Contacts of the helix formed by residues 769 - 776 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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754A HIS* 5.5 0.3 - - - -
756A ASP* 3.1 20.2 - - - +
757A GLY* 4.1 7.0 + - - +
767A ALA* 5.9 0.2 - - + -
768A LYS* 1.3 85.9 - - + +
770A PHE* 1.3 104.7 + - - +
771A LEU* 4.8 1.0 - - + +
772A PRO* 2.7 27.2 - - - +
773A LYS* 2.8 20.8 - - - +
1057A MET* 2.8 35.6 - - - +
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Residues in contact with PHE 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A PRO* 3.0 65.5 - - + -
754A HIS* 3.1 15.0 - + - -
755A LYS* 3.7 2.7 - - + -
756A ASP* 2.5 37.9 - - - -
768A LYS 3.2 0.6 + - - -
769A ASP* 1.3 101.8 + - - +
771A LEU* 1.3 69.9 + - + +
773A LYS* 2.8 38.8 + - + +
774A MET* 3.2 13.4 + - + +
968A GLN* 3.1 29.6 - - + -
1057A MET* 5.7 0.7 - - + -
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Residues in contact with LEU 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A TYR* 6.2 0.2 - - - +
751A LYS* 4.8 12.6 - - + +
752A LEU 4.7 8.7 - - - +
753A PRO 5.3 2.7 - - - +
762A VAL* 6.2 6.5 - - + -
764A SER 4.0 4.0 - - - +
765A PRO* 3.0 28.5 - - + +
766A PHE 4.0 1.1 - - - -
767A ALA* 2.9 39.7 - - + +
768A LYS 3.3 6.7 - - - +
769A ASP* 4.8 0.4 - - - +
770A PHE* 1.3 88.5 - - + +
772A PRO* 1.3 65.5 - - - +
774A MET* 3.1 28.9 + - + +
775A GLU* 3.0 25.7 + - - +
780A GLN* 4.0 5.4 + - - +
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Residues in contact with PRO 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A PHE 5.3 2.5 - - - +
767A ALA 3.2 4.0 - - - +
768A LYS* 3.1 20.0 - - + +
769A ASP* 2.7 42.4 - - - +
771A LEU* 1.3 80.4 - - - +
773A LYS* 1.3 60.4 + - + +
775A GLU* 2.7 41.2 + - - +
776A ASP* 3.3 10.7 + - - +
796A LYS* 5.0 5.4 - - + +
799A SER* 5.9 5.2 - - - +
800A PHE* 6.2 3.6 - - + -
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Residues in contact with LYS 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A ASP* 2.8 24.5 - - - +
770A PHE* 2.8 16.3 - - + +
772A PRO* 1.3 79.5 - - + +
774A MET* 1.3 51.3 + - + +
776A ASP* 2.6 30.4 - - - +
777A GLY* 2.6 10.4 + - - -
969A PHE* 3.5 43.6 - - + -
1057A MET* 2.8 37.7 - - - +
1064A ILE 4.1 9.7 + - - -
1065A ALA* 4.4 3.8 - - - +
1066A THR 5.2 5.6 - - - -
1071A ARG* 5.0 2.0 - - - +
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Residues in contact with MET 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ASP* 4.4 16.4 - - + +
614A TYR* 5.3 0.4 - - - +
751A LYS* 5.2 5.4 - - + -
752A LEU 4.5 11.7 - - - +
753A PRO* 5.2 4.7 - - + -
770A PHE* 3.6 13.0 - - + +
771A LEU* 3.1 34.8 + - + +
772A PRO 3.0 0.8 - - - -
773A LYS* 1.3 77.6 - - + +
775A GLU* 1.3 58.3 + - - +
777A GLY* 2.8 24.8 + - - -
779A LEU* 2.7 36.9 - - + +
780A GLN* 2.7 22.2 - - - +
968A GLN 6.1 1.1 - - - +
971A HIS* 6.4 0.9 - - - -
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Residues in contact with GLU 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A PRO 5.1 1.0 - - - +
766A PHE* 3.2 36.9 - - - +
771A LEU 3.1 16.2 - - - +
772A PRO* 2.7 23.0 + - - +
774A MET* 1.3 71.0 - - - +
776A ASP* 1.3 62.2 + - - +
777A GLY 2.8 7.6 - - - +
780A GLN* 3.1 31.0 - - + +
792A LEU* 3.5 14.9 - - + +
793A GLU* 4.3 1.9 - - - +
795A ASN* 3.2 9.8 + - - +
796A LYS* 2.8 54.2 + - + +
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Residues in contact with ASP 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A PRO 3.3 5.1 + - - +
773A LYS* 2.6 15.5 - - - +
775A GLU* 1.3 73.0 - - - +
777A GLY* 1.3 77.7 + - - +
793A GLU* 5.0 1.6 - - - -
796A LYS* 3.1 18.3 - - - +
866A ARG* 5.4 5.5 + - - -
1067A SER 5.6 1.4 - - - +
1068A ASP* 5.8 3.8 - - - +
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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