Contacts of the helix formed by residues 737 - 749 (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 HIS 737 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A GLU* 3.6 27.4 + - + +
733A ILE 3.9 1.7 - - - -
734A HIS* 3.4 53.1 - + + +
733D ILE* 3.3 18.6 - - + +
734D HIS* 3.1 22.7 + - + +
736D LEU* 1.3 79.1 - - - +
738D PRO* 1.3 74.5 - - + +
739D GLU* 3.0 55.2 + - + +
740D TYR* 2.9 12.3 + - - +
741D VAL* 3.1 11.4 + - - +
761D LYS* 6.4 0.2 - - - +
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Residues in contact with PRO 738 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734A HIS* 3.3 50.0 - - + +
736D LEU 3.5 5.4 - - - +
737D HIS* 1.3 84.7 - - + +
739D GLU* 1.4 57.0 + - + +
741D VAL* 3.4 9.3 + - + +
742D ARG* 2.9 30.2 + - - +
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Residues in contact with GLU 739 (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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733D ILE* 4.9 4.5 - - + -
737D HIS* 3.0 30.2 + - + +
738D PRO* 1.4 74.1 - - + +
740D TYR* 1.3 67.3 + - - +
742D ARG* 3.5 9.8 + - - +
743D VAL* 3.0 30.2 + - - +
761D LYS* 3.0 40.5 + - - +
889D TYR* 2.6 36.4 + - + +
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Residues in contact with TYR 740 (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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733D ILE* 3.5 32.2 - - + +
734D HIS 3.2 18.2 - - - +
735D HIS* 3.3 38.4 - - + +
737D HIS 2.9 7.1 + - - +
739D GLU* 1.3 77.5 - - - +
741D VAL* 1.3 52.8 + - - +
743D VAL* 3.3 1.5 + - - -
744D SER* 2.8 50.5 + - - -
756D ILE* 3.5 23.1 + - + +
757D GLU 5.0 3.8 + - - -
758D LYS* 4.7 1.6 - - - -
759D ILE* 3.7 49.6 - - + +
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Residues in contact with VAL 741 (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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735D HIS 3.9 14.8 - - - +
736D LEU* 4.2 12.1 - - + +
737D HIS 3.1 13.1 + - - +
738D PRO* 3.6 10.5 - - + +
740D TYR* 1.3 75.7 - - - +
742D ARG* 1.3 56.8 + - - +
744D SER* 3.7 5.0 - - - -
745D GLU* 3.0 47.7 + - + +
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Residues in contact with ARG 742 (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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738D PRO 2.9 18.0 + - - +
739D GLU* 3.7 9.3 - - - +
741D VAL* 1.3 77.1 - - - +
743D VAL* 1.3 66.9 + - - +
745D GLU* 3.4 4.5 + - - +
746D HIS* 3.0 44.9 + - + +
784D LEU* 3.5 31.7 - - - +
844D GLN* 4.0 15.2 + - - +
888D GLN* 4.4 18.4 + - - +
889D TYR* 4.8 8.1 + - - -
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Residues in contact with VAL 743 (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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739D GLU 3.0 18.8 + - - +
740D TYR 3.8 2.5 - - - +
742D ARG* 1.3 80.3 - - - +
744D SER* 1.3 63.8 + - - +
746D HIS* 3.1 8.7 + - - +
747D PHE* 3.0 21.8 + - - +
759D ILE* 3.9 18.6 - - + -
784D LEU* 4.9 7.0 - - + -
786D PHE* 5.1 0.7 - - - -
842D VAL* 3.8 13.0 - - + -
889D TYR* 3.3 39.0 - - + -
891D ILE* 3.6 29.6 - - + -
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Residues in contact with SER 744 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740D TYR* 2.8 40.3 + - - -
741D VAL* 3.7 5.6 - - - -
743D VAL* 1.3 71.4 - - - +
745D GLU* 1.3 55.9 + - - +
747D PHE* 3.4 1.7 + - - +
748D LYS* 2.9 59.4 + - - +
756D ILE* 3.4 26.5 - - - +
759D ILE* 3.9 1.5 - - - +
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Residues in contact with GLU 745 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741D VAL* 3.0 33.1 + - + +
742D ARG* 3.8 5.6 - - - +
743D VAL 3.3 0.2 - - - -
744D SER* 1.3 71.9 - - - +
746D HIS* 1.4 65.9 + - + +
748D LYS* 3.3 31.4 + - - +
749D ALA* 3.1 24.3 + - - +
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Residues in contact with HIS 746 (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* 3.0 46.3 + - + +
743D VAL* 3.1 8.0 + - - +
745D GLU* 1.4 76.5 - - - +
747D PHE* 1.3 61.8 + - - +
749D ALA* 3.6 15.5 + - - +
750D SER* 4.5 2.9 + - - -
784D LEU* 3.8 44.2 - - + +
786D PHE* 3.8 16.4 - + + -
823D ASP* 6.0 0.3 - - - -
824D ALA 5.4 0.3 + - - -
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Residues in contact with PHE 747 (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 3.0 12.6 + - - +
744D SER 3.5 8.1 - - - +
746D HIS* 1.3 75.9 - - - +
748D LYS* 1.4 64.5 + - + +
749D ALA 3.2 1.4 + - - -
750D SER* 3.4 5.0 + - - -
751D MET* 3.0 71.6 + - + +
754D PHE* 4.3 11.7 - - + -
756D ILE* 3.6 31.9 - - + -
786D PHE* 3.8 8.6 - + + -
824D ALA* 4.0 13.0 - - + +
840D MET* 4.1 14.6 - - + -
891D ILE* 3.7 26.7 - - + -
893D TYR* 3.6 33.4 - + + -
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Residues in contact with LYS 748 (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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744D SER* 2.9 42.0 + - - +
745D GLU* 3.3 28.5 + - - +
747D PHE* 1.4 78.5 - - + +
749D ALA* 1.4 60.5 + - - +
750D SER 3.2 3.6 + - - -
751D MET 3.7 16.0 + - - +
752D LYS* 2.9 28.8 + - - +
754D PHE 5.5 4.7 - - - +
756D ILE* 4.4 5.6 - - + -
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Residues in contact with ALA 749 (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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745D GLU 3.1 12.6 + - - +
746D HIS* 3.6 15.5 - - - +
747D PHE 3.2 0.8 - - - -
748D LYS* 1.4 76.6 - - - +
750D SER* 1.4 57.5 + - - +
752D LYS* 3.3 20.9 + - - +
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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