Contacts of the helix formed by residues 769 - 775 (chain D) in PDB entry 3IKM
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 ASP 769 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753D PRO 5.7 1.3 - - - -
754D HIS* 5.9 0.7 - - - -
756D ASP* 2.7 56.5 - - - +
757D GLY* 3.8 3.6 + - - -
767D ALA* 4.0 8.7 - - + +
768D LYS* 1.3 106.5 - - + +
770D PHE* 1.3 79.3 + - - +
771D LEU* 3.0 3.2 + - + +
772D PRO* 3.0 2.6 - - - +
773D LYS* 2.3 35.3 + - - +
1064D ILE* 4.6 13.3 - - - +
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Residues in contact with PHE 770 (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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752D LEU* 4.8 4.7 - - + -
753D PRO* 3.1 45.8 - - + -
756D ASP* 4.0 7.4 - - - +
769D ASP* 1.3 87.6 + - - +
771D LEU* 1.3 52.3 + - + +
773D LYS* 2.6 26.8 - - + +
774D MET* 2.5 71.9 + - + +
968D GLN* 2.5 66.2 - - + -
969D PHE* 3.7 11.4 - + - -
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Residues in contact with LEU 771 (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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751D LYS* 6.1 7.0 - - + +
752D LEU 4.5 5.4 - - - +
753D PRO* 3.6 35.4 - - + +
754D HIS* 6.4 0.9 - - + -
762D VAL* 5.5 8.7 - - + +
764D SER 2.7 31.0 - - - +
765D PRO* 3.5 19.7 - - + +
767D ALA* 3.0 22.2 - - + -
769D ASP* 3.0 3.0 + - + -
770D PHE* 1.3 79.4 - - + +
772D PRO* 1.3 56.9 - - + +
774D MET* 2.7 16.7 + - + +
775D GLU* 2.5 34.7 + - - +
780D GLN* 4.0 3.9 + - - +
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Residues in contact with PRO 772 (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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767D ALA 4.5 0.9 - - - +
768D LYS* 2.7 61.9 - - + +
769D ASP 3.0 7.4 - - - +
771D LEU* 1.3 72.3 - - + +
773D LYS* 1.3 65.9 + - - +
774D MET 2.8 1.1 - - - -
775D GLU* 1.9 53.7 - - + +
776D ASP* 4.0 1.2 - - - +
796D LYS* 5.0 9.9 - - + +
799D SER* 5.9 5.8 - - - +
800D PHE* 6.2 5.4 - - + -
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Residues in contact with LYS 773 (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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756D ASP* 5.7 0.7 - - - +
768D LYS* 3.8 17.9 - - - +
769D ASP* 2.3 38.8 + - - +
770D PHE* 2.6 31.0 - - + +
772D PRO* 1.3 88.0 - - - +
774D MET* 1.3 60.1 + - + +
776D ASP* 2.6 28.6 - - - +
777D GLY* 4.0 2.9 + - - -
800D PHE* 6.3 1.6 - - - -
969D PHE* 4.0 38.1 - - + -
1064D ILE 5.5 2.0 - - - -
1066D THR* 5.8 5.4 - - - +
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Residues in contact with MET 774 (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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620D TRP* 5.4 7.9 - - + -
751D LYS* 5.6 3.6 - - + -
752D LEU* 4.6 9.2 - - + +
753D PRO* 5.2 0.2 - - + -
770D PHE* 2.5 70.7 - - + +
771D LEU* 2.7 14.4 - - + +
773D LYS* 1.3 78.7 - - + +
775D GLU* 1.3 53.6 + - - +
776D ASP 2.2 20.1 + - - +
779D LEU* 2.1 59.4 + - + +
780D GLN* 3.8 3.6 - - - +
968D GLN 5.2 0.2 - - - +
971D HIS* 6.2 3.6 - - - -
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Residues in contact with GLU 775 (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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765D PRO 4.5 5.3 - - - +
766D PHE* 4.1 33.2 - - - +
771D LEU 2.5 14.1 + - - +
772D PRO* 1.9 49.2 + - + +
774D MET* 1.3 69.7 - - - +
776D ASP* 1.3 66.2 + - - +
780D GLN* 2.9 31.8 - - + +
781D ALA* 5.4 0.9 - - - +
792D LEU* 3.5 26.0 - - + +
795D ASN* 4.4 8.2 - - - +
796D LYS* 2.8 27.3 + - + +
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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