS* 3.8 3.1 - - - +
831D CYS* 3.9 17.2 - - + +
838D VAL* 4.0 11.2 - - + -
839D VAL 3.4 6.1 - - - -
840D MET* 3.8 17.5 - - + -
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Residues in contact with THR 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D TYR* 3.6 14.4 + - + -
788D ALA* 1.3 75.2 - - - +
790D SER* 1.3 76.0 + - - +
793D TYR* 3.5 20.2 - - + +
797D ILE* 3.8 14.1 - - + -
806D LEU* 4.2 5.2 - - - +
831D CYS* 4.0 10.2 - - - -
833D TYR* 4.0 11.2 - - - -
838D VAL* 3.3 4.9 - - - -
839D VAL* 2.9 33.8 + - + +
841D PHE* 3.7 33.0 - - + -
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Residues in contact with SER 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B ASN* 5.3 1.9 + - - -
789D THR* 1.3 91.7 + - - +
791D ARG* 1.3 61.6 + - - +
792D ALA* 3.1 20.3 + - - +
793D TYR* 3.0 33.3 + - - +
794D VAL 3.8 1.7 + - - -
833D TYR* 3.4 29.9 - - - -
837D ASN* 3.4 15.9 + - - +
839D VAL* 4.1 1.4 - - - +
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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