Contacts of the helix formed by residues 917 - 925 (chain I) in PDB entry 6LTJ
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 917 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887I LYS* 4.0 26.2 - - - +
915I GLN* 3.0 14.4 + - + +
916I ASN* 1.3 84.7 + - - +
918I LEU* 1.3 51.6 + - - +
919I PRO* 3.5 9.1 - - + +
920I GLU* 3.2 28.4 + - + +
921I LEU* 2.5 38.3 + - - +
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Residues in contact with LEU 918 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916I ASN* 3.0 12.2 + - - +
917I LYS* 1.3 75.1 - - - +
919I PRO* 1.4 69.6 - - + +
921I LEU* 3.1 10.2 + - + +
922I TRP* 3.1 33.4 + - + +
942I TRP 4.8 6.1 - - - +
971I VAL* 3.2 51.6 - - + +
972I LEU* 4.2 16.6 - - + -
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Residues in contact with PRO 919 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889I HIS* 4.9 0.2 - - - -
916I ASN 4.6 3.4 - - - +
917I LYS* 3.7 7.9 - - + +
918I LEU* 1.4 96.1 - - + +
920I GLU* 1.3 61.4 + - + +
922I TRP* 3.5 1.5 + - + +
923I ALA* 2.9 34.9 + - - +
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Residues in contact with GLU 920 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887I LYS* 3.0 28.3 - - - +
888I ASN* 4.0 14.0 + - - -
889I HIS* 3.1 30.2 + - - -
917I LYS* 3.2 36.1 + - + +
919I PRO* 1.3 80.8 - - + +
921I LEU* 1.3 57.6 + - - +
924I LEU* 2.8 36.6 + - + +
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Residues in contact with LEU 921 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912I THR* 6.3 1.6 - - + -
917I LYS 2.5 20.8 + - - +
918I LEU* 3.1 8.0 + - - +
920I GLU* 1.3 72.9 - - - +
922I TRP* 1.3 91.4 + - + +
924I LEU* 3.5 4.7 - - - +
925I LEU* 2.8 52.2 + - + +
972I LEU* 4.0 17.5 - - + -
976I LEU* 3.6 38.4 - - + -
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Residues in contact with TRP 922 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918I LEU* 3.1 30.0 + - + +
919I PRO* 4.6 1.8 - - + +
921I LEU* 1.3 80.9 - - + +
923I ALA* 1.3 60.7 + - - +
924I LEU 3.1 1.6 - - - -
925I LEU* 3.6 14.1 - - + -
926I ASN* 3.0 27.1 + - - -
936I CYS* 3.2 29.5 - - - -
939I PHE* 4.6 16.8 - - + +
940I GLU* 4.6 11.0 - - - +
942I TRP* 4.4 16.4 - - + +
971I VAL* 2.3 32.1 + - - +
972I LEU* 3.1 32.1 - - - -
974I PRO* 3.5 13.9 - - + -
975I PHE* 3.3 49.4 - + + -
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Residues in contact with ALA 923 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889I HIS* 3.1 39.3 - - + +
919I PRO 2.9 18.9 + - - +
922I TRP* 1.3 77.3 - - - +
924I LEU* 1.3 55.4 + - - +
926I ASN* 3.5 17.9 + - - +
927I PHE* 3.4 16.3 - - - -
940I GLU* 5.7 1.8 - - + -
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Residues in contact with LEU 924 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883I GLY 5.5 1.1 - - - +
886I MET* 3.2 38.1 - - + +
887I LYS* 3.3 15.0 - - - +
889I HIS* 3.1 35.0 + - + +
894I THR* 4.1 13.7 - - - -
920I GLU* 2.8 21.3 + - + +
921I LEU* 3.5 4.9 - - - +
923I ALA* 1.3 75.4 - - - +
925I LEU* 1.3 64.4 + - + +
926I ASN 2.8 11.0 + - - -
927I PHE* 3.3 21.9 + - + +
928I LEU* 5.3 0.3 - - - +
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Residues in contact with LEU 925 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776I ILE* 3.6 44.6 - - + -
921I LEU* 2.8 40.7 + - + +
922I TRP* 3.2 38.1 + - + -
924I LEU* 1.3 77.3 - - + +
926I ASN* 1.3 58.0 + - - +
927I PHE 3.1 6.6 + - - -
928I LEU* 4.0 15.6 - - + +
932I ILE* 3.9 11.8 - - - +
936I CYS* 3.2 16.0 - - - +
975I PHE* 3.8 8.8 - - + +
976I LEU* 4.5 1.8 - - + -
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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