Contacts of the helix formed by residues 757 - 768 (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 TYR 757 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756I GLN* 1.3 91.2 - - + +
758I GLN* 1.3 59.9 + - + +
759I ILE 3.2 1.3 - - - -
760I LYS* 3.1 15.2 + - - +
761I GLY* 3.0 19.2 + - - -
783I LEU* 3.5 52.7 - - + -
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Residues in contact with GLN 758 (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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755I LYS* 3.1 24.0 + - - +
756I GLN 5.1 0.4 - - - +
757I TYR* 1.3 78.0 - - + +
759I ILE* 1.3 60.7 + - - +
760I LYS 3.3 0.2 - - - -
761I GLY* 3.5 2.7 - - - +
762I LEU* 2.8 26.2 + - - +
783I LEU* 2.7 32.9 + - + +
784I GLY 2.8 16.4 + - - -
787I ILE* 2.9 47.8 - - + +
788I GLN* 3.2 14.1 + - - +
791I ALA* 3.8 11.6 - - + +
825I TRP* 6.4 2.0 - - + -
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Residues in contact with ILE 759 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755I LYS* 2.6 45.4 + - + +
756I GLN 4.8 2.9 - - - +
757I TYR 3.2 0.4 - - - -
758I GLN* 1.3 73.2 - - - +
760I LYS* 1.3 62.3 + - - +
762I LEU* 3.1 14.2 - - + +
763I GLU* 3.1 35.1 + - - +
791I ALA* 5.8 0.9 - - + -
795I TYR* 3.3 33.4 - - + +
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Residues in contact with LYS 760 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756I GLN 5.1 0.8 + - - +
757I TYR* 3.1 12.2 + - - +
759I ILE* 1.3 79.1 - - - +
761I GLY* 1.3 58.7 + - - +
763I GLU* 3.1 27.1 + - - +
764I TRP* 2.9 43.8 + - - +
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Residues in contact with GLY 761 (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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757I TYR 3.0 13.1 + - - -
758I GLN* 3.3 7.8 + - - -
759I ILE 3.2 0.4 - - - -
760I LYS* 1.3 74.6 - - - +
762I LEU* 1.3 59.0 + - - +
764I TRP* 3.3 0.4 + - - -
765I LEU* 2.9 25.5 + - - +
783I LEU 5.8 0.2 - - - -
788I GLN* 3.2 42.9 + - - +
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Residues in contact with LEU 762 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758I GLN* 2.8 17.9 + - - +
759I ILE* 3.1 24.9 - - + +
761I GLY* 1.3 70.4 - - - +
763I GLU* 1.3 62.2 + - + +
765I LEU* 5.6 0.2 - - - +
766I VAL* 2.9 46.5 + - + +
788I GLN* 4.6 9.2 - - - +
791I ALA* 3.3 27.8 - - + +
792I LEU* 3.6 15.7 - - - +
795I TYR* 3.6 31.4 - - + -
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Residues in contact with GLU 763 (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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759I ILE* 3.1 30.6 + - + +
760I LYS* 3.1 31.1 + - - +
762I LEU* 1.3 84.8 - - + +
764I TRP* 1.3 51.3 + - - +
766I VAL* 3.9 2.4 - - - -
767I SER* 2.7 36.8 + - - -
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Residues in contact with TRP 764 (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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760I LYS* 2.9 26.0 + - - +
761I GLY* 3.4 1.8 - - - +
763I GLU* 1.3 74.2 - - - +
765I LEU* 1.3 72.2 + - + +
767I SER* 2.4 30.5 + - - -
768I LEU* 3.0 32.6 + - + +
779I ASP* 3.1 33.1 + - + -
788I GLN* 3.0 41.8 + - - +
977I LEU* 4.6 10.3 - - + -
979I ARG* 4.1 28.3 - - - -
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Residues in contact with LEU 765 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I GLY 2.9 14.9 + - - +
762I LEU 4.8 0.2 - - - +
764I TRP* 1.3 84.8 - - + +
766I VAL* 1.3 60.1 + - - +
768I LEU* 3.2 12.3 - - + +
769I TYR* 3.1 27.2 + - - +
777I LEU* 4.0 13.2 - - + -
785I LYS* 3.7 22.7 - - + +
788I GLN* 3.2 33.2 - - + +
789I THR* 3.6 14.4 - - - +
792I LEU* 4.1 2.7 - - + +
907I LEU* 5.0 5.4 - - + -
909I LEU* 3.6 40.4 - - + -
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Residues in contact with VAL 766 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762I LEU* 2.9 32.6 + - + +
763I GLU* 4.4 2.2 - - - +
765I LEU* 1.3 75.7 - - - +
767I SER* 1.3 61.0 + - - +
768I LEU 3.1 1.6 + - - -
769I TYR* 4.1 15.7 - - + +
770I ASN* 3.3 27.7 + - + -
792I LEU* 3.5 36.8 - - + +
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Residues in contact with SER 767 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763I GLU 2.7 18.7 + - - -
764I TRP* 2.4 28.8 + - - -
766I VAL* 1.3 75.7 - - - +
768I LEU* 1.3 69.3 + - - +
769I TYR 3.6 0.4 - - - -
770I ASN* 3.4 20.2 + - - +
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Residues in contact with LEU 768 (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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764I TRP* 3.0 44.3 + - + +
765I LEU* 3.2 20.3 + - + +
766I VAL 3.1 0.2 - - - -
767I SER* 1.3 88.9 - - - +
769I TYR* 1.3 55.0 + - - +
770I ASN* 4.4 0.9 - - - -
771I ASN* 5.2 3.1 - - - +
777I LEU* 3.7 42.0 - - + +
779I ASP* 5.7 0.2 - - - +
907I LEU* 3.7 13.0 - - - +
977I LEU* 4.0 24.0 - - + -
979I ARG* 6.0 2.5 - - - +
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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