Contacts of the helix formed by residues 727 - 739 (chain D) in PDB entry 3TDU
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 727 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B GLU 2.9 27.5 + - - -
234B GLY* 3.1 26.8 + - - -
235B ALA* 3.6 12.3 - - + +
725D LEU 3.8 0.4 + - - -
726D LYS* 1.3 70.8 - - - +
728D GLN* 1.3 66.8 + - + +
730D LEU* 3.2 3.5 + - - +
731D LEU* 3.0 60.5 + - + +
750D LYS* 4.3 9.0 - - + -
753D ILE* 4.3 6.5 - - + -
770D ASP* 2.9 25.1 + - + +
772D TYR* 2.8 41.2 + - + -
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Residues in contact with GLN 728 (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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231B ASP* 5.1 8.1 + - - -
233B GLU 6.0 0.2 - - - +
726D LYS* 3.3 4.9 - - + +
727D HIS* 1.3 88.4 - - + +
729D GLN* 1.3 63.0 + - + +
731D LEU* 3.5 10.0 + - + +
732D GLY* 3.1 19.6 + - - -
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Residues in contact with GLN 729 (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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725D LEU* 3.5 24.6 - - + +
726D LYS* 3.1 40.1 + - + +
728D GLN* 1.3 78.5 - - + +
730D LEU* 1.3 62.1 + - - +
732D GLY* 3.3 2.8 + - - -
733D GLU* 3.0 32.1 + - - +
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Residues in contact with LEU 730 (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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715D ILE* 4.2 19.7 - - + -
718D ILE* 3.8 26.2 - - + -
719D MET* 4.1 19.3 - - + -
725D LEU* 3.6 11.2 - - + +
726D LYS 2.9 12.5 + - - +
727D HIS* 3.5 7.9 - - - +
729D GLN* 1.3 73.1 - - - +
731D LEU* 1.3 67.3 + - + +
733D GLU* 3.2 2.2 + - - -
734D VAL* 3.0 43.1 + - + +
753D ILE* 3.9 19.7 - - + -
762D LEU* 5.2 1.3 - - + -
772D TYR* 3.6 31.6 - - + -
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Residues in contact with LEU 731 (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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233B GLU* 3.8 11.4 - - + +
727D HIS* 3.0 56.4 + - + +
728D GLN* 3.8 10.1 - - + +
730D LEU* 1.3 76.9 - - + +
732D GLY* 1.3 63.1 + - - +
734D VAL* 3.4 6.8 + - - +
735D LEU* 3.2 29.9 + - + +
746D VAL* 4.0 24.7 - - + -
749D ILE* 3.7 35.3 - - + +
750D LYS* 5.2 1.1 - - + -
753D ILE* 4.2 7.0 - - + -
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Residues in contact with GLY 732 (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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728D GLN 3.1 15.0 + - - -
729D GLN* 3.7 3.4 - - - -
730D LEU 3.2 0.2 - - - -
731D LEU* 1.3 77.0 - - - +
733D GLU* 1.3 57.6 + - - +
735D LEU* 3.4 13.0 + - - +
736D THR* 3.2 29.0 + - - -
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Residues in contact with GLU 733 (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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718D ILE* 3.0 38.4 - - + +
721D MET* 5.3 0.9 - - - +
722D ARG* 3.6 32.6 + - - +
725D LEU* 3.4 17.3 - - - +
729D GLN* 3.0 22.9 + - - +
730D LEU 3.2 2.4 + - - +
732D GLY* 1.3 73.0 - - - +
734D VAL* 1.3 61.7 + - - +
736D THR* 3.4 7.6 + - - -
737D GLN* 3.0 35.0 + - + +
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Residues in contact with VAL 734 (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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711D ILE* 4.3 7.9 - - + -
714D ALA* 4.7 3.8 - - + -
715D ILE* 3.7 28.9 - - + +
718D ILE* 3.8 16.4 - - + -
730D LEU* 3.0 26.2 + - + +
731D LEU 3.7 5.6 - - - +
732D GLY 3.3 0.2 - - - -
733D GLU* 1.3 72.1 - - - +
735D LEU* 1.3 64.9 + - - +
737D GLN* 3.3 3.0 + - - +
738D LEU* 3.1 42.2 + - + +
744D PRO* 4.2 3.4 - - + -
749D ILE* 4.0 30.3 - - + -
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Residues in contact with LEU 735 (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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731D LEU* 3.2 20.9 + - + +
732D GLY* 3.5 14.6 - - - +
734D VAL* 1.3 77.7 - - - +
736D THR* 1.3 57.3 + - - +
738D LEU 3.3 0.7 + - - -
739D SER* 2.8 34.2 + - - -
743D LYS* 3.8 27.4 - - + -
744D PRO* 3.5 45.5 - - + +
746D VAL* 6.2 4.7 - - + -
749D ILE* 4.7 5.6 - - + -
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Residues in contact with THR 736 (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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732D GLY 3.2 12.7 + - - -
733D GLU* 3.8 11.4 - - - -
734D VAL 3.3 0.2 - - - -
735D LEU* 1.3 77.3 - - - +
737D GLN* 1.3 64.8 + - - +
739D SER* 2.9 22.9 + - - +
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Residues in contact with GLN 737 (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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714D ALA* 4.3 16.6 - - + -
717D ARG* 3.9 27.1 + - - +
718D ILE* 3.9 20.6 - - + +
733D GLU* 3.0 21.7 + - + +
734D VAL 3.8 4.9 - - - +
735D LEU 3.3 0.4 - - - -
736D THR* 1.3 82.7 - - - +
738D LEU* 1.3 62.8 + - - +
739D SER 3.5 0.4 - - - -
740D SER* 4.9 5.4 + - - -
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Residues in contact with LEU 738 (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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710D LEU* 3.9 35.0 - - + +
711D ILE* 3.6 31.9 - - + -
714D ALA* 4.4 8.5 - - + -
717D ARG* 5.4 4.3 - - - +
734D VAL* 3.1 21.4 + - + +
735D LEU 3.7 0.4 - - - -
737D GLN* 1.3 81.3 - - - +
739D SER* 1.3 64.2 + - - +
740D SER* 3.2 4.0 - - - -
741D ARG* 2.9 23.2 + - - +
742D PHE* 2.9 32.1 + - + +
744D PRO* 3.5 32.3 - - + -
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Residues in contact with SER 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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735D LEU 2.8 17.1 + - - -
736D THR* 2.9 19.0 + - - +
737D GLN 3.5 0.6 - - - -
738D LEU* 1.3 76.7 - - - +
740D SER* 1.3 61.8 + - - +
741D ARG 3.3 1.2 + - - -
742D PHE* 3.9 12.2 + - - +
743D LYS* 5.8 0.4 - - - +
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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