Contacts of the helix formed by residues 778 - 790 (chain A) in PDB entry 3LLT
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 GLU 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738A ARG* 3.6 7.4 - - - +
776A THR* 3.3 6.2 + - - +
777A HIS* 1.3 103.1 + - + +
779A HIS* 1.3 65.4 + - - +
780A MET* 3.5 9.9 + - - +
781A GLU* 3.5 31.7 + - + +
782A HIS* 3.0 21.2 + - - +
819A TRP* 5.3 0.2 - - - -
822A ASN 4.9 2.6 - - - +
823A ALA* 5.3 1.2 - - - -
824A SER* 2.8 39.4 + - - -
828A SER* 4.7 3.5 + - - -
876A ACT 3.8 18.2 - - + +
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Residues in contact with HIS 779 (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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734A ILE* 4.6 17.5 - - + -
738A ARG* 3.6 18.8 + - - -
741A ARG* 3.1 33.7 + - - -
746A ILE* 3.6 39.2 - - + +
778A GLU* 1.3 72.5 - - - +
780A MET* 1.3 58.8 + - - +
782A HIS* 3.1 9.8 + + - +
783A LEU* 2.8 34.8 + - - +
809A TYR* 2.9 35.3 + - + +
876A ACT 3.4 13.5 + - + +
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Residues in contact with MET 780 (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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778A GLU* 3.4 11.8 - - - +
779A HIS* 1.3 76.6 - - - +
781A GLU* 1.3 63.2 + - - +
783A LEU* 3.3 5.2 + - + -
784A ALA* 3.1 21.5 + - - +
808A LYS* 4.9 0.9 - - + +
809A TYR* 3.4 56.3 - - + +
817A LEU* 3.8 19.7 - - + -
818A ALA 3.7 15.0 - - - +
819A TRP* 4.2 14.1 - - + -
822A ASN* 3.7 39.7 - - + +
876A ACT 3.6 7.7 + - - +
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Residues in contact with GLU 781 (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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776A THR* 2.7 35.3 + - - +
777A HIS* 4.1 6.4 + - - -
778A GLU* 3.5 20.9 + - + +
779A HIS 3.4 0.4 - - - -
780A MET* 1.3 74.2 - - - +
782A HIS* 1.3 60.5 + - - +
784A ALA* 3.2 3.3 + - - +
785A MET* 2.9 35.4 + - - +
819A TRP* 4.0 10.0 - - + -
828A SER* 2.7 42.4 + - - +
831A HIS* 4.0 20.2 - - - +
832A VAL* 3.6 16.6 - - + -
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Residues in contact with HIS 782 (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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738A ARG* 3.0 33.5 + - + -
739A GLN* 4.0 7.7 + - - -
741A ARG* 4.0 8.6 + - + -
746A ILE* 3.8 16.8 - - + -
774A PHE* 3.5 34.4 - + + +
776A THR* 3.6 22.8 + - + -
778A GLU 3.0 15.0 + - - +
779A HIS* 3.1 15.7 - + - +
781A GLU* 1.3 75.6 - - - +
783A LEU* 1.3 62.2 + - - +
785A MET* 3.3 6.9 + - - +
786A MET* 3.2 42.6 + - + +
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Residues in contact with LEU 783 (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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743A PRO* 4.8 3.4 - - + +
746A ILE* 3.8 29.8 - - + -
747A LEU* 3.8 21.3 - - + -
779A HIS 2.8 19.3 + - - +
780A MET* 3.6 10.1 - - + +
781A GLU 3.2 0.2 - - - -
782A HIS* 1.3 73.5 - - - +
784A ALA* 1.3 62.5 + - - +
786A MET* 3.2 33.9 + - - +
787A GLU* 3.4 6.8 + - - +
793A ILE* 4.1 17.8 - - + +
809A TYR* 3.7 37.0 - - + -
817A LEU* 3.6 23.3 - - + +
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Residues in contact with ALA 784 (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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780A MET 3.1 10.3 + - - +
781A GLU 3.2 6.9 + - - +
783A LEU* 1.3 76.7 - - - +
785A MET* 1.3 61.2 + - - +
787A GLU* 3.4 6.2 + - - +
788A SER* 3.2 25.5 + - - -
817A LEU* 3.7 9.5 - - + +
819A TRP* 3.5 47.8 - - + +
832A VAL* 3.8 9.8 - - + +
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Residues in contact with MET 785 (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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773A LEU 3.9 7.9 - - - +
774A PHE* 3.7 19.1 - - + -
775A ARG* 3.5 41.7 - - + +
776A THR* 3.9 20.0 - - - -
781A GLU* 2.9 16.4 + - - +
782A HIS 3.4 9.2 - - - +
783A LEU 3.2 0.2 - - - -
784A ALA* 1.3 75.0 - - - +
786A MET* 1.3 58.7 + - - +
788A SER* 3.3 3.4 + - - +
789A ILE* 3.0 37.7 + - + +
831A HIS* 4.3 12.1 - - + +
832A VAL* 3.9 15.7 - - + -
835A CYS* 3.6 30.1 - - - -
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Residues in contact with MET 786 (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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741A ARG 3.6 18.2 - - - +
743A PRO* 3.6 29.2 - - + -
746A ILE* 3.9 11.9 - - + -
758A TRP* 3.7 19.1 - - + -
774A PHE* 3.7 21.8 - - + -
782A HIS* 3.2 41.2 + - + +
783A LEU* 3.2 21.3 + - - +
785A MET* 1.3 76.4 - - - +
787A GLU* 1.3 58.0 + - + +
790A ILE* 3.0 28.0 + - - +
791A GLN 3.3 10.9 + - - +
793A ILE* 5.4 2.5 - - + -
857A ILE* 4.2 14.0 - - + +
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Residues in contact with GLU 787 (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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783A LEU 3.4 12.4 + - - +
784A ALA* 3.4 8.5 + - - +
785A MET 3.2 0.4 - - - -
786A MET* 1.3 77.7 - - - +
788A SER* 1.3 61.9 + - - +
790A ILE 4.4 1.0 - - - -
791A GLN* 3.2 28.5 + - - +
792A PRO* 3.8 14.8 - - + +
793A ILE* 3.1 35.4 + - + +
798A LEU* 5.1 2.4 - - - +
817A LEU* 3.6 33.6 + - + +
819A TRP* 6.1 0.3 - - - +
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Residues in contact with SER 788 (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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784A ALA 3.2 16.1 + - - -
785A MET* 3.3 4.9 + - - -
787A GLU* 1.3 79.8 - - - +
789A ILE* 1.3 60.0 + - - +
832A VAL* 3.6 27.5 + - - +
835A CYS* 4.2 14.8 - - - +
836A LEU 4.3 0.2 - - - -
837A PRO* 3.6 22.0 - - - +
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Residues in contact with ILE 789 (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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773A LEU* 3.6 44.2 - - + +
774A PHE* 3.9 12.8 - - + -
785A MET* 3.0 20.5 + - + +
788A SER* 1.3 80.7 - - - +
790A ILE* 1.3 77.9 + - + +
835A CYS* 4.0 26.5 - - + -
836A LEU 3.5 20.0 - - - +
837A PRO* 3.4 6.8 - - - +
838A LEU* 2.8 40.9 + - + +
841A ILE* 4.6 3.1 - - + -
852A TYR* 4.0 1.9 + - - -
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Residues in contact with ILE 790 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758A TRP* 4.1 13.7 - - + -
773A LEU* 4.5 6.5 - - + -
774A PHE* 3.5 32.1 - - + -
786A MET 3.0 15.1 + - - +
787A GLU 4.4 2.7 - - - -
788A SER 5.3 0.2 - - - -
789A ILE* 1.3 94.5 - - + +
791A GLN* 1.3 79.2 + - + +
838A LEU* 4.8 6.3 - - + -
852A TYR* 4.1 28.0 + - + -
855A LEU* 3.2 41.5 - - + +
857A ILE* 5.0 2.7 - - + -
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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