Contacts of the helix formed by residues 784 - 795 (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 GLY 784 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758I GLN* 2.8 8.9 + - - -
781I MET* 3.7 22.7 - - - +
782I GLY 3.9 0.2 - - - +
783I LEU* 1.3 75.0 - - - +
785I LYS* 1.3 55.8 + - - +
786I THR 3.3 2.2 - - - -
787I ILE* 3.0 26.5 + - - -
788I GLN* 2.5 33.9 + - - +
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Residues in contact with LYS 785 (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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765I LEU* 3.8 6.7 - - + -
777I LEU* 2.4 41.0 + - - +
779I ASP* 2.5 39.7 + - - +
780I GLU 4.8 8.5 - - - +
781I MET* 4.3 9.3 - - + +
784I GLY* 1.3 70.7 - - - +
786I THR* 1.3 61.8 + - - +
788I GLN* 3.2 27.4 + - - +
789I THR* 2.9 28.6 + - - -
909I LEU* 3.3 32.7 - - + +
910I THR 2.5 20.7 + - - +
911I GLY* 5.2 6.1 - - - -
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Residues in contact with THR 786 (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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781I MET* 4.5 16.6 - - + +
785I LYS* 1.3 75.7 - - - +
787I ILE* 1.3 75.4 + - + +
789I THR* 2.8 25.6 + - - -
790I ILE* 3.0 28.2 + - - +
815I LEU* 5.8 1.9 - - - +
818I TRP* 4.9 25.7 - - + -
822I PHE* 4.0 11.6 - - + -
881I ASP* 5.5 2.8 + - - -
909I LEU* 4.3 4.6 - - - +
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Residues in contact with ILE 787 (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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758I GLN* 2.9 33.2 - - + +
781I MET* 3.8 16.8 - - + -
783I LEU 5.3 0.7 - - - -
784I GLY* 3.0 23.0 + - - +
786I THR* 1.3 82.9 - - + +
788I GLN* 1.3 59.3 + - - +
790I ILE* 3.8 15.7 - - + -
791I ALA* 2.9 25.3 + - + +
821I GLU* 4.3 24.7 - - + +
822I PHE* 5.9 2.0 - - + -
825I TRP* 5.8 12.1 - - + -
1192I ARG* 5.7 2.7 - - - +
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Residues in contact with GLN 788 (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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758I GLN* 3.2 9.4 - - - +
761I GLY* 3.2 41.2 + - - +
762I LEU* 4.6 3.8 - - - -
764I TRP* 3.0 38.9 - - - +
765I LEU* 3.2 14.3 - - + +
783I LEU 4.7 2.9 + - - +
784I GLY 2.5 21.1 + - - +
785I LYS* 3.2 28.7 - - - +
786I THR 3.1 0.4 - - - -
787I ILE* 1.3 73.7 - - - +
789I THR* 1.3 58.5 + - - +
791I ALA* 3.8 1.2 - - - +
792I LEU* 2.9 29.7 + - - +
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Residues in contact with THR 789 (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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765I LEU* 3.6 3.2 - - - +
785I LYS 2.9 14.0 + - - -
786I THR* 2.8 9.9 + - - -
788I GLN* 1.3 75.7 - - - +
790I ILE* 1.3 64.7 + - + +
792I LEU* 3.2 19.8 - - + +
793I ILE* 3.2 17.7 + - + +
879I ILE* 4.4 22.2 - - + -
907I LEU* 4.5 10.8 - - + -
908I LEU* 6.5 0.2 - - + -
909I LEU* 3.0 36.0 - - + +
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Residues in contact with ILE 790 (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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786I THR* 3.0 29.1 + - - +
787I ILE* 3.8 15.7 - - + +
788I GLN 3.2 0.2 - - - -
789I THR* 1.3 76.3 - - - +
791I ALA* 1.3 59.6 + - - +
792I LEU 3.1 1.3 - - - -
793I ILE* 3.0 11.8 + - + +
794I THR* 2.8 27.7 + - - -
808I ILE* 6.1 4.3 - - + -
822I PHE* 3.5 44.2 - - + -
826I ALA* 4.9 17.0 - - + -
879I ILE* 6.4 2.0 - - + -
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Residues in contact with ALA 791 (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* 5.8 3.1 - - + -
758I GLN* 3.8 33.0 - - + +
759I ILE* 5.8 0.7 - - + -
762I LEU* 3.3 18.1 - - + +
787I ILE* 2.9 17.9 + - + +
788I GLN 4.1 1.8 - - - +
790I ILE* 1.3 73.8 - - - +
792I LEU* 1.3 66.1 + - - +
794I THR* 3.2 30.4 + - + +
795I TYR* 3.6 4.0 - - + -
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Residues in contact with LEU 792 (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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762I LEU* 3.6 16.6 - - - +
765I LEU* 4.1 7.2 - - + +
766I VAL* 3.5 28.2 - - + +
769I TYR* 3.9 26.7 - - + +
788I GLN 2.9 14.6 + - - +
789I THR* 3.2 15.0 - - + +
790I ILE 3.1 0.2 - - - -
791I ALA* 1.3 79.1 - - - +
793I ILE* 1.3 79.8 + - + +
794I THR 3.7 0.2 + - - -
795I TYR* 4.4 3.3 + - - +
796I LEU* 4.1 10.0 - - + +
907I LEU* 3.7 30.1 - - + -
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Residues in contact with ILE 793 (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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789I THR* 3.2 20.8 + - + +
790I ILE* 3.0 12.3 + - + +
792I LEU* 1.3 92.2 - - + +
794I THR* 1.3 62.7 + - - +
795I TYR 3.3 3.6 + - - -
796I LEU* 3.6 22.9 - - + +
806I PHE* 3.5 37.2 - - + -
877I TYR* 6.0 0.7 - - + -
878I MET 4.9 3.1 - - - +
879I ILE* 4.0 33.9 - - + -
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Residues in contact with THR 794 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755I LYS* 6.4 2.0 - - + -
790I ILE* 2.8 15.7 + - - -
791I ALA* 3.2 29.6 + - + +
793I ILE* 1.3 76.0 - - - +
795I TYR* 1.3 82.1 + - + +
796I LEU 3.0 11.3 + - - -
797I MET* 4.0 15.8 + - - +
826I ALA* 5.8 3.5 - - - +
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Residues in contact with TYR 795 (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* 4.5 9.1 - - + +
759I ILE* 3.3 32.3 - - + +
762I LEU* 3.6 33.0 - - + -
791I ALA* 3.6 15.4 + - + -
792I LEU 4.4 3.1 + - - +
793I ILE 3.3 1.8 - - - -
794I THR* 1.3 94.0 - - + +
796I LEU* 1.4 67.4 + - + +
797I MET* 3.9 9.6 - - + +
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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